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Rydal MP, Poulsen LL, Nielsen JP. The early-life fecal microbiota is associated with litter of origin but not with susceptibility to ETEC F4ab-mediated post-weaning diarrhea in CHCF1 genotyped pigs. PLoS One 2025; 20:e0323875. [PMID: 40440292 PMCID: PMC12121822 DOI: 10.1371/journal.pone.0323875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 04/16/2025] [Indexed: 06/02/2025] Open
Abstract
INTRODUCTION Universal biomarkers in the fecal microbiota that predict susceptibility to post-weaning diarrhea (PWD) would be valuable for future intervention strategies. Genetic susceptibility to enterotoxigenic E. coli (ETEC) infection in pigs is a major determinant of PWD and may unfavourably alter early-life gut microbiota composition. We investigated whether pigs genetically susceptible to ETEC F4ab/ac had different fecal microbiota composition and diversity pre- and post-weaning compared to genetically resistant pigs. METHOD Fecal microbiotas were characterized using long-read sequencing of the 16S rRNA gene in 24 CHCF1 heterozygous susceptible (RS) and 24 CHCF1 homozygous resistant (RR) pigs. These pigs were tested at early lactation (post-natal day (PND) 8) and late lactation (PND 22), which are critical periods for microbiota development and immune maturation. Twelve pigs from each group were weaned and transported to an experimental facility at PND 23, and were tested again at PND 24, prior to an ETEC F4ab challenge. This enabled studying immediate fecal microbiota changes after weaning and investigating whether CHCF1 RS pigs had compromised microbiotas compared to CHCF1 RR pigs preceding infection. RESULTS Across time, CHCF1 RS pigs had a higher number of observed OTUs (coef: 103, 95% CI [18.90; 192.76], p = 0.01) compared to CHCF1 RR pigs. There were no significant differences in the overall bacterial communities or differentially abundant taxa between genotypes. Littermates had bacterial communities more similar to each other compared to non-littermates during lactation (PND 8: R2 = 0.2, p = 0.001 and PND 22: R2 = 0.23, p = 0.001) and the litter effect persisted after weaning (PND 24: R2 = 0.4, p = 0.001). CONCLUSION We did not find major differences in the fecal microbiota between CHCF1 genotypes, pre- or post-weaning, that could help explain subsequent susceptibility to ETEC F4ab-mediated PWD. Litter explained a major part of the variation in the overall fecal bacterial community between pigs in the study.
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Affiliation(s)
- Martin Peter Rydal
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Louise Ladefoged Poulsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Peter Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Yang T, Zhou X, Wu Y, Liang Y, Zeng X, Yu Z. Metagenomic analyses of aerobic bacterial enrichment cultures that degraded Tris(2-chloroethyl) phosphate (TCEP) and its transformation products. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124825. [PMID: 39197646 DOI: 10.1016/j.envpol.2024.124825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/23/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Tris(2-chloroethyl) phosphate (TCEP) is of growing public concern worldwide because of its ubiquitous contamination, toxicity, and persistence. In this study, we investigated bacterial communities in aerobic enrichment cultures with TCEP and its two major transformation products bis(2-chloroethyl) phosphate (BCEP) and 2-chloroethanol (2-CE) as the sole carbon source. Burkholderiales and Rhizobiales were likely two main bacterial guilds involved in the hydrolysis of TCEP, while Rhizobiales and Sphingomonadales may play an important role in the hydrolysis of BCEP, given the increase of Rhizobiales and Sphingomonadales-related phosphoesterase genes when the carbon source was switched from TCEP to BCEP. All Burkholderiales, Rhizobiales, Sphingomonadales were probably efficient in 2-CE metabolism, because their dehydrogenase genes and dehalogenase genes increased after 2-CE enrichment. The different substrate preference of different bacterial guilds highlighted the importance to understand the diversity and collaboration among functional bacteria. Meanwhile, two TCEP-degrading strains affiliated with Xanthobacter and Ancylobacter were isolated. Xanthobacter sp. strain T2-1 was able to degrade both TCEP and BCEP following the pseudo-first-order kinetics with reaction rates of 1.66 h-1 for TCEP and 1.02 h-1 for BCEP, respectively. Ancylobacter sp. strain T3-4 could degrade TCEP following the pseudo-first-order kinetics with a reaction rate of 2.54 h-1, but is unable to degrade BCEP. Additionally, strains that were phylogenetically closely related were found to have different degradation capabilities toward TCEP and/or BCEP, indicating the importance to investigate functional genes such as phosphoesterase genes.
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Affiliation(s)
- Tianyue Yang
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangyu Zhou
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiding Wu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Liang
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Xiangying Zeng
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
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Ko GP, Jo H, Kim J, Kim JS, Boo KH, Kim CS. Enterotype-Specific Effects of Red Beetroot ( Beta vulgaris L.) Powder and Betanin on Human Gut Microbiota: A Preliminary Study Based on In Vitro Fecal Fermentation Model. Life (Basel) 2024; 14:1391. [PMID: 39598189 PMCID: PMC11595470 DOI: 10.3390/life14111391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 10/11/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024] Open
Abstract
Red beetroots, rich in betanin, may act as prebiotics and impact gut microbiota. Because the human gut microbiota is unique to each person, the effectiveness of prebiotics varies with the enterotype. In this study, we hypothesized that the effects of red beetroot powder (RP) and betanin pigment (BP) would differ depending on the enterotype. Fecal samples from 30 subjects were analyzed and categorized into three enterotypes: Phocaeicola, Prevotella, and Bifidobacterium. Feces were collected from one representative subject from each enterotype cluster for fermentation. Results showed that RP and BP affected microbiota composition and short-chain fatty acid (SCFA) production differently across enterotypes. The Bifidobacterium cluster showed significantly reduced alpha diversity, with the direction of change in the gut microbiota composition being different from that of other subjects. Additionally, SCFAs significantly increased, with the highest increase in the Bifidobacterium cluster. In this cluster, metabolic pathways related to SCFAs (i.e., starch and sucrose metabolism and glycolysis/gluconeogenesis) were altered. Conversely, Prevotella-dominant feces exhibited fewer changes in SCFAs and a lower increase in Bifidobacterium abundance than the others. These findings highlight that RP and BP elicit enterotype-specific responses in the gut microbiota composition and SCFA production, emphasizing the importance of enterotypes in personalized nutrition.
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Affiliation(s)
- Gwang-Pyo Ko
- Faculty of Biotechnology, Jeju National University, Jeju 63243, Republic of Korea; (G.-P.K.); (H.J.); (K.-H.B.)
| | - Hyejun Jo
- Faculty of Biotechnology, Jeju National University, Jeju 63243, Republic of Korea; (G.-P.K.); (H.J.); (K.-H.B.)
| | - Jungman Kim
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Republic of Korea;
- Jeju Institute of Korean Medicine, Jeju 63309, Republic of Korea
| | - Jeong Seon Kim
- Jeju Special Self-Governing Province Agricultural Research & Extension Services, Seogwipo-si 63556, Republic of Korea;
| | - Kyung-Hwan Boo
- Faculty of Biotechnology, Jeju National University, Jeju 63243, Republic of Korea; (G.-P.K.); (H.J.); (K.-H.B.)
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Republic of Korea;
| | - Chang Sook Kim
- Faculty of Biotechnology, Jeju National University, Jeju 63243, Republic of Korea; (G.-P.K.); (H.J.); (K.-H.B.)
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Republic of Korea;
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Yang Z, Shan Y, Liu X, Chen G, Pan Y, Gou Q, Zou J, Chang Z, Zeng Q, Yang C, Kong J, Sun Y, Li S, Zhang X, Wu WC, Li C, Peng H, Holmes EC, Guo D, Shi M. VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization. Mol Biol Evol 2024; 41:msae202. [PMID: 39331699 PMCID: PMC11523140 DOI: 10.1093/molbev/msae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 09/10/2024] [Accepted: 09/24/2024] [Indexed: 09/29/2024] Open
Abstract
RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.
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Affiliation(s)
- Ziyue Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yongtao Shan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Guowei Chen
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
| | - Yuanfei Pan
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qinyu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jie Zou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zilong Chang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qiang Zeng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chunhui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jianbin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
| | - Shaochuan Li
- Goodwill Institute of Life Sciences, Guangzhou, China
| | - Xu Zhang
- Goodwill Institute of Life Sciences, Guangzhou, China
| | - Wei-chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chunmei Li
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Hong Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong (SAR), China
| | - Deyin Guo
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
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Ko G, Unno T, Kim Y, Kim J. Dietary Polycan, a β-glucan originating from Aureobasidium pullulansSM-2001, attenuates high-fat-diet-induced intestinal barrier damage in obese mice by modulating gut microbiota dysbiosis. Food Sci Nutr 2024; 12:5824-5835. [PMID: 39139941 PMCID: PMC11317661 DOI: 10.1002/fsn3.4235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 08/15/2024] Open
Abstract
Various metabolic diseases caused by a high-fat diet (HFD) are closely related to gut microbiota dysbiosis and epithelial barrier dysfunction. Polycan, a type of β-glucan, is effective in treating anti-obesity and metabolic diseases caused by HFD. However, the effect of Polycan on dysbiosis and epithelial barrier damage is still unknown. In this study, the effects of Polycan on dysbiosis and intestinal barrier damage were investigated using HFD-induced obese model mice. C57BL/6 mice were fed a HFD for 12 weeks and treated with two different doses of Polycan (250 and 500 mg/kg) orally administered during weeks 9 to 12. Polycan supplementation increased the expression of tight junction genes (zonula occludens-1, occludin, and claudin-3) and short-chain fatty acid (SCFA) content while reducing toxic substances (phenol, p-cresol, and skatole). Most significantly, Polycan enriched SCFA-producing bacteria (i.e., Phocaeicola, Bacteroides, Faecalibaculum, Oscillibacter, Lachnospiraceae, and Muribaculaceae), and decreased the Firmicutes/Bacteroidetes ratio and toxic substances-producing bacteria (i.e., Olsenella, Clostridium XVIII, and Schaedlerella). Furthermore, microbial functional capacity prediction of the gut microbiota revealed that Polycan enriched many SCFA-related KEGG enzymes while toxic substance-related KEGG enzymes were depleted. These findings indicated that Polycan has the potential to alleviate HFD-induced intestinal barrier damage by modulating the function and composition of the gut microbiota.
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Affiliation(s)
- Gwang‐Pyo Ko
- Faculty of Biotechnology, School of Life SciencesSARI Jeju National UniversityJejuKorea
| | - Tatsuya Unno
- Department of MicrobiologyChungbuk National UniversityCheongjuKorea
| | | | - Jungman Kim
- Subtropical/Tropical Organism Gene Bank Jeju National UniversityJejuKorea
- Jeju Institute of Korean MedicineJejuKorea
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Lennon S, Lackie T, Miltko A, Kearns ZC, Paquette MR, Bloomer RJ, Wang A, van der Merwe M. Safety and efficacy of a probiotic cocktail containing P. acidilactici and L. plantarum for gastrointestinal discomfort in endurance runners: randomized double-blinded crossover clinical trial. Appl Physiol Nutr Metab 2024; 49:890-903. [PMID: 38427981 DOI: 10.1139/apnm-2023-0449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Probiotics are increasingly used to treat conditions associated with gastrointestinal injury and permeability, including exercise-induced gastrointestinal discomfort. This study assessed safety and efficacy of a probiotic in altering the intestinal milieu and mitigating gastrointestinal symptoms (GIS) in endurance runners. In a double blind, crossover study, 16 runners were randomized to 4 weeks of daily supplementation with a probiotic cocktail containing Pediococcus acidilactici bacteria and Lactobacillus plantarum or placebo. Fasting blood and stool samples were collected for measurement of gut permeability markers, immune parameters, and microbiome analyses. Treadmill run tests were performed before and after treatment; participants ran at 65%-70% of VO2max at 27 °C for a maximum of 90 min or until fatigue/GIS developed. A blood sample was collected after the treadmill run test. In healthy individuals, 4 weeks of probiotic supplementation did not alter health parameters, although a marginal reduction in aspartate aminotransferase levels was observed with probiotic treatment only (p = 0.05). GIS, gut permeability-associated parameters (intestinal fatty acid binding protein, lipopolysaccharide binding protein, zonulin, and cytokines), and intestinal microbial content were not altered by the probiotic supplementation. Post-run measurements of GIS and gut-associated parameters did not differ between groups; however, the observed lack of differences is confounded by an absence of measurable functional outcome as GIS was not sufficiently induced during the run. Under the current study conditions, the probiotic was safe to use, and did not affect gut- or immune-associated parameters, or intestinal symptoms in a healthy population. The probiotic might reduce tissue damage, but more studies are warranted.
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Affiliation(s)
- Sarah Lennon
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Thomas Lackie
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Adriana Miltko
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Zoey C Kearns
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Maxime R Paquette
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Richard J Bloomer
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
| | - Anyou Wang
- Harry Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA
| | - Marie van der Merwe
- Center for Nutraceuticals and Dietary Supplement Research, College of Health Sciences, University of Memphis, Memphis, TN, USA
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Ristinmaa AS, Tafur Rangel A, Idström A, Valenzuela S, Kerkhoven EJ, Pope PB, Hasani M, Larsbrink J. Resin acids play key roles in shaping microbial communities during degradation of spruce bark. Nat Commun 2023; 14:8171. [PMID: 38071207 PMCID: PMC10710418 DOI: 10.1038/s41467-023-43867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.
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Affiliation(s)
| | - Albert Tafur Rangel
- Department of Life Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Alexander Idström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, NO-1433, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1433, Ås, Norway
| | - Merima Hasani
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Johan Larsbrink
- Department of Life Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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Tang X, Yang L, Miao Y, Ha W, Li Z, Mi D. Angelica polysaccharides relieve blood glucose levels in diabetic KKAy mice possibly by modulating gut microbiota: an integrated gut microbiota and metabolism analysis. BMC Microbiol 2023; 23:281. [PMID: 37784018 PMCID: PMC10546737 DOI: 10.1186/s12866-023-03029-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Angelica polysaccharides (AP) have numerous benefits in relieving type 2 diabetes (T2D). However, the underlying mechanisms have yet to be fully understood. Recent many reports have suggested that altering gut microbiota can have adverse effects on the host metabolism and contribute to the development of T2D. Here, we successfully established the T2D model using the male KKAy mice with high-fat and high-sugar feed. Meanwhile, the male C57BL/6 mice were fed with a normal feed. T2D KKAy mice were fed either with or without AP supplementation. In each group, we measured the mice's fasting blood glucose, weight, and fasting serum insulin levels. We collected the cecum content of mice, the gut microbiota was analyzed by targeted full-length 16S rRNA metagenomic sequencing and metabolites were analyzed by untargeted-metabolomics. RESULTS We found AP effectively alleviated glycemic disorders of T2D KKAy mice, with the changes in gut microbiota composition and function. Many bacteria species and metabolites were markedly changed in T2D KKAy mice and reversed by AP. Additionally, 16 altered metabolic pathways affected by AP were figured out by combining metagenomic pathway enrichment analysis and metabolic pathway enrichment analysis. The key metabolites in 16 metabolic pathways were significantly associated with the gut microbial alteration. Together, our findings showed that AP supplementation could attenuate the diabetic phenotype. Significant gut microbiota and gut metabolite changes were observed in the T2D KKAy mice and AP intervention. CONCLUSIONS Administration of AP has been shown to improve the composition of intestinal microbiota in T2D KKAy mice, thus providing further evidence for the potential therapeutic application of AP in the treatment of T2D.
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Affiliation(s)
- Xiaolong Tang
- The First Clinical Medical College, Lanzhou University, Lanzhou City, Gansu Province, China
- The Second Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, Sichuan Province, Nanchong City, China
| | - Lixia Yang
- Gansu Academy of Traditional Chinese Medicine, Lanzhou City, Gansu Province, China
| | - Yandong Miao
- The First Clinical Medical College, Lanzhou University, Lanzhou City, Gansu Province, China
- Department of Oncology, Yantai Affiliated Hospital of Binzhou Medical University, The Second Clinical Medical College of Binzhou Medical University, Yantai City, Shandong Province, China
| | - Wuhua Ha
- The First Clinical Medical College, Lanzhou University, Lanzhou City, Gansu Province, China
| | - Zheng Li
- Department of Radiotherapy, Cancer Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Denghai Mi
- The First Clinical Medical College, Lanzhou University, Lanzhou City, Gansu Province, China.
- Gansu Academy of Traditional Chinese Medicine, Lanzhou City, Gansu Province, China.
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9
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Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE, Lee JN, Yeo ZY, Zahn G. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival. ENVIRONMENTAL MICROBIOME 2023; 18:47. [PMID: 37264467 DOI: 10.1186/s40793-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/01/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival. CONCLUSION The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.
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Affiliation(s)
- Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Trevor Millar
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lacee Bowen
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lauren Semon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Zhi Yi Yeo
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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10
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Wang AJ, Song D, Hong YM, Liu NN. Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age. Mol Omics 2023; 19:283-296. [PMID: 36916422 DOI: 10.1039/d2mo00288d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.
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Affiliation(s)
- An-Jun Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Dingka Song
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Yue-Mei Hong
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
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11
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Liu Z, Michalet R, Wang C, Wang Y, Chen J, Cui H, Song H, Wang J, Yang Z, An L, Xiao S, Chen S. Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160154. [PMID: 36375548 DOI: 10.1016/j.scitotenv.2022.160154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In alpine systems, cushion plants act as foundation species by ameliorating local environmental conditions. Empirical studies indicate that contrasting phenotypes of alpine cushion species have different effects on understory plant species, either facilitative or competitive. Furthermore, dependent species within each community type might also exhibit different responses to each cushion phenotype, which can be clustered into several "response groups". Additionally, these species-groups specific responses to alpine cushion species phenotypes could alter community assembly. However, very few studies have assessed responses of dependent communities at species-group levels, in particular for both above- and below-ground communities. Here, we selected a loose and a tight phenotype of the alpine cushion species Thylacospermum caespitosum in two sites of northwest China, and use the relative intensity of interactions index to quantify cushion plant effects on subordinate communities of plants and soil fungi and bacteria. We assessed variations in responses of both above- and below-ground organisms to cushion plant effects at species-group level. Species-group level analyses showed that the effects of the phenotype varied among groups of each of the three community types, and different species-groups were composed by unique taxa. Additionally, we found that loose cushions enhanced stochastic processes in community assembly, for plants and soil fungi but not for soil bacteria. These variations of phenotypic effects on different species-group induced contrasting taxonomic composition between groups, and alter community assembly thereby. Our study highlights the occurrence of contrasting effects of two phenotypes of a foundation cushion plant on understory plants, soil fungi and bacteria community composition, but not necessarily on their richness. We also showed that assessing responses of understory species at the species-group level allows a more realistic and mechanistic understanding of biotic interactions both for above- and below-ground communities.
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Affiliation(s)
- Ziyang Liu
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Richard Michalet
- Environnements et Paléoenvironnements Océaniques et Continentaux, University of Bordeaux, Bordeaux, France
| | - Chenyue Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Yajun Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Lizhe An
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China.
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12
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Motteran F, Varesche MBA, Lara-Martin PA. Assessment of the aerobic and anaerobic biodegradation of contaminants of emerging concern in sludge using batch reactors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:84946-84961. [PMID: 35789461 DOI: 10.1007/s11356-022-21819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
This work explores the degradation of xenobiotic compounds in aerobic and anaerobic batch reactors. Different inoculums were spiked with nine emerging contaminants at nominal concentrations ranging between 1 to 2 mg/L (ibuprofen, diclofenac, naproxen, acesulfame, sucralose, aspartame, cyclamate, linear alkylbenzene sulfonates, and secondary alkyl sulfonates). Ethanol was used as co-substrate in the anaerobic reactors. We found that the kinetic decay was faster in the aerobic reactors inoculated with a Spanish (Spn) inoculum compared to a Brazilian (Brz) inoculum, resulting in rection rates for LAS and SAS of 2.67 ± 3.6 h-1 and 5.09 ± 6 h-1 for the Brz reactors, and 1.3 ± 0.1 h-1 and 1.5 ± 0.2 h-1 for the Spn reactors, respectively. There was no evidence of LAS and SAS degradation under anaerobic conditions within 72 days; nonetheless, under aerobic conditions, these surfactants were removed by both the Brz and Spn inoculums (up to 86.2 ± 9.4% and 74.3 ± 0.7%, respectively) within 10 days. The artificial sweeteners were not removed under aerobic conditions, whereas we could observe a steady decrease in the anaerobic reactors containing the Spn inoculum. Ethanol aided in the degradation of surfactants in anaerobic environments. Proteiniphilum, Paraclostridium, Arcobacter, Proteiniclasticum, Acinetobacter, Roseomonas, Aquamicrobium, Moheibacter, Leucobacter, Synergistes, Cyanobacteria, Serratia, and Desulfobulbus were the main microorganisms identified in this study.
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Affiliation(s)
- Fabricio Motteran
- Geosciences Technology Center, Department of Civil and Environmental Engineering, Environmental Sanitation Laboratory and Laboratory of Molecular Biology and Environmental Technology, Federal University of Pernambuco, Ave. Arquitetura, s/n, Cidade Universitária, Recife, PA, Zipcode 50740-550, Brazil.
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, n°. 400, São Carlos, São Paulo, Zipcode 13566-590, Brazil
| | - Pablo A Lara-Martin
- Department of Physical Chemistry, Faculty of Environmental and Marine Sciences, University of Cadiz (UCA), Campus Río San Pedro, 11510, Puerto Real (Cádiz), Andalusia, Spain
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13
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Kim JH, Ko GP, Son KH, Ku BH, Bang MA, Kang MJ, Park HY. Arazyme in combination with dietary carbohydrolases influences odor emission and gut microbiome in growing-finishing pigs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157735. [PMID: 35926625 DOI: 10.1016/j.scitotenv.2022.157735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the effects of supplementing feed with arazyme and dietary carbohydrolases derived from invertebrate gut-associated symbionts on the noxious gas emissions, gut microbiota, and host-microbiome interactions of pigs. Here, 270 and 260 growing pigs were assigned to control and treatment groups, respectively. The tested feed additives contained a mixture of arazyme (2,500,000 Unit/kg) and synergetic enzymes, xylanase (200,000 Unit/kg) and mannanase (200,000 Unit/kg), derived from insect gut-associated symbionts in a 7.5:1:1 ratio. The control group was fed a basal diet and the treatment group was fed the basal diet supplemented with 0.1 % enzyme mixture (v/v) for 2 months. Odorous gases were monitored in ventilated air from tested houses. Fecal samples were collected from steel plate under the cage at the completion of the experiment to determine chemical composition, odor emissions, and bacterial communities. There was a significant decrease in the concentration of NH3 (22.5 vs. 11.2 ppm; P < 0.05), H2S (7.35 vs. 3.74 ppm; P < 0.05), trimethylamine (TMA) (0.066 vs. 0.001 ppm; P < 0.05), and p-cresol (0.004 ppm vs. 0 ppm; P < 0.05) at 56 d in treatment group compared with the control group. Moreover, fecal analysis results showed that exogenous enzyme supplementation caused a reduction in VFAs and indole content with approximately >60 % and 72.7 %, respectively. The result of gas emission analysis showed that NH3 (9.9 vs. 5.3 ppm; P < 0.05) and H2S (5.8 vs. 4.1 ppm; P < 0.05) were significantly reduced in the treatment group compared to the control group. The gut microbiota of the treatment group differed significantly from that of the control group, and the treatment group altered predicted metabolic pathways, including sulfur and nitrogen related metabolism, urea degradation. The results demonstrated that supplementing feed with arazyme with dietary carbohydrolases effectively controls noxious gas emissions and improves health and meat quality of pigs.
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Affiliation(s)
- Jong-Hoon Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Gwang-Pyo Ko
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kwang-Hee Son
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Bon-Hwan Ku
- Insect Biotech Co. Ltd., Daejeon 34054, Republic of Korea
| | - Mi-Ae Bang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Jong Kang
- Department of Food Industry Research Center, Jeonnam Bioindustry Foundation, Naju 58275, Republic of Korea.
| | - Ho-Yong Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
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14
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Wang D, Li X, Yang X, Chen S, Li L, Wang Y, Pan C, Zhao Y. Unraveling the effect of the combination of modified atmosphere packaging and ε-polylysine on the physicochemical properties and bacterial community of greater amberjack (Seriola dumerili). Front Nutr 2022; 9:1035714. [DOI: 10.3389/fnut.2022.1035714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The combined effect of ε-polylysine (PL) and modified atmosphere packaging (MAP; 60% CO2/40% N2) on the bacterial community of greater amberjack filets and their physicochemical properties was evaluated at 4°C. The total viable counts (TVC), psychrotrophic bacterial count, sensory index, texture analysis, and total volatile basic nitrogen (TVB-N) revealed that PL, MAP, and MAP + PL treatment delayed the deterioration of greater amberjack filets. These treatment groups also showed decreased accumulation of biogenic amines. High-throughput 16S rRNA gene sequencing results indicated that these treatments suppressed the growth of Pseudomonas in greater amberjack filets. Furthermore, the MAP + PL treatment group was observed to be more effective than the PL and MAP groups, extending the shelf life of greater amberjack filets by 6 days. This investigation showed that the combination of PL and MAP has the potential to retain the quality and extend the shelf life of greater amberjack.
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15
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Yang YZ, Luo MX, Yan HX, Gao RH, Chang JT, Chao CT, Liao PC. Physicochemical and Biotic Changes and the Phylogenetic Evenness of Microbial Community in Soil Subjected to Phytoreclamation. MICROBIAL ECOLOGY 2022; 84:1182-1194. [PMID: 34741194 DOI: 10.1007/s00248-021-01890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Phytoreclamation is the intervention of plants to improve degraded soil quality, changing soil biotic and abiotic properties. Many studies have focused on microbial composition and bioactivity, but few explored the changes in phylogenetic assemblages of soil microbiota after phytoreclamation. This study compared microbiomes of bare land to those of planted soils and investigated how the rhizosphere environment affects microbial assemblages from monocot Poa pratensis and eudicot Dianthus plumarius plantings using 16S rRNA metabarcoding. The results showed that the biotic susceptibility of soil to the rhizosphere environment was higher than that of the abiotic. A noticeable change was in some soil physicochemical properties like Na, P, Zn, Cu, C, and sand-to-silt proportion before and after phytoreclamation, but not between the rhizosphere and bulk soil of plantings. Contrastingly, microbial composition and diversity were significantly affected by both turfing and rhizosphere effects and were more susceptible to differences in turfing or not than in planting species. In the turfgrass, the microbiome differences between plants were greater in the rhizosphere than in the surrounding bulk soil, indicating the proximal influence of root exudates. We also found that the main abiotic factors that influenced microbial composition were Na, Zn, NOx, N, and S; as for the phylogenetic assemblages, were by K levels and the increase of silt. Turfgrass decomposes soil aggregates and changes the physicochemical properties, thereby evens the phylogenetic clustering of the soil microbial community. We demonstrated that the deterministic process affects the microbial assemblage and acts as a selective agent of the soil microbiota in fundamental and realized niches. Phytoreclamation may lead to abiotic soil changes that reallocate resources to microbes. This could affect the phylogeny of the microbial assemblages and increase microbial richness.
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Affiliation(s)
- Yong-Zhi Yang
- College of Forestry, Inner Mongolia Agricultural University, Huhhot, 010019, China
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Hai-Xia Yan
- Inner Mongolia Autonomous Region Hohhot Ecological Environment Monitoring Station, Hohhot, 010030, China
| | - Run-Hong Gao
- College of Forestry, Inner Mongolia Agricultural University, Huhhot, 010019, China.
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan.
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16
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Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
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17
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Qin Z, Li B, Xu F, Chen K, Chen C, Wan J, Yu C, Yang J, Shen C. Metagenomic study of humic acid promoting the dechlorination of polychlorinated biphenyls. CHEMOSPHERE 2022; 301:134688. [PMID: 35489463 DOI: 10.1016/j.chemosphere.2022.134688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants that degrade slowly in the environment. Humic acid (HA), the main component of soil organic matter, or more specifically, the quinone moieties in HA, is generally regarded as an "electron shuttle" between pollutants and microorganisms, which could promote microbial remediation of contamination. In this study, we examined the dechlorination of PCB153 by adding HA and anthraquinone-2,6-disulfonate (AQDS, a model compound of quinones) to systems containing PCB dechlorinators, analyzed the composition and functional gene network of the microbial community by metagenomics, and explored the role of HA by modifying or substituting carbon sources or electron donors. However, this study found that HA accelerated microbial dechlorination of PCBS, while AQDS did not. Moreover, HA without quinone activity still promoted dechlorination, but not without carbon source or electron donor. Metagenomic analysis showed that HA did not promote the growth of PCB dechlorinator (Dehalococcoides), but the transmembrane electron carriers in the HA group were higher than those in the AQDS group and the control group, so HA may have promoted the electron transport process. This study is helpful for microbial remediation of PCB contamination, and provides new insights into the role that HA plays in the biogeochemical cycle.
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Affiliation(s)
- Zhihui Qin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Binglu Li
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengjun Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jixing Wan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chunna Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiawen Yang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
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18
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Schneider KM, Mohs A, Gui W, Galvez EJC, Candels LS, Hoenicke L, Muthukumarasamy U, Holland CH, Elfers C, Kilic K, Schneider CV, Schierwagen R, Strnad P, Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, de Vos W, Strowig T, Trebicka J, Trautwein C. Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment. Nat Commun 2022; 13:3964. [PMID: 35803930 PMCID: PMC9270328 DOI: 10.1038/s41467-022-31312-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, and therapeutic options for advanced HCC are limited. Here, we observe that intestinal dysbiosis affects antitumor immune surveillance and drives liver disease progression towards cancer. Dysbiotic microbiota, as seen in Nlrp6-/- mice, induces a Toll-like receptor 4 dependent expansion of hepatic monocytic myeloid-derived suppressor cells (mMDSC) and suppression of T-cell abundance. This phenotype is transmissible via fecal microbiota transfer and reversible upon antibiotic treatment, pointing to the high plasticity of the tumor microenvironment. While loss of Akkermansia muciniphila correlates with mMDSC abundance, its reintroduction restores intestinal barrier function and strongly reduces liver inflammation and fibrosis. Cirrhosis patients display increased bacterial abundance in hepatic tissue, which induces pronounced transcriptional changes, including activation of fibro-inflammatory pathways as well as circuits mediating cancer immunosuppression. This study demonstrates that gut microbiota closely shapes the hepatic inflammatory microenvironment opening approaches for cancer prevention and therapy.
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Affiliation(s)
- Kai Markus Schneider
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Antje Mohs
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Wenfang Gui
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Eric J C Galvez
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | | | - Lisa Hoenicke
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Uthayakumar Muthukumarasamy
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Christian H Holland
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Carsten Elfers
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Kilic
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Carolin Victoria Schneider
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert Schierwagen
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), 08021, Barcelona, Spain
- Translational Hepatology, Department of Internal Medicine I, Goethe University Frankfurt, 60323, Frankfurt, Germany
| | - Pavel Strnad
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Theresa H Wirtz
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127, Bonn, Germany
- Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
- German Center for Neurodegenerative Diseases, 53127, Bonn, Germany
| | | | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Jonel Trebicka
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), 08021, Barcelona, Spain
- Translational Hepatology, Department of Internal Medicine I, Goethe University Frankfurt, 60323, Frankfurt, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
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19
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Liang Y, Zhou X, Wu Y, Wu Y, Gao S, Zeng X, Yu Z. Rhizobiales as the Key Member in the Synergistic Tris (2-chloroethyl) Phosphate (TCEP) Degradation by Two Bacterial Consortia. WATER RESEARCH 2022; 218:118464. [PMID: 35461102 DOI: 10.1016/j.watres.2022.118464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Tris(2-chloroethyl) phosphate (TCEP) is of growing concern because of its ubiquitous occurrence, potential toxicity, and persistence in the environment. In this study, two efficient TCEP degradation consortia (AT1 and AT3) were developed and were able to completely hydrolyze TCEP within 20-25 h. Rhizobiales was identified as the key degrader in both consortia, because Rhizobiales-related phosphoesterase genes were enriched by one to two orders of magnitude when the carbon source was changed from acetate to TCEP. In addition, the increase in Rhizobiales abundance was related to the development of TCEP degradation. The isolation of Xanthobacter strains confirmed the efficient TCEP and bis(2-chloroethyl) phosphate (BCEP) degradation of Rhizobiales. The higher abundances of phosphoesterase genes affiliated with Rhizobiales genera (Bradyrhizobium and Ancylobacter), Cytophagales genus (Spirosoma), Sphingobacteriales genus (Pedobacter), and Burkholderia genus (Methylibium), may be related to the faster TCEP degradation in AT3, while the higher abundance of Rhizobiales genus (Hyphomicrobium)-related phosphodiesterase (PDE) genes may contribute to the faster BCEP degradation in AT1. The stepwise hydrolysis of TCEP was likely catalyzed by different bacterial guilds, which was confirmed by the coculture of TCEP- and BCEP-degrading isolates and highlighted the importance of synergistic interactions during TCEP degradation.
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Affiliation(s)
- Yi Liang
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Xiangyu Zhou
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yiding Wu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Shutao Gao
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Xiangying Zeng
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
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20
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Ye L, Dong N, Xiong W, Li J, Li R, Heng H, Chan EWC, Chen S. High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly. Front Microbiol 2022; 13:801587. [PMID: 35633679 PMCID: PMC9134245 DOI: 10.3389/fmicb.2022.801587] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms. Assembly was achieved using four assemblers, including Flye (Nanopore), metaSPAdes (Illumina), hybridSPAdes (Illumina and Nanopore), and OPERA-MS (Illumina and Nanopore). Hybrid metagenome assembly was shown to generate contigs with almost same sizes comparable to those produced using Illumina reads alone, but was more contiguous, informative, and longer compared with those assembled with Illumina reads only. In addition, hybrid metagenome assembly enables us to obtain complete plasmid sequences and much more AMR gene-encoding contigs than the Illumina method. Most importantly, using our workflow, 58 novel high-quality metagenome bins were obtained from four assembly algorithms, particularly hybrid assembly (47/58), although metaSPAdes could provide 11 high-quality bins independently. Among them, 29 bins were currently uncultured bacterial metagenome-assembled genomes. These findings were highly consistent and supported by mock community data tested. In the analysis of biosynthetic gene clusters (BGCs), the number of BGCs in the contigs from hybridSPAdes (241) is higher than that of contigs from metaSPAdes (233). In conclusion, hybrid metagenome assembly could significantly enhance the efficiency of contig assembly, taxonomic binning, and genome construction compared with procedures using Illumina short-read data alone, indicating that nanopore long reads are highly useful in metagenomic applications. This technique could be used to create high-resolution references for future human metagenome studies.
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Affiliation(s)
- Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Wenguang Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Heng Heng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Edward Wai Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Sheng Chen,
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21
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Mwirichia R. Amplicon-Based Analysis of the Fungal Diversity across Four Kenyan Soda Lakes. SCIENTIFICA 2022; 2022:9182034. [PMID: 35572347 PMCID: PMC9098348 DOI: 10.1155/2022/9182034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms have been able to colonize and thrive in extreme environments characterized by low/high pH, temperature, salt, or pressure. Examples of extreme environments are soda lakes and soda deserts. The objective of this study was to explore the fungal diversity across soda lakes Magadi, Elmenteita, Sonachi, and Bogoria in Kenya. A new set of PCR primers was designed to amplify a fragment long enough for the 454-pyrosequencing technology. Analysis of the amplicons generated showed that the new primers amplified for diverse fungal groups. A total of 153,634 quality-filtered, nonchimeric sequences derived from the 18S region of the rRNA region were used for community diversity analysis. The sequence reads were clustered into 502 OTUs at 97% similarity cut-off using BLASTn analysis of which 432 were affiliated to known fungal phylotypes and the rest to other eukaryotes. Fungal OTUs were distributed across 107 genera affiliated to the phyla Ascomycota, Basidiomycota, Glomeromycota, and and other unclassified groups refred to as Incertae sedis. The phylum Ascomycota was the most abundant in terms of OTUs. Overall, fifteen genera (Chaetomium, Monodictys, Arthrinium, Cladosporium, Fusarium, Myrothecium, Phyllosticta, Coniochaeta, Diatrype, Sarocladium, Sclerotinia, Aspergillus, Preussia, and Eutypa) accounted for 65.3% of all the reads. The genus Cladosporium was detected across all the samples at varying percentages with the highest being water from Lake Bogoria (51.4%). Good's coverage estimator values ranged between 97 and 100%, an indication that the dominant phylotypes were represented in the data. These results provide useful insights that can guide cultivation-dependent studies to understand the physiology and biochemistry of the as-yet uncultured taxa.
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Affiliation(s)
- Romano Mwirichia
- Department of Biological Sciences, University of Embu, P.O Box 6-60100, Embu, Kenya
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22
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Li Z, Li A, Dai W, Leng H, Liu S, Jin L, Sun K, Feng J. Skin Microbiota Variation Among Bat Species in China and Their Potential Defense Against Pathogens. Front Microbiol 2022; 13:808788. [PMID: 35432245 PMCID: PMC9009094 DOI: 10.3389/fmicb.2022.808788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Host-associated skin bacteria are essential for resisting pathogen infections and maintaining health. However, we have little understanding of how chiropteran skin microbiota are distributed among bat species and their habitats, or of their putative roles in defending against Pseudogymnoascus destructans in China. In this study, we characterized the skin microbiomes of four bat species at five localities using 16S rRNA gene amplicon sequencing to understand their skin microbial composition, structure, and putative relationship with disease. The alpha- and beta-diversities of skin microbiota differed significantly among the bat species, and the differences were affected by environmental temperature, sampling sites, and host body condition. The chiropteran skin microbial communities were enriched in bacterial taxa that had low relative abundances in the environment. Most of the potential functions of skin microbiota in bat species were associated with metabolism. Focusing on their functions of defense against pathogens, we found that skin microbiota could metabolize a variety of active substances that could be potentially used to fight P. destructans. The skin microbial communities of bats in China are related to the environment and the bat host, and may be involved in the host's defense against pathogens.
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Affiliation(s)
- Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Sen Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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23
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Hou Q, Wang Y, Ni H, Cai W, Liu W, Yang S, Zhang Z, Shan C, Guo Z. Deep sequencing reveals changes in prokaryotic taxonomy and functional diversity of pit muds in different distilleries of China. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01671-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Purpose
The microbial community in the pit mud correlated closely with the quality of the final product of Chinese strong-flavored Baijiu (CSFB). However, environmental conditions and brewing processes can vary by region and distilleries. This may lead to differences in microbial composition and function in pit mud. Therefore, revealing the features of the pit mud microbial community structure and functions of different distilleries will provide key information for understanding the diversity and difference of microbes in the brewing of CSFB, which will be beneficial for the improvement of the quality of pit mud and CSFB in the future.
Methods and results
Illumina MiSeq sequencing of 16S rRNA gene amplicons was used to analyze the similarities and differences in microbial community structure and function in pit muds of different distilleries located in Shihezi (Xinjiang), Xiangyang (Hubei), and Yibin (Sichuan). At the genus level, Clostridium, Lactobacillus, Aminobacterium, Petrimonas, Syntrophomonas, Methanoculleus, Syntrophaceticus, Sedimentibacter, Caloramator, Ruminococcus, Bacillus, Methanosarcina, and Garciella were the dominated genera of pit muds. There were great differences in the composition of microorganisms in pit muds used by different distilleries. The significantly enriched prokaryotic microbiotas of pit muds collected in the distilleries of Xiangyang were mainly affiliated with Bacillus, Lactobacillus, and Croceifilum, and the relative abundance of methanogens, such as Methanomicrobia and Methanobacteria, were only significantly enriched in the pit mud collected from the distilleries of Yibin (P < 0.05). Functional analysis indicated that the difference of microbial composition in pit mud will further lead to significant differences in various metabolic functions.
Conclusion
The compositions and functions of dominant microorganisms in pit mud used for the production of CSFB by different enterprises across regions in China were greatly different, and there was a close relationship between the compositions and functions of microorganisms in pit mud. Therefore, it may be an effective method to improve CSFB fermentation processes by directionally regulating the microbial community functions of pit mud using specific strains.
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24
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Xue Y, Tang F, Cai W, Zhao X, Song W, Zhong J, Liu Z, Guo Z, Shan C. Bacterial Diversity, Organic Acid, and Flavor Analysis of Dacha and Ercha Fermented Grains of Fen Flavor Baijiu. Front Microbiol 2022; 12:769290. [PMID: 35058895 PMCID: PMC8765705 DOI: 10.3389/fmicb.2021.769290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/29/2021] [Indexed: 01/12/2023] Open
Abstract
Fen flavor Baijiu needs two rounds of fermentation, which will obtain Dacha after initial fermentation and Ercha after secondary fermentation. The quality of Baijiu is closely related to the microbes within fermented grains. However, the bacterial diversity in Dacha and Ercha fermented grains of Fen flavor Baijiu has not been reported. In the present study, the structure and diversity of bacteria communities within fermented grains of Fen flavor Baijiu were analyzed and evaluated using MiSeq platform's HTS with a sequencing target of the V3-V4 region of the 16S rRNA gene. Through the analysis of physical and chemical indexes and electronic senses, the relationship between bacterial flora, organic acid, taste, and aroma in fermented grains was clarified. The results indicated that Lactobacillus was the main bacteria in Dacha, and the mean relative content was 97.53%. The bacteria within Ercha samples were Pseudomonas and Bacillus, mean relative content was 37.16 and 28.02%, respectively. The diversity of bacterial communities in Ercha samples was significantly greater than that in Dacha samples. The correlation between Lactobacillus and organic acids, especially lactic acid, led to the difference between Dacha and Ercha organic acids, which also made the pH value of Dacha lower and the sour taste significantly higher than Ercha. Lactobacillus was significantly positively correlated with a variety of aromas, which made Dacha the response value of aromas higher. In addition, Bacillus had a significant positive correlation with bitterness and aromatic compounds, which led to a higher response value of bitterness in Ercha and made it present an aromatic aroma. This study provides an in-depth analysis of the difference between different stages of Fen flavor Baijiu, and theoretical support for the standard production and improvement in quality of Fen flavor Baijiu in the future.
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Affiliation(s)
- Yu'ang Xue
- School of Food Science, Shihezi University, Shihezi, China.,School of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China.,Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, China
| | - Fengxian Tang
- School of Food Science, Shihezi University, Shihezi, China
| | - Wenchao Cai
- School of Food Science, Shihezi University, Shihezi, China
| | - Xinxin Zhao
- School of Food Science, Shihezi University, Shihezi, China
| | - Wen Song
- School of Food Science, Shihezi University, Shihezi, China
| | - Ji'an Zhong
- Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, China.,Xiangyang Fen-Flavor Baijiu Biotechnology Key Laboratory, Xiangyang, China
| | - Zhongjun Liu
- Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, China.,Xiangyang Fen-Flavor Baijiu Biotechnology Key Laboratory, Xiangyang, China
| | - Zhuang Guo
- School of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China.,Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, China
| | - Chunhui Shan
- School of Food Science, Shihezi University, Shihezi, China
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25
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Zhao X, Xiang F, Tang F, Cai W, Guo Z, Hou Q, Yang X, Song W, Shan C. Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China. Front Microbiol 2022; 12:748779. [PMID: 35046909 PMCID: PMC8762310 DOI: 10.3389/fmicb.2021.748779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023] Open
Abstract
Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.
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Affiliation(s)
- Xinxin Zhao
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Fanshu Xiang
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Fengxian Tang
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Wenchao Cai
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Sciences, Xiangyang, China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Sciences, Xiangyang, China
| | - Xinquan Yang
- School of Food Science, Shihezi University, Shihezi, China
| | - Wen Song
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Chunhui Shan
- School of Food Science, Shihezi University, Shihezi, China.,Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
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26
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Lüdemann M, Sulastyanto S, Raab P, Schoen C, Rudert M. Periprosthetic joint infection: Comparison of automated multiplex-PCR Unyvero i60 ITI cartridge system with bacterial culture and real-time PCR. Technol Health Care 2022; 30:1005-1015. [DOI: 10.3233/thc-213248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: In the past, various efforts have been made to investigate diagnostic tools for periprosthetic-joint-infection (PJI). It is little-known about the diagnostic utility of polymerase-chain-reaction (PCR) in this context, especially concerning the role of multiplex-PCR assays comparing with conventional tissue culture. OBJECTIVE: Evaluation of an automated-multiplex-PCR cartridge system for patients with suspicion of PJI in comparison with conventional microbiological culture and 16S-rDNA-PCR. METHODS: On suspicion of PJI synovial fluid specimen were taken preoperatively or periprosthetic tissue was collected intraoperatively. Microbiological analysis included conventional culture, 16S-rDNA-PCR and automated-multiplex-PCR (Unyvero-i60-ITI®). The European-Bone-and-Joint-Infection-Society (EBJIS) criteria were used for PJI diagnosis. Positive and negative percent agreement was calculated. Total percentage agreement and Cohen’s kappa coefficient were calculated. Sensitivity, specificity and positive predictive value of conventional culture, 16S-rDNA-PCR and multiplex-PCR were calculated. Ten specimens of proved PJI were used as control group. RESULTS: Fifty specimen were suitable for culture. 14 (28%) were classified as PJI, 36 (72%) were aseptic. Coagulase-negative staphylococci was the most frequent detected pathogen. Concordance-rate between mPCR and culture results was 75.6% with a Cohen’s kappa of 0.28. Concordance-rate between mPCR and 16S-rDNA was 82.9%, Cohen’s kappa was 0.13. Concordance analysis between culture results and 16S-rDNA lead to a concordance-rate of 88.9%. Cohen’s kappa was calculated with 0.6. With regard to the microbiological culture as reference, sensitivity of the mPCR was 0.33 and specificity was 0.91. Sensitivity and specificity of the 16S-rDNA-PCR was 0.55 and 0.97. The positive predictive value was 0.57 for the mPCR and 0.83 for the 16S-rDNA-PCR. CONCLUSIONS: Due to fair agreement between mPCR and conventional microbiological culture, the tested multiplex-PCR could be an additional instrument for the detection of PJI but is not superior over the conventional culture.
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Affiliation(s)
- Martin Lüdemann
- Department of Orthopaedic Surgery, University of Wuerzburg, Wuerzburg, Germany
| | - Saskia Sulastyanto
- Department of Orthopaedic Surgery, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Raab
- Department of Orthopaedic Surgery, University of Wuerzburg, Wuerzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Maximilian Rudert
- Department of Orthopaedic Surgery, University of Wuerzburg, Wuerzburg, Germany
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27
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Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae. Sci Rep 2022; 12:169. [PMID: 34997021 PMCID: PMC8742107 DOI: 10.1038/s41598-021-03973-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.
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Cai W, Xue Y, Tang F, Wang Y, Yang S, Liu W, Hou Q, Yang X, Guo Z, Shan C. The Depth-Depended Fungal Diversity and Non-depth-Depended Aroma Profiles of Pit Mud for Strong-Flavor Baijiu. Front Microbiol 2022; 12:789845. [PMID: 35069486 PMCID: PMC8770870 DOI: 10.3389/fmicb.2021.789845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/03/2021] [Indexed: 01/09/2023] Open
Abstract
Microorganisms in pit mud are the essential factor determining the style of strong flavor Baijiu. The spatial distribution characteristics of fungal communities and aroma in the pit mud for strong flavor Baijiu from Xinjiang, China, were investigated using Illumina MiSeq high-throughput sequencing and electronic nose technology. A total of 138 fungal genera affiliated with 10 fungal phyla were identified from 27 pit mud samples; of these, Saccharomycopsis, Aspergillus, and Apiotrichum were the core fungal communities, and Aspergillus and Apiotrichum were the hubs that maintain the structural stability of fungal communities in pit mud. The fungal richness and diversity, as well as aroma of pit mud, showed no significant spatial heterogeneity, but divergences in pit mud at different depths were mainly in pH, total acid, and high abundance fungi. Moisture, NH4 +, and lactate were the main physicochemical factors involved in the maintenance of fungal stability and quality in pit mud, whereas pH had only a weak effect on fungi in pit mud. In addition, the fungal communities of pit mud were not significantly associated with the aroma. The results of this study provide a foundation for exploring the functional microorganisms and dissecting the brewing mechanism of strong flavor Baijiu in Xinjiang, and also contributes to the improvement of pit mud quality by bioaugmentation and controlling environmental physicochemical factors.
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Affiliation(s)
- Wenchao Cai
- School of Food Science, Shihezi University, Shihezi, China
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Yu’ang Xue
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Fengxian Tang
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Shaoyong Yang
- Hubei Guxiangyang Baijiu Co., Ltd., Xiangyang, China
| | - Wenhui Liu
- Hubei Guxiangyang Baijiu Co., Ltd., Xiangyang, China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Xinquan Yang
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Chunhui Shan
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
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Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD. Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Nat Microbiol 2022; 7:169-179. [PMID: 34952941 PMCID: PMC8732310 DOI: 10.1038/s41564-021-01011-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.
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Affiliation(s)
- Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Diana M Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Martin Hölzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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Cai W, Wang Y, Ni H, Liu Z, Liu J, Zhong J, Hou Q, Shan C, Yang X, Guo Z. Diversity of microbiota, microbial functions, and flavor in different types of low-temperature Daqu. Food Res Int 2021; 150:110734. [PMID: 34865753 DOI: 10.1016/j.foodres.2021.110734] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/06/2021] [Accepted: 09/28/2021] [Indexed: 02/01/2023]
Abstract
Light-flavor Baijiu is made from grain materials using a combination of three types of low-temperature Daqu (Hongxin, Houhuo, and Qingcha). This study comprehensively examined the microbial structure, microbial functions, and flavor characteristics of the three types of low-temperature Daqu using high-throughput sequencing and electronic senses, and it further clarified the relationship between the microbiota and flavor in low-temperature Daqu. The results showed that Hongxin had the highest bacterial richness and diversity, while Houhuo had the lowest. Both fungal richness and diversity were significantly higher in Qingcha than in Hongxin and Houhuo. The differences in peak temperature during Daqu-making led to significant differences in the structure of microbial communities, microbial functions, and flavor quality in the three types of low-temperature Daqu, and could be leveraged for screening and enriching functional microorganisms for Baijiu-making. Co-exclusion patterns between lactic acid bacteria and Bacillus in low-temperature Daqu resulted in a negative correlation between amino acid transport metabolism and carbohydrate transport metabolism. The different types of low-temperature Daqu had distinct flavor profiles, and the differences in the taste profiles were more significant. Dominated by Thermoactinomyces and Lactobacillus, and together with Saccharopolyspora, Bacillus, Streptomyces, Saccharomycopsis, and Thermoascus, they formed the core microbiota that influencing the flavor of low-temperature Daqu. The bacteria mainly influenced the taste of low-temperature Daqu, whereas the fungi mainly influenced the aroma. Each type of low-temperature Daqu contributed to the flavor of light-flavor Baijiu: Hongxin could elevate the levels of aromatic compounds, Houhuo could regulate the bitterness and sourness, and Qingcha could inhibit the generation of sulfur organic compounds. The results of the present study enrich and refine our knowledge of low-temperature Daqu, promoting the further evolution of traditional brewing methods.
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Affiliation(s)
- Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, PR China; School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, PR China; Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, PR China; Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China
| | - Hui Ni
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, PR China; School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, PR China; Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China
| | - Zhongjun Liu
- Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China; Xiangyang Fen-flavor Baijiu Biotechnology Key Laboratory, Xiangyang, Hubei Province, PR China
| | - Jiming Liu
- Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China; Xiangyang Fen-flavor Baijiu Biotechnology Key Laboratory, Xiangyang, Hubei Province, PR China
| | - Ji'an Zhong
- Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China; Xiangyang Fen-flavor Baijiu Biotechnology Key Laboratory, Xiangyang, Hubei Province, PR China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, PR China; Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China
| | - Chunhui Shan
- School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, PR China
| | - Xinquan Yang
- School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, PR China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, PR China; Xiangyang Liquor Brewing Biotechnology and Application Enterprise-University Joint Innovation Center, Xiangyang, Hubei Province, PR China.
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Cai W, Xue Y, Wang Y, Wang W, Shu N, Zhao H, Tang F, Yang X, Guo Z, Shan C. The Fungal Communities and Flavor Profiles in Different Types of High-Temperature Daqu as Revealed by High-Throughput Sequencing and Electronic Senses. Front Microbiol 2021; 12:784651. [PMID: 34925290 PMCID: PMC8674350 DOI: 10.3389/fmicb.2021.784651] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/01/2021] [Indexed: 02/01/2023] Open
Abstract
Polymicrobial co-fermentation is among the distinct character of high-temperature Daqu. However, fungal communities in the three types of high-temperature Daqu, namely, white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, are yet to be characterized. In this study, the fungal diversity, taste, and aroma profiles in the three types of high-temperature Daqu were investigated by Illumina MiSeq high-throughput sequencing, electronic tongue, and electronic nose, respectively. Ascomycota and Basidiomycota were detected as the absolute dominant fungal phylum in all types of high-temperature Daqu samples, whereas Thermomyces, Thermoascus, Aspergillus, Rasamsonia, Byssochlamys, and Trichomonascus were identified as the dominant fungal genera. The fungal communities of the three types of high-temperature Daqu differed significantly (p < 0.05), and Thermomyces, Thermoascus, and Monascus could serve as the biomarkers in white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, respectively. The three types of high-temperature Daqu had an extremely significant difference (p < 0.01) in flavor: white high-temperature Daqu was characterized by sourness, bitterness, astringency, richness, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds; black high-temperature Daqu was characterized by aftertaste-A, aftertaste-B, methane-aliph, hydrogen, and aromatic compounds; and yellow high-temperature Daqu was characterized by saltiness, umami, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds. The fungal communities in the three types of high-temperature Daqu were significantly correlated with taste but not with aroma, and the aroma of high-temperature Daqu was mainly influenced by the dominant fungal genera including Trichomonascus, Aspergillus, Thermoascus, and Thermomyces. The result of the present study enriched and refined our knowledge of high-temperature Daqu, which had positive implications for the development of traditional brewing technique.
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Affiliation(s)
- Wenchao Cai
- School of Food Science, Shihezi University, Shihezi, China
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Yu’ang Xue
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Wenping Wang
- Xiangyang Maotai-Flavor Baijiu Solid-State Fermentation Enterprise-University Joint Innovation Center, Xiangyang, China
| | - Na Shu
- Xiangyang Maotai-Flavor Baijiu Solid-State Fermentation Enterprise-University Joint Innovation Center, Xiangyang, China
| | - Huijun Zhao
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Fengxian Tang
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Xinquan Yang
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, China
| | - Chunhui Shan
- School of Food Science, Shihezi University, Shihezi, China
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Shihezi, China
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Zhao F, Jin H, Shen X, Li Q, Liu X, Zhang L, Sun Z, Yu J. Effect of the administration of probiotics on the fecal microbiota of adult individuals. Food Sci Nutr 2021; 9:6471-6479. [PMID: 34925778 PMCID: PMC8645741 DOI: 10.1002/fsn3.2547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022] Open
Abstract
Probiotics have been used to ameliorate ailments by modulating gut microbiota. However, to date, the effects of probiotic supplementation on the composition of fecal microbiota in healthy adults remain obscure. In this study, nine healthy volunteers were recruited to take probiotics (a mixture of Lactobacillus casei Zhang, L. plantarum P-8, and Bifidobacterium lactis V9, 2:2:3, 1 × 1010 CFU/day) for 28 days. The fecal samples were collected at 0 and 28 days, and V4 of the 16S rRNA gene sequenced by Illumina MiSeq was used to analyze the fecal microbiota. The enterotype has been used to characterize the composition of gut microbiota. Nine adults were divided into Type P (fecal microbiota dominated by Prevotella, 4 adults) and Type B (fecal microbiota dominated by Bacteroides, 5 adults) based on an enterotype analysis. The responses of variation had been found in two enterotypes. The α-diversity was not changed significantly after the administration of probiotics in both Type P and B. However, the community structure in Type B was substantially influenced. After the administration of probiotics, Weissella and Leuconostoc were significantly higher in Type P, while Collinsella significantly increased in Type B. The different pathways involving pathogen infections were downregulated at 28 days. The Type VI secretion system and the EHEC/EPEC pathogenicity signature were downregulated in Type B and Type P, respectively.
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Affiliation(s)
- Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Hao Jin
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Xin Shen
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Qi Li
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Xiaoye Liu
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lei Zhang
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and EngineeringKey Laboratory of Dairy Products ProcessingInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
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Succession of Microbial Communities of Corn Silage Inoculated with Heterofermentative Lactic Acid Bacteria from Ensiling to Aerobic Exposure. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To further explore the effects of heterofermentative lactic acid bacteria (LAB) on silage fermentation and aerobic stability, whole-plant corn at around the 1/2 milk-line stage was freshly chopped and ensiled in laboratory silos with deionized water (control), Lactobacillus buchneri (LB), or L. rhamnosus (LR). Each treatment was prepared in triplicate for 3, 14, and 60 d of fermentation, followed by 3 and 7 days of aerobic exposure. The dynamic changes in microbial community were studied by single molecule real-time (SMRT) sequencing. The results showed that the two LAB inoculants altered the microbial communities in different ways. Succession from L. plantarum to L. buchneri and L. rhamnosus was observed in LB- and LR-treated silage, respectively. Both silages improved aerobic stability (82 and 78 h vs. 44 h) by occupying the microbial niche to produce higher levels of acetic acid at terminal fermentation. Because Acetobacter fabarum dominated in the silages after aerobic exposure, beta diversity dramatically decreased. In this study, a. fabarum was reported for the first time in silage and was related to aerobic spoilage. The two heterofermentative LAB produced acetic acid and improved the aerobic stability of the corn silage by occupying the microbial niche at terminal fermentation. Inoculated L. rhamnosus had a greater pH for a longer period of time after opening and less DM loss at day 7.
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34
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Xu D, Wang W, Wang P, Zhang X, Zhang J, Xu C, Wang F. Soy whey as a promising substrate in the fermentation of soy sauce: a study of microbial community and volatile compounds. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Dandan Xu
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Wenping Wang
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Peng Wang
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Xin Zhang
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Jian Zhang
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Chunyan Xu
- Beijing Academy of Food Sciences Beijing 100068 China
| | - Fenghuan Wang
- Beijing Laboratory of Food Quality and Safety Beijing Technology and Business University Beijing 100050 China
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Ha J, Gao Y, Zhang R, Li K, Zhang Y, Niu X, Chen X, Luo K, Chen Y. Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava ( Manihot esculenta Crantz) Genotypes. Front Microbiol 2021; 12:729022. [PMID: 34659156 PMCID: PMC8515189 DOI: 10.3389/fmicb.2021.729022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
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Affiliation(s)
- Jingwen Ha
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yu Gao
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Rui Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Ke Li
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yijie Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiaolei Niu
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Luo
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinhua Chen
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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Webster TM, McFarland A, Gebert MJ, Oliverio AM, Nichols LM, Dunn RR, Hartmann EM, Fierer N. Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14105-14114. [PMID: 34606240 DOI: 10.1021/acs.est.1c03309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.
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Affiliation(s)
- Tara M Webster
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
| | - Alexander McFarland
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Matthew J Gebert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
| | - Angela M Oliverio
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina 27607, United States
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1050, Denmark
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
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The diversity and composition of the human gut lactic acid bacteria and bifidobacterial microbiota vary depending on age. Appl Microbiol Biotechnol 2021; 105:8427-8440. [PMID: 34625821 DOI: 10.1007/s00253-021-11625-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/25/2022]
Abstract
Aging is associated with gut microbiota alterations, characterized by changes in intestinal microbial diversity and composition. However, no study has yet focused on investigating age-related changes in the low-abundant but potentially beneficial subpopulations of gut lactic acid bacteria (LAB) and Bifidobacterium. Our study found that the subjects' age correlated negatively with the alpha diversity of the gut bifidobacterial microbiota, and such correlation was not observed in the gut LAB subpopulation. Principal coordinate analysis (PCoA) and analysis of distribution of operational taxonomic units (OTUs) revealed that the structure and composition of the gut bifidobacterial subpopulation of the longevous elderly group were rather different from that of the other three age groups. The same analyses were applied to identify age-dependent characteristics of the gut LAB subpopulation, and the results revealed that the gut LAB subpopulation of young adults was significantly different from that of all three elderly groups. Our study identified several potentially beneficial bacteria (e.g., Bifidobacterium breve and Bifidobacterium longum) that were enriched in the longevous elderly group (P < 0.05), and the relative abundance of Bifidobacterium adolescentis decreased significantly with the increase in age (P < 0.05). Although both bifidobacteria and LAB are generally considered as health-promoting taxa, their age-dependent distribution varied from each other, suggesting their different life stage changes and potentially different functional roles. This study provided novel species-level gut bifidobacterial and LAB microbiota profiles of a large cohort of subjects and identified several age-or longevity-associated features and biomarkers. KEY POINTS: • The alpha diversity of the gut bifidobacterial microbiota decreased with age, while LAB did not change. • The structure and composition of the gut bifidobacterial subpopulation of the longevous elderly group were rather different from that of the other three age groups. • Several potentially beneficial bacteria (e.g., Bifidobacterium breve and Bifidobacterium longum) that were enriched in the longevous elderly group.
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Zhen-Dong Z, Yu-Rong W, Fan-Shu X, Qiang-Chuan H, Zhuang G. Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing. Food Sci Biotechnol 2021; 30:1233-1241. [PMID: 34603822 DOI: 10.1007/s10068-021-00963-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 11/24/2022] Open
Abstract
Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00963-3.
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Affiliation(s)
- Zhang Zhen-Dong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Wang Yu-Rong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Xiang Fan-Shu
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Hou Qiang-Chuan
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Guo Zhuang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
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Yu Z, Peng C, Kwok LY, Zhang H. The Bacterial Diversity of Spontaneously Fermented Dairy Products Collected in Northeast Asia. Foods 2021; 10:foods10102321. [PMID: 34681370 PMCID: PMC8535065 DOI: 10.3390/foods10102321] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022] Open
Abstract
Spontaneously fermented dairy products have a long history, and present diverse microorganisms and unique flavors. To provide insight into the bacterial diversity, 80 different types of spontaneously fermented dairy product samples’ sequence data that were downloaded from MG-RAST and NCBI and 8 koumiss and 4 shubat were sequenced by the PacBio SMRT sequencing platform. All samples including butter, sour cream, cottage cheese, yogurt, koumiss, shubat, and cheese, were collected from various regions in Russia, Kazakhstan, Mongolia and Inner Mongolia (China). The results revealed that Firmicutes and Proteobacteria were the most dominant phyla (>99%), and 11 species were identified with a relative abundance exceeding 1%. Furthermore, Streptococcus salivarius, Lactobacillus helveticus, Lactobacillus delbrueckii, Enterobacter xiangfangensis, and Acinetobacter baumannii were the primary bacterial species in the fermented dairy product samples. Principal coordinates analysis showed that koumiss and shubat stood out from the other samples. Moreover, permutational ANOVA tests revealed that the types of fermented dairy products and geographical origin significantly affected microbial diversity. However, different processing techniques did not affect microbial diversity. In addition, results of hierarchical clustering and canonical analysis of the principal coordinates were consistent. In conclusion, geographical origin and types of fermented dairy products determined the bacterial diversity in spontaneously fermented dairy product samples.
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Affiliation(s)
- Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.Y.); (C.P.); (L.-y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Chuantao Peng
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.Y.); (C.P.); (L.-y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.Y.); (C.P.); (L.-y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.Y.); (C.P.); (L.-y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
- Correspondence:
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40
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Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing. Mol Biol Rep 2021; 48:7203-7214. [PMID: 34559376 DOI: 10.1007/s11033-021-06712-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Antibiotic resistance poses a grave threat to One-Health. By replacing antibiotics with non-antibiotic additives (are alternatives to antibiotics, ATAs) like phytogenic feed additives and organic acids in poultry feed. ATAs are a potential alternative as these decline the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. In this study, we use 16S rRNA amplicon sequencing of the V3-V4 region to evaluate phytogenic feed additives and organic acids on the cecal microbial diversity of broiler chickens. METHODS AND RESULTS Two hundred & forty broiler chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG), and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with increased microbial diversity in AB, ORG, and COM (p < 0.05). The synergistic effects of PHY and ORG increased bacterial population of phyla: Firmicutes, Bacteroides, and Proteobacteria in the cecum. The presence of species, Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups. CONCLUSIONS Treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens, led to healthy and economical broiler meat.
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41
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Ma T, Shen L, Wen Q, Lv R, Hou Q, Kwok LY, Sun Z, Zhang H. PacBio sequencing revealed variation in the microbiota diversity, species richness and composition between milk collected from healthy and mastitis cows. MICROBIOLOGY-SGM 2021; 167. [PMID: 34292863 DOI: 10.1099/mic.0.000968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mastitis is the economically most important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length 16S rRNAs from 27 milk samples (18 from mastitis and nine from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota of different groups also varied greatly. The healthy cow milk microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii, and Bacteroides dorei, while the milk from mastitis cows was predominantly comprised of Bacillus cereus. The prevalence of L. lactis and B. cereus in the milk samples was confirmed by digital droplets PCR. Differences in the milk microbiota diversity and composition could suggest an important role for some these microbes in protecting the host from mastitis while others associated with mastitis. The results of our research serve as useful references for designing strategies to prevent and treat mastitis.
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Affiliation(s)
- Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Lai Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, PR China.,Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot, PR China
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42
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Guo X, Yu Z, Zhao F, Sun Z, Kwok LY, Li S. Both sampling seasonality and geographic origin contribute significantly to variations in raw milk microbiota, but sampling seasonality is the more determining factor. J Dairy Sci 2021; 104:10609-10627. [PMID: 34253372 DOI: 10.3168/jds.2021-20480] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/28/2021] [Indexed: 11/19/2022]
Abstract
Accurately profiling and characterizing factors shaping raw milk microbiota would provide practical information for detecting microbial contamination and unusual changes in milk. The current work was an observational study aiming to profile the microbiota of raw milk collected across wide geographic regions in China in different seasons and to investigate the contribution of geographical, seasonal, and environmental factors in shaping the raw milk microbiota. A total of 355 raw cow milk samples from healthy Holsteins and 41 environmental samples (farm soil and surface of milking room floor) were collected from 5 dairy farms in 5 Chinese provinces (namely, Daqing in Heilongjiang province, Jiaozuo in Henan province, Qingyuan in Guangdong province, Suqian in Jiangsu province, and Yinchuan in Ningxia Hui Autonomous Region) in January, May, and September 2018. The microbial communities in raw milk and farm environmental samples were determined using the PacBio small-molecule real-time circular consensus sequencing, which generated high-fidelity microbiota profiles based on full-length 16S rRNA genes; such technology was advantageous in producing accurate species-level information. Our results showed that both seasonality and sampling region were significant factors influencing the milk microbiota; however, the raw milk microbiota was highly diverse according to seasonality, and sampling region was the less determining factor. The wide variation in raw milk microbial communities between samples made it difficult to define a representative species-level core milk microbiota. Nevertheless, 3 most universal milk-associated species were identified: Lactococcus lactis, Enhydrobacter aerosaccus, and Acinetobacter lwoffii, which were consistently detected in 99%, 95%, and 94% of all analyzed milk samples, respectively (n = 355). The top taxa accounting for the overall seasonal microbiota variation were Bacillus (Bacillus cereus, Bacillus flexus, Bacillus safensis), Lactococcus (Lactococcus lactis, Lactococcus piscium, Lactococcus raffinolactis), Lactobacillus (Lactobacillus helveticus, Lactobacillus delbrueckii), Lactiplantibacillus plantarum, Streptococcus agalactiae, Enhydrobacter aerosaccus, Pseudomonas fragi, and Psychrobacter cibarius. Unlike the milk microbiota, the environmental microbiota did not exhibit obvious pattern of seasonal or geographic variation. However, this study was limited by the relatively low number and types of environmental samples, making it statistically not meaningful to perform further correlation analysis between the milk and environmental microbiota. Nevertheless, this study generated novel information on raw milk microbiota across wide geographic regions of China and found that seasonality was more significant in shaping the raw milk microbiota compared with geographic origin.
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Affiliation(s)
- Xiaocen Guo
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhongjie Yu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Feiyan Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Zhang D, Chen S, Abd-Alla AMM, Bourtzis K. The Effect of Radiation on the Gut Bacteriome of Aedes albopictus. Front Microbiol 2021; 12:671699. [PMID: 34305838 PMCID: PMC8299835 DOI: 10.3389/fmicb.2021.671699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
The sterile insect technique (SIT) has been developed as a component of area-wide integrated pest management approaches to control the populations of Aedes albopictus, a mosquito vector capable of transmission of dengue, Zika and chikungunya viruses. One of the key factors for the success of SIT is the requirement of high biological quality sterile males, which upon their release would be able to compete with wild males for matings with wild females in the field. In insects, gut bacteriome have played a catalytic role during evolution significantly affecting several aspects of their biology and ecology. Given the importance of gut-associated bacterial species for the overall ecological fitness and biological quality of their hosts, it is of interest to understand the effects of radiation on the gut-associated bacteriome of Ae. albopictus. In this study, the effect of radiation on the composition and density levels of the gut-associated bacterial species at the pupal stage as well as at 1- and 4-day-old males and females was studied using 16S rRNA gene-based next generation sequencing (NGS) and quantitative PCR (qPCR) approaches. Age, diet, sex, and radiation were shown to affect the gut-associated bacterial communities, with age having the highest impact triggering significant changes on bacterial diversity and clustering among pupae, 1- and 4-day-old adult samples. qPCR analysis revealed that the relative density levels of Aeromonas are higher in male samples compared to all other samples and that the irradiation triggers an increase in the density levels of both Aeromonas and Elizabethkingia in the mosquito gut at specific stages. Our results suggest that Aeromonas could potentially be used as probiotics to enhance protandry and sex separation in support of SIT applications against Ae. albopictus, while the functional role of Elizabethkingia in respect to oxidative stress and damage in irradiated mosquitoes needs further investigation.
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Affiliation(s)
- Dongjing Zhang
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria.,Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-sen University, Guangzhou, China
| | - Shi Chen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria.,Institute of Biological Control, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
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Changes in physico-chemical characteristics and viable bacterial communities during fermentation of alfalfa silages inoculated with Lactobacillus plantarum. World J Microbiol Biotechnol 2021; 37:127. [PMID: 34181131 DOI: 10.1007/s11274-021-03095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 06/18/2021] [Indexed: 10/21/2022]
Abstract
This study investigated the effect of inoculating Lactobacillus (L.) plantarum PS-8 in fermentation of alfalfa silages. We monitored the fermentation characteristics and bacterial population dynamics during the ensiling process. PacBio single molecule real time sequencing was combined with propidium monoazide (PMA) treatment to monitor the viable microbiota dynamics. We found that inoculating L. plantarum PS-8 may improve the silage quality by accelerating acidification, reducing the amounts of clostridia, coliform bacteria, molds and yeasts, elevating the protein and organic acid contents (except butyrate), and enhancing lactic acid bacteria (LAB) while suppressing harmful microorganisms. Some significant differential abundant taxa were found between the PMA-treated and non-treated microbiota. For example, the relative abundances of L. brevis, L. plantarum, and Pediococcus pentosaceus were significantly higher in the PMA-treated group than the non-PMA-treated group, suggesting obvious differences between the viable and non-viable microbiota. It would thus be necessary to distinguish between the viable and non-viable microbial communities to further understand their physiological contribution in silage fermentation. By tracking the dynamics of viable microbiota in relation with changes in the physico-chemical parameters, our study provided novel insights into the beneficial effects of inoculating L. plantarum PS-8 in silage fermentation and the physiological function of the viable bacterial communities.
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Zhang Z, Wang Y, Zhang Y, Chen K, Chang H, Ma C, Jiang S, Huo D, Liu W, Jha R, Zhang J. Synergistic Effects of the Jackfruit Seed Sourced Resistant Starch and Bifidobacterium pseudolongum subsp. globosum on Suppression of Hyperlipidemia in Mice. Foods 2021; 10:foods10061431. [PMID: 34205515 PMCID: PMC8235523 DOI: 10.3390/foods10061431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 02/07/2023] Open
Abstract
Approximately 17 million people suffer from cardiovascular diseases caused by hyperlipidemia, making it a serious global health concern. Among others, resistant starch (RS) has been widely used as a prebiotic in managing hyperlipidemia conditions. However, some studies have reported limited effects of RS on body weight and blood lipid profile of the host, suggesting further investigation on the synergistic effects of RS in combination with probiotics as gut microbes plays a role in lipid metabolism. This study evaluated the effects of jackfruit seed sourced resistant starch (JSRS) as a novel RS on mice gut microbes and hyperlipidemia by performing 16s rRNA and shotgun metagenomic sequencing. The results showed that 10% JSRS had a limited preventive effect on bodyweight and serum lipid levels. However, the JSRS promoted the growth of Bifidobacterium pseudolongum, which indicated the ability of B. pseudolongum for JSRS utilization. In the validation experiment, B. pseudolongum interacted with JSRS to significantly reduce bodyweight and serum lipid levels and had a therapeutic effect on hepatic steatosis in mice. Collectively, this study revealed the improvements of hyperlipidemia in mice by the synergistic effects of JSRS and B. pseudolongum, which will help in the development of “synbiotics” for the treatment of hyperlipidemia in the future.
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Affiliation(s)
- Zeng Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Yuanyuan Wang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Yanjun Zhang
- Spice and Beverages Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning 571533, China;
| | - Kaining Chen
- Hainan Provincial People’s Hospital, Haikou 570311, China;
| | - Haibo Chang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Chenchen Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Dongxue Huo
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China; (Z.Z.); (Y.W.); (H.C.); (C.M.); (S.J.); (D.H.)
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
- Correspondence:
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Chen X, Zhang D, Sun H, Jiang F, Shen Y, Wei P, Shen X. Characterization of the gut microbiota in Chinese children with overweight and obesity using 16S rRNA gene sequencing. PeerJ 2021; 9:e11439. [PMID: 34164233 PMCID: PMC8194416 DOI: 10.7717/peerj.11439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 04/21/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Childhood obesity constitutes a worldwide health problem, and the gut microbiota play extremely important roles in obesity. Herein, we aimed to characterize the gut microbiota in children of normal weight, overweight, and obesity. METHODS Thirty children of normal weight, 35 who were overweight, and 35 with obesity were enrolled from Nanjing, China. We isolated DNA from fecal samples, and employed 16S rRNA gene sequencing to explore the diversity and composition of gut microbiota. RESULTS The operational taxonomic unit (OTU) numbers exhibited a reduction in the gut microbiota abundance with the increase in the body weight. Alpha diversity analysis revealed a sharp decrease in the mean microbial abundance among the three groups (Chao1: F = 5.478, P = 0.006; observed species: F = 7.271, P = 0.001; PD whole tree: F = 8.735, P < 0.001). Beta diversity analysis indicated notable differences in the gut microbial composition between children of normal weight and obesity. However, overweight children had little difference in gut microbiota compared to either children of normal weight or obesity. At the genus level, Oscillospira decreased among the three groups (χ2 = 10.062, P = 0.001), and Sutterella increased (F = 4.052, P = 0.020). There were many remarkably increased species of gut bacteria in the comparison among three groups, 31 in the normal weight group, 32 in the obese group, and only three species of bacteria were identified in the overweight group. These significantly increased species of gut bacteria may have a close relationship with the progression of obesity. CONCLUSIONS The abundance of species decreased significantly as the BMI increased. Although the gut microbial composition between children of normal weight and obesity was notably different, due to the changing ratio of some microbial communities, gut microbiota in overweight children showed similarities to that of children with normal weight and obesity.
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Affiliation(s)
- Xiaowei Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Dawei Zhang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Haixiang Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Fei Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yan Shen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Pingmin Wei
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Xiaobing Shen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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Rahmeh R, Akbar A, Kumar V, Al-Mansour H, Kishk M, Ahmed N, Al-Shamali M, Boota A, Al-Ballam Z, Shajan A, Al-Okla N. Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment. Evol Bioinform Online 2021; 17:11769343211016887. [PMID: 34163126 PMCID: PMC8191072 DOI: 10.1177/11769343211016887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/16/2021] [Indexed: 11/15/2022] Open
Abstract
Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.
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Affiliation(s)
- Rita Rahmeh
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Abrar Akbar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Vinod Kumar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Hamad Al-Mansour
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mohamed Kishk
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Nisar Ahmed
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mustafa Al-Shamali
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anwar Boota
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Zainab Al-Ballam
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anisha Shajan
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Naser Al-Okla
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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48
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Zhang K, Jia M, Guo Z, Li Y, Li B, Li X. Evaluation of bacterial diversity of traditional cheese in Tarbagatay Prefecture, China, and its correlation with cheese quality. Food Sci Nutr 2021; 9:3155-3164. [PMID: 34136180 PMCID: PMC8194751 DOI: 10.1002/fsn3.2275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
In Xinjiang, China, traditional handmade cheese is made from fresh milk under natural environmental conditions and is a common fermented dairy product in the region. Due to differences in production methods between regions, the research conducted on the bacterial diversity of traditional handmade cheese is not comprehensive. Hence, little is known about the relationship between bacteria and cheese quality. Therefore, in this study, cheese samples from Tarbagatay Prefecture, Xinjiang, were chosen for investigation. The bacteria in 17 cheese samples were analyzed by sequencing 16S rRNA using Illumina MiSeq technology. The results showed that there were two dominant bacterial phyla and six dominant bacterial genera in the cheeses. Of these, Lactobacillus and Lactococcus displayed the most significant positive correlation with cheese quality. This study provides data to support the improvement of traditional cheese quality via microbial diversity and lays a foundation for the industrialization of traditional cheese production.
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Affiliation(s)
- Kaili Zhang
- School of Food Science and Technology/Key laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
| | - Mengzhen Jia
- School of Food Science and Technology/Key laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHu Bei University of Arts and ScienceXiangyangChina
| | - Yuhui Li
- School of Food Science and Technology/Key laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
| | - Baokun Li
- School of Food Science and Technology/Key laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
| | - Xu Li
- School of Food Science and Technology/Key laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
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49
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Boscaini S, Cabrera‐Rubio R, Golubeva A, Nychyk O, Fülling C, Speakman JR, Cotter PD, Cryan JF, Nilaweera KN. Depletion of the gut microbiota differentially affects the impact of whey protein on high-fat diet-induced obesity and intestinal permeability. Physiol Rep 2021; 9:e14867. [PMID: 34057306 PMCID: PMC8165735 DOI: 10.14814/phy2.14867] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 01/13/2023] Open
Abstract
Whey protein isolate (WPI) is considered a dietary solution to obesity. However, the exact mechanism of WPI action is still poorly understood but is probably connected to its beneficial effect on energy balance, adiposity, and metabolism. More recently its ability to modulate the gut microbiota has received increasing attention. Here, we used a microbiota depletion, by antibiotic cocktail (ABX) administration, to investigate if the gut microbiota mediates the physiological and metabolic changes observed during high-fat diet (HFD)-WPI consumption. C57BL/6J mice received a HFD containing WPI (HFD-WPI) or the control non-whey milk protein casein (HFD-CAS) for 5 or 10 weeks. HFD-fed mice supplemented with WPI showed reduced body weight gain, adiposity, Ob gene expression level in the epidydimal adipose tissue (eWAT) and plasma leptin relative to HFD-CAS-fed mice, after 5- or 10-weeks intervention both with or without ABX treatment. Following 10-weeks intervention, ABX and WPI had an additive effect in lowering adiposity and leptin availability. HFD-WPI-fed mice showed a decrease in the expression of genes encoding pro-inflammatory markers (MCP-1, TNFα and CD68) within the ileum and eWAT, compared to HFD-CAS-fed mice, without showing alterations following microbiota depletion. Additionally, WPI supplementation decreased HFD-induced intestinal permeability disruption in the distal ileum; an effect that was reversed by chronic ABX treatment. In summary, WPI reverses the effects of HFD on metabolic and physiological functions through mainly microbiota-independent mechanisms. Moreover, we demonstrate a protective effect of WPI on HFD-induced inflammation and ileal permeability disruption, with the latter being reversed by gut microbiota depletion.
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Affiliation(s)
- Serena Boscaini
- Teagasc Food Research CentreMooreparkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
| | - Raul Cabrera‐Rubio
- Teagasc Food Research CentreMooreparkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Anna Golubeva
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
| | | | - Christine Fülling
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
| | - John R. Speakman
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenScotland
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Paul D. Cotter
- Teagasc Food Research CentreMooreparkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - John F. Cryan
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
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Zhang N, Li C, Xie H, Yang Y, Hu Z, Gao M, Liang S, Feng K. Mn oxides changed nitrogen removal process in constructed wetlands with a microbial electrolysis cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144761. [PMID: 33736424 DOI: 10.1016/j.scitotenv.2020.144761] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/20/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Intensified Mn redox cycling could enhance nutrient removal in constructed wetlands (CWs). In this study, Mn oxides (birnessite-coated sand) were used as the matrix in horizontal flow CWs (HFCWs) with a microbial electrolysis cell (MEC) (E-B-CW) or without an MEC (B-CW). The model CWs were developed to investigate the capacities and mechanisms of nitrogen removal with increased Mn redox cycling. The results showed that E-B-CW had the highest average removal efficiencies for NH4-N, NO3-N and TN, followed by B-CW and control HFCW (C-CW). The Mn(III) oxides (MnOOH or Mn2O3) and the Mn(IV) oxide (MnO2) were all detected in E-B-CW and B-CW, while the matrix in E-B-CW had much more Mn(IV) oxides than B-CW. Interestingly, clustering heat map showed that ammonification and nitrate reduction were related to Mn-oxidizing bacteria and the relative abundance of Mn-oxidizing bacteria in E-B-CW was highest due to the re-oxidation of Mn(II) by the MEC.
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Affiliation(s)
- Ning Zhang
- Environment Research Institute, Shandong University, Jinan 250100, China
| | - Chaoyu Li
- Environment Research Institute, Shandong University, Jinan 250100, China
| | - Huijun Xie
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Yixiao Yang
- Environment Research Institute, Shandong University, Jinan 250100, China
| | - Zhen Hu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Mingming Gao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Shuang Liang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Kuishuang Feng
- Institute of Blue and Green Development, Weihai Institute of Interdisciplinary Research, Shandong University, Weihai 264209, China
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