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Gao R, He H, Yang X, Wang W, Gao J, Yang C. Cold atmospheric plasma and skin wound healing: influence on microbial diversity and composition. BMC Microbiol 2025; 25:260. [PMID: 40301741 PMCID: PMC12042303 DOI: 10.1186/s12866-025-03965-x] [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: 07/17/2024] [Accepted: 04/14/2025] [Indexed: 05/01/2025] Open
Abstract
BACKGROUND Skin wound healing presents a complex challenge, often compounded by the risk of infection. Cold atmospheric plasma (CAP) emerged as a novel therapeutic for reducing bacterial load and expediting wound healing. However, its effect on the wound microbiome remained unclear. This study aimed to characterize the microbiome of different types of wounds and determine whether CAP influenced microbial diversity. METHODS Twenty-five patients (ten with acute, fifteen with chronic skin wounds) and ten healthy controls were enrolled. CAP was tailored to individual clinical conditions. Skin samples were collected before and after CAP, and microbiota composition was determined by 16 S ribosomal RNA sequencing. RESULTS Microbial communities differed between acute and chronic groups. CAP could accelerate wound healing. However, it did not change microbial α and β-diversity in acute wounds. In chronic wounds, α-diversity indices, including the chao and ACE, were significantly increased, and a significant clustering was observed in post-CAP group. In addition, CAP led to higher abundance of Staphylococcus, lower levels of Proteobacteria and Pseudomonas in chronic wounds. CONCLUSIONS This study provided novel insights into the impact of CAP on skin wound microbiota. Further research was required to ascertain causality between microbiota and CAP and to develop personalized CAP treatment strategies.
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Affiliation(s)
- Ruidi Gao
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
- Department of Dermatology and Venereology, Fuyang People's Hospital, Fuyang, China
| | - Houyu He
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
- Joint Laboratory for Plasma Clinical Applications, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xingyu Yang
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
- Joint Laboratory for Plasma Clinical Applications, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wang
- Department of Dermatology and Venereology, Fuyang People's Hospital, Fuyang, China
| | - Jing Gao
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
- Joint Laboratory for Plasma Clinical Applications, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chunjun Yang
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China.
- Joint Laboratory for Plasma Clinical Applications, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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Ye X, Sahana G, Lund MS, Li B, Cai Z. Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle. Anim Microbiome 2025; 7:24. [PMID: 40069804 PMCID: PMC11899718 DOI: 10.1186/s42523-025-00386-z] [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: 07/26/2024] [Accepted: 02/23/2025] [Indexed: 03/14/2025] Open
Abstract
BACKGROUND Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies. RESULTS This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles. CONCLUSIONS The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.
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Affiliation(s)
- Xiaoxing Ye
- Center for Quantitative Genetics and Genomics, Aarhus University, CF Møllers Allé 3, 8000, Aarhus, Denmark.
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, CF Møllers Allé 3, 8000, Aarhus, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, CF Møllers Allé 3, 8000, Aarhus, Denmark
| | - Bingjie Li
- Department of Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, CF Møllers Allé 3, 8000, Aarhus, Denmark
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Xiao Y, Zhang Y, Deng S, Yang X, Yao X. Immune and Non-immune Interactions in the Pathogenesis of Androgenetic Alopecia. Clin Rev Allergy Immunol 2025; 68:22. [PMID: 40024940 DOI: 10.1007/s12016-025-09034-5] [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] [Accepted: 02/17/2025] [Indexed: 03/04/2025]
Abstract
Androgenetic alopecia (AGA), a leading cause of progressive hair loss, affects up to 50% of males aged 50 years, causing significant psychological burden. Current treatments, such as anti-androgen drugs and minoxidil, show heterogeneous effects, even with long-term application. Meanwhile, the large-scale adoption of other adjuvant therapies has been slow, partly due to insufficient mechanistic evidence. A major barrier to developing better treatment for AGA is the incomplete understanding of its pathogenesis. The predominant academic consensus is that AGA is caused by abnormal expression of androgens and their receptors in individuals with a genetic predisposition. Emerging evidence suggests the contributing role of factors such as immune responses, oxidative stress, and microbiome changes, which were not previously given due consideration. Immune-mediated inflammation and oxidative stress disrupt hair follicles' function and damage the perifollicular niche, while scalp dysbiosis influences local metabolism and destabilizes the local microenvironment. These interconnected mechanisms collectively contribute to AGA pathogenesis. These additional aspects enhance our current understanding and confound the conventional paradigm, bridging the gap in developing holistic solutions for AGA. In this review, we gather existing evidence to discuss various etiopathogenetic factors involved in AGA and their possible interconnections, aiming to lay the groundwork for the future identification of therapeutic targets and drug development. Additionally, we summarize the advantages and disadvantages of AGA research models, ranging from cells and tissues to animals, to provide a solid basis for more effective mechanistic studies.
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Affiliation(s)
- Yu Xiao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China
| | - Yi Zhang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China
| | - Shuting Deng
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China
| | - Xueyuan Yang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China
| | - Xu Yao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China.
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, 210042, Jiangsu, China.
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Potbhare R, RaviKumar A, Munukka E, Lahti L, Ashma R. Skin microbiota variation in Indian families. PeerJ 2025; 13:e18881. [PMID: 40034669 PMCID: PMC11874944 DOI: 10.7717/peerj.18881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 12/28/2024] [Indexed: 03/05/2025] Open
Abstract
Background In India, joint families often encompass members spanning multiple generations cohabiting in the same household, thereby sharing the same ethnicity, genetics, dietary habits, lifestyles, and other living conditions. Such an extended family provides a unique opportunity to evaluate the effect of genetics and other confounding factors like geographical location, diet and age on the skin microbiota within and between families across three generations. Methods The present study involved seventy-two individuals from fifteen families from two geographical regions of Maharashtra, India. The 16S rRNA sequencing of V3-V4 regions was performed and the generated taxonomic profiles were used for downstream analysis. Results Our study highlights a significant difference in community composition (beta diversity) between families (PERMANOVA; p = 0.001) and geographical locations (p = 0.001). We observed geographical location-wise differences in the relative abundances Staphylococcus in the families from Pune (Wilcoxon test, p = 0.007), and Bacillus in the Ahmednagar families (Wilcoxon test, p = 0.004). When within and between-family comparisons of skin microbiota composition were carried out between different generations (G1-G2, G2-G3, and G1-G3); we observed skin microbiota tended to be more similar within than between families but this difference was not significant. Conclusion This study underscores the diversity and commonalities in skin microbiota composition within and between families. Our result suggests that geographical location is significantly associated with the genus composition of skin microbiota, which is quantitatively unique for a family and likely explained by co-habitation.
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Affiliation(s)
- Renuka Potbhare
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Eveliina Munukka
- Turku Clinical Microbiome Bank, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
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Lei Y, Li M, Zhang H, Deng Y, Dong X, Chen P, Li Y, Zhang S, Li C, Wang S, Tao R. Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference. mSphere 2025; 10:e0067224. [PMID: 39699186 PMCID: PMC11774049 DOI: 10.1128/msphere.00672-24] [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: 08/11/2024] [Accepted: 11/22/2024] [Indexed: 12/20/2024] Open
Abstract
The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.
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Affiliation(s)
- Yinlei Lei
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Min Li
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Han Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yu Deng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Xinyu Dong
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, China
| | - Pengyu Chen
- Department of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Ye Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Shouyu Wang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai, China
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Srila W, Sripilai K, Binlateh T, Thammanichanon P, Tiskratok W, Noisa P, Jitprasertwong P. Relationship Between the Salivary Microbiome and Oral Malodor Metabolites in Older Thai Individuals with Periodontitis and the Cytotoxic Effects of Malodor Compounds on Human Oral Squamous Carcinoma (HSC-4) Cells. Dent J (Basel) 2025; 13:36. [PMID: 39851614 PMCID: PMC11764442 DOI: 10.3390/dj13010036] [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: 12/05/2024] [Revised: 12/24/2024] [Accepted: 01/14/2025] [Indexed: 01/26/2025] Open
Abstract
Background/Objectives: Halitosis is primarily caused by the activity of oral microorganisms. In this study, we employed metagenomic sequencing and metabolomic approaches to investigate the differences in salivary microbiota and metabolite profiles between individuals with halitosis and periodontitis and healthy controls. Additionally, we expanded the study to examine how oral malodorous compounds interact with human oral squamous carcinoma (HSC-4) cells. Methods: Saliva samples were collected and analyzed using Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) to identify metabolites. We then assessed the correlations between the microbiota and metabolites. Furthermore, the impact of oral malodorous substances on HSC-4 cells was investigated by evaluating apoptosis, antioxidant activity, and inflammatory properties. Results: The microbiota and metabolite profiles showed significant differences between the halitosis with periodontitis group and the periodontally healthy group. The halitosis with periodontitis group exhibited significantly higher relative abundances of eight genera: Tannerella, Selenomonas, Bacteroides, Filifactor, Phocaeicola, Fretibacterium, Eubacterium saphenum, and Desulfobulbus. In contrast, the periodontally healthy group showed significantly higher relative abundances of Family XIII UCG-001, Haemophilus, and Streptobacillus. Two metabolites, 2,3-dihydro-1H-indole and 10,11-dihydro-12R-hydroxy-leukotriene E4, were significantly higher in individuals with halitosis and periodontitis. In the treatment of HSC-4 cells with metabolites, dimethyl sulfide (DMS) did not show significant effects while indole appeared to induce cell death in HSC-4 cells by triggering apoptotic pathways. Additionally, both indole and DMS affected the inflammatory and antioxidant properties of HSC-4 cells. Conclusions: This study provides insights into the mechanisms of halitosis by exploring the correlations between microbiota and metabolite profiles. Furthermore, oral metabolites were shown to impact the cellular response of HSC-4 cells.
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Affiliation(s)
- Witsanu Srila
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Pathum Thani 12110, Thailand;
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (K.S.); (P.N.)
| | - Kritsana Sripilai
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (K.S.); (P.N.)
| | - Thunwa Binlateh
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - Peungchaleoy Thammanichanon
- Institute of Dentistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (P.T.); (W.T.)
| | - Watcharaphol Tiskratok
- Institute of Dentistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (P.T.); (W.T.)
| | - Parinya Noisa
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (K.S.); (P.N.)
| | - Paiboon Jitprasertwong
- Institute of Dentistry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (P.T.); (W.T.)
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Manurung THP, Sitohang IBS, Agustin T. Staphylococcus caprae and Staphylococcus epidermidis define the skin microbiome among different grades of acne vulgaris. Arch Dermatol Res 2024; 317:156. [PMID: 39738874 DOI: 10.1007/s00403-024-03581-1] [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: 09/29/2024] [Revised: 11/09/2024] [Accepted: 11/26/2024] [Indexed: 01/02/2025]
Abstract
Acne vulgaris (AV) has been associated with Cutibacterium acnes (C. acnes) colonization in sebaceous follicles. However, recent studies have revealed the role of skin microbiome dysbiosis in acne pathogenesis. AV grading, which is classified by the sum of noninflammatory and inflammatory lesions, is essential in making clinical decisions about AV management. Henceforth, a better understanding of the skin microorganism profile in AV is needed. Our purpose was to compare microbiome profiles between different grades of AV severity. The microbiome samples were collected by swabbing from 108 participants with various AV grades in accordance with the classification from Lehmann. The V3-V4 regions of the 16 S rRNA gene were sequenced and analysed. The difference in the percentage of C. acnes among different grades of AV severity was not significant. However, the proportion of Staphylococcus epidermidis (S. epidermidis) was significantly greater in severe AV than in mild AV (0,3 vs. 0,1%; p = 0,046). The difference in the Shannon index between the groups was not remarkable. Several skin commensals were also found in the samples. However, only the proportion of Staphylococcus caprae (S. caprae) was significantly greater in mild AV than in moderate and severe AV (1.5% vs. 0.7% vs. 1.1%, p = 0.004). These results indicate that the degree of AV severity may be distinguished from the degree of dysbiosis associated with changes in skin commensal microorganisms, specifically S. epidermidis and S. caprae. This study was registered at ClinicalTrials.gov on April 28, 2023, under registration number NCT05838534.
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Affiliation(s)
- Teguh Hopkop Putera Manurung
- Faculty of Medicine, Department of Dermatology and Venereology, University of Indonesia, Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Irma Bernadette S Sitohang
- Faculty of Medicine, Department of Dermatology and Venereology, University of Indonesia, Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia.
| | - Triana Agustin
- Faculty of Medicine, Department of Dermatology and Venereology, University of Indonesia, Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
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Perveen N, Cabezas-Cruz A, Iliashevich D, Abuin-Denis L, Sparagano OA, Willingham AL. Microbiome of Hyalomma dromedarii (Ixodida: Ixodidae) Ticks: Variation in Community Structure with Regard to Sex and Host Habitat. INSECTS 2024; 16:11. [PMID: 39859594 PMCID: PMC11766007 DOI: 10.3390/insects16010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/06/2024] [Accepted: 12/13/2024] [Indexed: 01/27/2025]
Abstract
Hyalomma dromedarii ticks are the main hematophagous ectoparasites of camels, harboring a variety of microbes that can affect tick vector competence and pathogen transmission. To better understand the tick microbiome influenced by sex and host habitat, we analyzed the bacterial community of H. dromedarii male and female ticks collected from camel farms, livestock markets, and slaughterhouses, representing the range of major habitats in the UAE, by sequencing the 16S rRNA gene. Tick samples were collected during 2022 and 2023. A total of 40 ticks (male (15), female (15), and nymph (10)) were selected from tick samples collected from camels and processed for genomic DNA and next-generation sequencing using the Illumina MiSeq platform. We obtained 151,168 read counts, and these formed 237 operational taxonomic units representing 11 phyla, 22 classes, 77 families, and 164 genera. The phyla Actinomycetota, Bacillota, Bacteroidota, Pseudomonadota, and Fusobacteriota were the most abundant. The bacterial genus Corynebacterium dominated the microbiomes of farm-collected female H. dromedarii ticks, while Proteus dominated the microbiomes of farm-collected male H. dromedarii ticks. In comparison, the microbiomes of H. dromedarii ticks collected from slaughterhouse samples were dominated by genus Francisella in both males and females. Our results confirm that the bacterial microbiomes of H. dromedarii ticks vary by sex and habitat settings. Furthermore, recent findings could deliver insight into the differences in the ability of camel ticks to acquire, maintain, and transmit pathogens in various habitats that may impact the tick vector competence of medically and agriculturally important species in the Middle East and North Africa (MENA) region and Asia.
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Affiliation(s)
- Nighat Perveen
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, F-94700 Maisons-Alfort, France; (A.C.-C.); (L.A.-D.)
| | - Daniil Iliashevich
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
| | - Lianet Abuin-Denis
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, F-94700 Maisons-Alfort, France; (A.C.-C.); (L.A.-D.)
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 Between 158 and 190, Havana CU-10600, Cuba
| | - Olivier Andre Sparagano
- 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;
- UK Management College, Manchester M11 1AA, UK
| | - Arve Lee Willingham
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
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Chatthanathon P, Leelahavanichkul A, Cheibchalard T, Wilantho A, Hirankarn N, Somboonna N. Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation. Sci Rep 2024; 14:26371. [PMID: 39487198 PMCID: PMC11530527 DOI: 10.1038/s41598-024-77672-4] [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: 06/18/2024] [Accepted: 10/24/2024] [Indexed: 11/04/2024] Open
Abstract
Although the association between gut dysbiosis (imbalance of the microbiota) in systemic lupus erythematosus (SLE) is well-known, the simultaneous exploration in gut dysbiosis in fecal and different intestinal sections before and after lupus onset (at 2, 4, 6, 8, and 10 months old) resulting from the loss of inhibitory Fc gamma receptor IIb (FcGIIb) and pristane induction have never been conducted. Anti-dsDNA (an important lupus autoantibody) and proteinuria developed as early as 6 months old in both models, with higher levels in FcGRIIb deficient (FcGRIIb-/-) mice. Compared to the healthy control at 2 and 4 months, the lupus mice (both FcGRRIIb-/- and pristane) and healthy mice at 6 months old demonstrated an alteration as indicated by the Shannon alpha diversity index, highlighting influences of lupus- and age-induced dysbiosis, respectively. Non-metric multidimensional scaling (NMDS) revealed that the fecal microbiota of FcGRIIb-/- mice were distinct from the age-matched healthy control at all timepoints (at 6 month, p < 0.05), while pristane mice showed divergence at only some timepoints. Analyses of different intestinal sections revealed similarity among microbiota in the cecum, colon, and feces, contrasting with those in the small intestines (duodenum, jejunum, and ileum). Subtle differences were found between FcGRIIb-/- and pristane mice in feces and the intestinal sections as assessed by several analyses, for examples, the similar or dissimilar distances (NMDS), the neighbor-joining clustering, and the potential metabolisms (KEGG pathway analysis). Due to the differences between the gut microbiota (feces and intestinal sections) in the lupus mice and the healthy control, rebalancing of the microbiota using rectal administration of feces from the healthy control (fecal transplantation; FMT) to 7-month-old FcGIIb-/- mice (the established lupus; positive anti-dsDNA and proteinuria) was performed. In comparison to FcGRIIb-/- mice without FMT, FMT mice (more effect on the female than the male mice) showed the lower anti-dsDNA levels with similar fecal microbiome diversity (16s DNA gene copy number) and microbiota patterns to the healthy control. In conclusion, gut microbiota (feces and intestinal sections) of lupus mice (FcGRIIb-/- and pristane) diverged from the control as early as 4-6 months old, correlating with lupus characteristics (anti-dsDNA and proteinuria). The different gut microbiota in FcGRIIb-/- and pristane suggested a possible different gut microbiota in lupus with various molecular causes. Furthermore, FMT appeared to mitigate gut dysbiosis and reduce anti-dsDNA, supporting the benefit of the rebalancing gut microbiota in lupus, with more studies are warranted.
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Affiliation(s)
- Piraya Chatthanathon
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Multi-Omics for Functional Products in Food, Cosmetics and Animals Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Thanya Cheibchalard
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alisa Wilantho
- National Biobank of Thailand, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Multi-Omics for Functional Products in Food, Cosmetics and Animals Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand.
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, 10330, Thailand.
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10
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Cinca-Morros S, Garcia-Rey S, Álvarez-Herms J, Basabe-Desmonts L, Benito-Lopez F. A physiological perspective of the relevance of sweat biomarkers and their detection by wearable microfluidic technology: A review. Anal Chim Acta 2024; 1327:342988. [PMID: 39266058 DOI: 10.1016/j.aca.2024.342988] [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] [Received: 02/02/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 09/14/2024]
Abstract
The great majority of published microfluidic wearable platforms for sweat sensing focus on the development of the technology to fabricate the device, the integration of sensing materials and actuators and the fluidics of sweat within the device. However, very few papers have discussed the physiological relevance of the metabolites measured using these novel approaches. In fact, some of the analytes present in sweat, which serve as biomarkers in blood, do not show a correlation with blood levels. This discrepancy can be attributed to factors such as contamination during measurements, the metabolism of sweat glands, or challenges in obtaining significant samples. The objective of this review is to present a critical and meaningful insight into the real applicability and potential use of wearable technology for improving health and sport performance. It also discusses the current limitations and future challenges of microfluidics, aiming to provide accurate information about the actual needs in this field. This work is expected to contribute to the future development of more suitable wearable microfluidic technology for health and sports science monitoring, using sweat as the biofluid for analysis.
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Affiliation(s)
- Sergi Cinca-Morros
- Microfluidics Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip (AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Spain; Microfluidics Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Sandra Garcia-Rey
- Microfluidics Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip (AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Spain; Microfluidics Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Jesús Álvarez-Herms
- Research Group in Sports Genomics, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain; PHYMOlab Research & Exercise Performance, Segovia, Spain
| | - Lourdes Basabe-Desmonts
- Microfluidics Cluster UPV/EHU, BIOMICs Microfluidics Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Basque Foundation of Science, IKERBASQUE, María Díaz Haroko Kalea, 3, 48013 Bilbao, Spain.
| | - Fernando Benito-Lopez
- Microfluidics Cluster UPV/EHU, Analytical Microsystems & Materials for Lab-on-a-Chip (AMMa-LOAC) Group, Analytical Chemistry Department, University of the Basque Country UPV/EHU, Spain.
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11
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Nemes-Nikodém É, Gyurok GP, Dunai ZA, Makra N, Hofmeister B, Szabó D, Sótonyi P, Hidi L, Szappanos Á, Kovács G, Ostorházi E. Relationship between Gut, Blood, Aneurysm Wall and Thrombus Microbiome in Abdominal Aortic Aneurysm Patients. Int J Mol Sci 2024; 25:8844. [PMID: 39201529 PMCID: PMC11354423 DOI: 10.3390/ijms25168844] [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: 07/05/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
Previous research confirmed gut dysbiosis and translocation of selected intestinal bacteria into the vessel wall in abdominal aortic aneurysm patients. We studied the stool, blood, thrombus and aneurysm microbiomes of 21 abdominal aortic aneurysm patients using 16S rRNA sequencing. Our goals were to determine: 1. whether the microbiome characteristic of an aneurysm differs from that of a healthy vessel, 2. whether bacteria detectable in the aneurysm are translocated from the gut through the bloodstream, 3. whether the enzymatic activity of the aneurysm microbiome can contribute to the destruction of the vessel wall. The abundance of Acinetobacter, Burkholderia, Escherichia, and Sphingobium in the aneurysm samples was significantly higher than that in the microbiome of healthy vessels, but only a part of these bacteria can come from the intestine via the blood. Environmental bacteria due to the oral cavity or skin penetration route, such as Acinetobacter, Sphingobium, Enhydrobacter, and Aquabacterium, were present in the thrombus and aneurysm with a significantly higher abundance compared to the blood. Among the enzymes of the microbiome associated with the healthy vessel wall, Iron-chelate-transporting ATPase and Polar-amino-acid-transporting ATPase have protective effects. In addition, bacterial Peptidylprolyl isomerase activity found in the aneurysm has an aggravating effect on the formation of aneurysm.
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Affiliation(s)
- Éva Nemes-Nikodém
- Department of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary; (É.N.-N.); (N.M.); (B.H.); (D.S.)
| | - Gergő Péter Gyurok
- Department of Vascular and Endovascular Surgery, Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary; (G.P.G.); (P.S.); (L.H.); (Á.S.)
| | | | - Nóra Makra
- Department of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary; (É.N.-N.); (N.M.); (B.H.); (D.S.)
| | - Bálint Hofmeister
- Department of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary; (É.N.-N.); (N.M.); (B.H.); (D.S.)
| | - Dóra Szabó
- Department of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary; (É.N.-N.); (N.M.); (B.H.); (D.S.)
- HUN-REN-SU Human Microbiota Research Group, 1052 Budapest, Hungary;
| | - Péter Sótonyi
- Department of Vascular and Endovascular Surgery, Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary; (G.P.G.); (P.S.); (L.H.); (Á.S.)
| | - László Hidi
- Department of Vascular and Endovascular Surgery, Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary; (G.P.G.); (P.S.); (L.H.); (Á.S.)
| | - Ágnes Szappanos
- Department of Vascular and Endovascular Surgery, Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary; (G.P.G.); (P.S.); (L.H.); (Á.S.)
- Department of Rheumatology and Clinical Immunology, Semmelweis University, 1023 Budapest, Hungary
| | - Gergely Kovács
- Department of Vascular and Endovascular Surgery, Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary; (G.P.G.); (P.S.); (L.H.); (Á.S.)
| | - Eszter Ostorházi
- Department of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary; (É.N.-N.); (N.M.); (B.H.); (D.S.)
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
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12
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Older CE, Rodrigues Hoffmann A. Considerations for performing companion animal skin microbiome studies. Vet Dermatol 2024; 35:367-374. [PMID: 38654617 DOI: 10.1111/vde.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/16/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.
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Affiliation(s)
- Caitlin E Older
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Aline Rodrigues Hoffmann
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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13
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Zhang H, Wang X, Chen A, Li S, Tao R, Chen K, Huang P, Li L, Huang J, Li C, Zhang S. Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling. mSystems 2024; 9:e0039924. [PMID: 38934545 PMCID: PMC11264597 DOI: 10.1128/msystems.00399-24] [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: 03/19/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an in silico experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA.IMPORTANCESkin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.
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Affiliation(s)
- Han Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning, China
| | - Anqi Chen
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Shilin Li
- Institute of Forensic Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Science, Shanghai, China
| | - Kaiqin Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Ping Huang
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Liliang Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiang Huang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, China
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14
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Ockert LE, McLennan EA, Fox S, Belov K, Hogg CJ. Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females. Sci Rep 2024; 14:15188. [PMID: 38956276 PMCID: PMC11220038 DOI: 10.1038/s41598-024-66097-8] [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: 01/11/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female's pouch, pouch young skin, and through the milk, are thought to boost the neonate's immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.
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Affiliation(s)
- Lucy E Ockert
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, TAS, 7001, Australia
- Toledo Zoo, 2605 Broadway, Toledo, OH, 43609, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia.
- San Diego Zoo Wildlife Alliance, PO BOX 120551, San Diego, CA, 92112, USA.
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15
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Song Q, Zhu Y, Liu X, Liu H, Zhao X, Xue L, Yang S, Wang Y, Liu X. Changes in the gut microbiota of patients with sarcopenia based on 16S rRNA gene sequencing: a systematic review and meta-analysis. Front Nutr 2024; 11:1429242. [PMID: 39006102 PMCID: PMC11239431 DOI: 10.3389/fnut.2024.1429242] [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: 05/07/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024] Open
Abstract
Introduction Sarcopenia, an age-related disease, has become a major public health concern, threatening muscle health and daily functioning in older adults around the world. Changes in the gut microbiota can affect skeletal muscle metabolism, but the exact association is unclear. The richness of gut microbiota refers to the number of different species in a sample, while diversity not only considers the number of species but also the evenness of their abundances. Alpha diversity is a comprehensive metric that measures both the number of different species (richness) and the evenness of their abundances, thereby providing a thorough understanding of the species composition and structure of a community. Methods This meta-analysis explored the differences in intestinal microbiota diversity and richness between populations with sarcopenia and non-sarcopenia based on 16 s rRNA gene sequencing and identified new targets for the prevention and treatment of sarcopenia. PubMed, Embase, Web of Science, and Google Scholar databases were searched for cross-sectional studies on the differences in gut microbiota between sarcopenia and non-sarcopenia published from 1995 to September 2023 scale and funnel plot analysis assessed the risk of bias, and performed a meta-analysis with State v.15. 1. Results A total of 17 randomized controlled studies were included, involving 4,307 participants aged 43 to 87 years. The alpha diversity of intestinal flora in the sarcopenia group was significantly reduced compared to the non-sarcopenia group: At the richness level, the proportion of Actinobacteria and Fusobacteria decreased, although there was no significant change in other phyla. At the genus level, the abundance of f-Ruminococcaceae; g-Faecalibacterium, g-Prevotella, Lachnoclostridium, and other genera decreased, whereas the abundance of g-Bacteroides, Parabacteroides, and Shigella increased. Discussion This study showed that the richness of the gut microbiota decreased with age in patients with sarcopenia. Furthermore, the relative abundance of different microbiota changed related to age, comorbidity, participation in protein metabolism, and other factors. This study provides new ideas for targeting the gut microbiota for the prevention and treatment of sarcopenia. Systematic Review Registration https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=475887, CRD475887.
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Affiliation(s)
- Qi Song
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Youkang Zhu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Xiao Liu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Hai Liu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | | | - Liyun Xue
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Shaoying Yang
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Yujia Wang
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
- Xi'an Physical Education University, Xi'an, China
| | - Xifang Liu
- Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
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16
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Tunsakul N, Wongsaroj L, Janchot K, Pongpirul K, Somboonna N. Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults. PeerJ 2024; 12:e17270. [PMID: 38650647 PMCID: PMC11034497 DOI: 10.7717/peerj.17270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
Background The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data. Methods This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions. Results Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).
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Affiliation(s)
- Naruemon Tunsakul
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Lampet Wongsaroj
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kantima Janchot
- Center of Excellence in Preventive and Integrative Medicine (CE-PIM) and Department of Preventive and Social Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Krit Pongpirul
- Center of Excellence in Preventive and Integrative Medicine (CE-PIM) and Department of Preventive and Social Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Multi-Omics for Functional Products in Food, Cosmetics and Animals Research Unit, Chulalongkorn University, Bangkok, Thailand
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17
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Parekh T, Tsai M, Spiro S. Choline degradation in Paracoccus denitrificans: identification of sources of formaldehyde. J Bacteriol 2024; 206:e0008124. [PMID: 38501746 PMCID: PMC11025334 DOI: 10.1128/jb.00081-24] [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] [Received: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Paracoccus denitrificans is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so growth on C1 substrates induces the expression of genes encoding enzymes required for the oxidation of formaldehyde and formate. This induction involves a histidine kinase response regulator pair (FlhSR) that is likely triggered by formaldehyde. Catabolism of some complex organic substrates (e.g., choline and L-proline betaine) also generates formaldehyde. Thus, flhS and flhR mutants that fail to induce expression of the formaldehyde catabolic enzymes cannot grow on methanol, methylamine, and choline. Choline is oxidized to glycine via glycine betaine, dimethylglycine, and sarcosine. By exploring flhSR growth phenotypes and the activities of a promoter and enzyme known to be upregulated by formaldehyde, we identify the oxidative demethylations of glycine betaine, dimethylglycine, and sarcosine as sources of formaldehyde. Growth on glycine betaine, dimethylglycine, and sarcosine is accompanied by the production of up to three, two, and one equivalents of formaldehyde, respectively. Genetic evidence implicates two orthologous monooxygenases in the oxidation of glycine betaine. Interestingly, one of these appears to be a bifunctional enzyme that also oxidizes L-proline betaine (stachydrine). We present preliminary evidence to suggest that growth on L-proline betaine induces expression of a formaldehyde dehydrogenase distinct from the enzyme induced during growth on other formaldehyde-generating substrates.IMPORTANCEThe bacterial degradation of one-carbon compounds (methanol and methylamine) and some complex multi-carbon compounds (e.g., choline) generates formaldehyde. Formaldehyde is toxic and must be removed, which can be done by oxidation to formate and then to carbon dioxide. These oxidations provide a source of energy; in some species, the CO2 thus generated can be assimilated into biomass. Using the Gram-negative bacterium Paracoccus denitrificans as the experimental model, we infer that oxidation of choline to glycine generates up to three equivalents of formaldehyde, and we identify the three steps in the catabolic pathway that are responsible. Our work sheds further light on metabolic pathways that are likely important in a variety of environmental contexts.
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Affiliation(s)
- Trusha Parekh
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Marcus Tsai
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Stephen Spiro
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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18
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Long DR, Bryson-Cahn C, Waalkes A, Holmes EA, Penewit K, Tavolaro C, Bellabarba C, Zhang F, Chan JD, Fang FC, Lynch JB, Salipante SJ. Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery. Sci Transl Med 2024; 16:eadk8222. [PMID: 38598612 PMCID: PMC11634388 DOI: 10.1126/scitranslmed.adk8222] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.
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Affiliation(s)
- Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Celeste Tavolaro
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlo Bellabarba
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fangyi Zhang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jeannie D. Chan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pharmacy, Harborview Medical Center; University of Washington School of Pharmacy, Seattle, WA 98104, USA
| | - Ferric C. Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA
| | - John B. Lynch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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19
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Chen D, Cheng K, Wan L, Cui C, Li G, Zhao D, Yu Y, Liao X, Liu Y, D'Souza AW, Lian X, Sun J. Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome. IMETA 2024; 3:e158. [PMID: 38868515 PMCID: PMC10989081 DOI: 10.1002/imt2.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 06/14/2024]
Abstract
Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.
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Affiliation(s)
- Dong‐Rui Chen
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Ke Cheng
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Chao‐Yue Cui
- Laboratory Animal CentreWenzhou Medical UniversityWenzhouChina
| | - Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Dong‐Hao Zhao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Yang Yu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Ya‐Hong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Alaric W. D'Souza
- Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Xin‐Lei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
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Kim D, Jeon J, Kim M, Jeong J, Heo YM, Lee DG, Yon DK, Han K. Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms. Genomics Inform 2023; 21:e52. [PMID: 38224719 PMCID: PMC10788361 DOI: 10.5808/gi.23068] [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: 08/17/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 01/17/2024] Open
Abstract
Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.
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Affiliation(s)
- Dongwan Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Junhyeon Jeon
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Minseo Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
| | | | - Dong-Geol Lee
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- R&I Center, COSMAX BTI, Seongnam 13486, Korea
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute, Kyung Hee University Medical Center, Kyung Hee University College of Medicine, Seoul 02447, Korea
- Department of Pediatrics, Kyung Hee University College of Medicine, Seoul 02447, Korea
| | - Kyudong Han
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
- HuNbiome Co., Ltd, R&D Center, Seoul 08503, Korea
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21
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Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Lahner E, Pivetta G, Turroni F, Ventura M, Milani C. Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses. MICROBIOME RESEARCH REPORTS 2023; 3:4. [PMID: 38455080 PMCID: PMC10917613 DOI: 10.20517/mrr.2023.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024]
Abstract
Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host's DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Edith Lahner
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Giulia Pivetta
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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22
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Ogai K, Nana BC, Lloyd YM, Arios JP, Jiyarom B, Awanakam H, Esemu LF, Hori A, Matsuoka A, Nainu F, Megnekou R, Leke RGF, Ekali GL, Okamoto S, Kuraishi T. Skin microbiome profile in people living with HIV/AIDS in Cameroon. Front Cell Infect Microbiol 2023; 13:1211899. [PMID: 38029259 PMCID: PMC10644231 DOI: 10.3389/fcimb.2023.1211899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The presence of pathogens and the state of diseases, particularly skin diseases, may alter the composition of human skin microbiome. HIV infection has been reported to impair gut microbiome that leads to severe consequences. However, with cutaneous manifestations, that can be life-threatening, due to the opportunistic pathogens, little is known whether HIV infection might influence the skin microbiome and affect the skin homeostasis. This study catalogued the profile of skin microbiome of healthy Cameroonians, at three different skin sites, and compared them to the HIV-infected individuals. Taking advantage on the use of molecular assay coupled with next-generation sequencing, this study revealed that alpha-diversity of the skin microbiome was higher and beta-diversity was altered significantly in the HIV-infected Cameroonians than in the healthy ones. The relative abundance of skin microbes such as Micrococcus and Kocuria species was higher and Cutibacterium species was significantly lower in HIV-infected people, indicating an early change in the human skin microbiome in response to the HIV infection. This phenotypical shift was not related to the number of CD4 T cell count thus the cause remains to be identified. Overall, these data may offer an important lead on the role of skin microbiome in the determination of cutaneous disease state and the discovery of safe pharmacological preparations to treat microbial-related skin disorders.
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Affiliation(s)
- Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center (ai@ku), Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
- Department of Bio-engineering Nursing, Graduate School of Nursing, Ishikawa Prefectural Nursing University, Kahoku, Japan
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Benderli Christine Nana
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Yukie Michelle Lloyd
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - John Paul Arios
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Boonyanudh Jiyarom
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Honore Awanakam
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
| | - Livo Forgu Esemu
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, University of Yaoundé I, Yaoundé, Cameroon
| | - Aki Hori
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Ayaka Matsuoka
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Firzan Nainu
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Rosette Megnekou
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rose Gana Fomban Leke
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Shigefumi Okamoto
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
- Division of Health Sciences, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Takayuki Kuraishi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
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23
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Ghosh A, Panda S. Cutaneous Dysbiosis and Dermatophytosis: The Unexplored Link. Indian J Dermatol 2023; 68:508-514. [PMID: 38099124 PMCID: PMC10718259 DOI: 10.4103/ijd.ijd_828_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
The skin, besides being the largest interface between the body and the external environment, also forms an ecological niche which is populated by almost a trillion microorganisms. These, collectively known as the cutaneous microbiome, form a dynamic yet well-controlled system that resists invasion by pathogenic microorganisms, functioning as the so-called 'microbiological barrier', modulating the body's immune response, indirectly playing a crucial role in the pathogenesis of several inflammatory diseases. The composition and complexity of the microbiome are yet to be fully understood. The term 'dysbiosis' originally was coined in 1908 for a change in the gut microbiome. The potential role of 'cutaneous dysbiosis' in human dermatophytic infections, especially in the backdrop of the current epidemic of chronic, recurrent and treatment-resistant dermatophytosis, is understandably a topic of interest. The purpose of this review was to assess all studies using culture-independent methods for analysing the skin microbiome in various dermatophyte infections. The PubMed and Google Scholar databases were searched using the terms 'microbiome', 'dysbiosis', 'dermatophytes', 'dermatophytosis' and 'tinea'. All studies involving the use of standard sequencing methods for the study of the microbiome in various dermatophytoses were included. A total of four studies assessing the local skin microbiome associated with dermatophytic infections were found-one for tinea capitis, one for onychomycosis (in both psoriatic and nonpsoriatic nails) and two studying patients of tinea pedis. The studies determined the microbiological patterns in patients and compared them with healthy individuals using sequencing methods. Significant differences in the species diversity and counts of the various microorganisms between patient and control groups were demonstrated in all. However, cross-sectional design and the absence of pre- and post-treatment data along with a limited sample size were the major limitations in all of them. No data regarding other forms of tinea, most importantly, tinea cruris, corporis, faciei, etc. were found. The existing studies demonstrate a change in the microbiome or dysbiosis associated with cases of dermatophytosis, but are inadequate to determine a causal association. The changes may also be wholly or partly attributed to the effect of the infection. Further longitudinal studies from different regions of the world, also involving other forms of dermatophytosis, are required to provide a clearer insight and a more representative picture.
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Affiliation(s)
- Aparajita Ghosh
- From the Department of Dermatology, K.P.C Medical College and Hospital, Kolkata, West Bengal, India
| | - Saumya Panda
- Department of Dermatology, JIMS Hospital and Medical College, Kolkata, West Bengal, India
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24
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Flocco CG, Methner A, Burkart F, Geppert A, Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol 2023; 14:1197837. [PMID: 37601377 PMCID: PMC10435870 DOI: 10.3389/fmicb.2023.1197837] [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: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
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Affiliation(s)
- Cecilia G. Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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25
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Stupak A, Kwaśniewski W. Evaluating Current Molecular Techniques and Evidence in Assessing Microbiome in Placenta-Related Health and Disorders in Pregnancy. Biomolecules 2023; 13:911. [PMID: 37371491 PMCID: PMC10296270 DOI: 10.3390/biom13060911] [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] [Received: 03/24/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal-fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women.
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Affiliation(s)
- Aleksandra Stupak
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, Staszica Str. 16, 20-081 Lublin, Poland
| | - Wojciech Kwaśniewski
- Department of Gynecological Oncology and Gynecology, Medical University of Lublin, 20-081 Lublin, Poland
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Borrego BB, Gracioso LH, Karolski B, Cardoso LOB, Melo LBU, Castro ÍB, Perpetuo EA. Tributyltin degrading microbial enzymes: A promising remediation approach. MARINE POLLUTION BULLETIN 2023; 189:114725. [PMID: 36805770 DOI: 10.1016/j.marpolbul.2023.114725] [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: 10/31/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Brazil is one of the countries most impacted along the entire coastline by the presence of tributyltin (TBT), a biocide used in antifouling paints. Despite being banned since 2008, its use is still registered in the country, and it is possible to find recent inputs of this substance in places under the influence of shipyards, marinas, and fishing ports. In this study, a bacterium isolated from TBT-contaminated sediment from Santos and São Vicente Estuarine System (SESS) in Brazil, identified as Achromobacter sp., proved to be resistant to this compound. Furthermore, its crude enzymatic extract presented the ability to reduce up to 25 % of the initial TBT concentration in the liquid phase in 1 h, demonstrating to be a simple, fast, effective procedure and a potential tool for the environmental attenuation of TBT.
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Affiliation(s)
- Bruna Bacaro Borrego
- The Interunits Postgraduate Program in Biotechnology, University of São Paulo, PPIB-USP, Lineu Prestes Ave, 2415, São Paulo, SP, Brazil; Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil.
| | - Louise Hase Gracioso
- Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil; School of Arts, Science and Humanities of University of São Paulo, EACH-USP, Arlindo Bettio Ave, 1000, São Paulo, SP, Brazil
| | - Bruno Karolski
- Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil
| | - Letícia Oliveira Bispo Cardoso
- Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil; Chemical Engineering Department, Escola Politécnica, University of São Paulo, POLI-USP, Prof. Luciano Gualberto Ave, 380, São Paulo, SP, Brazil
| | - Letícia Beatriz Ueda Melo
- Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil; Graduate Interdisciplinary Program in Marine Science and Technology, PPG-ICTMar-UNIFESP, Carvalho de Mendonça Ave, 144, Santos, SP, Brazil
| | - Ítalo Braga Castro
- Institute of Marine Sciences, Federal University of São Paulo, IMar-UNIFESP, Carvalho de Mendonça Ave, 144, Santos, SP, Brazil
| | - Elen Aquino Perpetuo
- Bio4Tec Lab, Environmental Research and Education Center, University of São Paulo, CEPEMA-POLI-USP, Cônego Domênico Rangoni Rd, 270 km, Cubatão, SP, Brazil; Graduate Interdisciplinary Program in Marine Science and Technology, PPG-ICTMar-UNIFESP, Carvalho de Mendonça Ave, 144, Santos, SP, Brazil; Institute of Marine Sciences, Federal University of São Paulo, IMar-UNIFESP, Carvalho de Mendonça Ave, 144, Santos, SP, Brazil
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Paradoxical Reactions to Anti-TNFα and Anti-IL-17 Treatment in Psoriasis Patients: Are Skin and/or Gut Microbiota Involved? Dermatol Ther (Heidelb) 2023; 13:911-933. [PMID: 36929119 DOI: 10.1007/s13555-023-00904-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
Psoriasis is a chronic, immune-mediated, inflammatory disease primarily affecting the skin. It is currently coming to light that patients with psoriasis have disrupted intestinal barrier and often suffer from comorbidities associated with the gastrointestinal tract. Moreover, there is growing evidence of both cutaneous and intestinal paradoxical reactions during biologic treatment in patients with psoriasis. This review focuses on barrier defects and changes in immune responses in patients with psoriasis, which play an important role in the development of the disease but are also influenced by modern biological treatments targeting IL-17 and TNFα cytokines. Here, we highlight the relationship between the gut-skin axis, microbiota, psoriasis treatment, and the incidence of paradoxical reactions, such as inflammatory bowel disease in patients with psoriasis. A better understanding of the interconnection of these mechanisms could lead to a more personalized therapy and lower the incidence of treatment side effects, thereby improving the quality of life of the affected patients.
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28
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He C, Yue Y, Li R, Huang Y, Shu L, Lv H, Wang J, Zhang Z. Sodium hyaluronates applied in the face affects the diversity of skin microbiota in healthy people. Int J Cosmet Sci 2023. [PMID: 36710533 DOI: 10.1111/ics.12845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
OBJECTIVE A healthy and stable microbiome has many beneficial effects on the host, while an unbalanced or disordered microbiome can lead to various skin diseases. Hyaluronic acid is widely used in the cosmetics and pharmaceutical industries; however, specific reports on its effect on the skin microflora of healthy people have not been published. This study aimed to determine the effect of sodium hyaluronate on the facial microflora of healthy individuals. METHODS Face of 20 healthy female volunteers between 18 and 24 years was smeared with sodium hyaluronate solution once per day. Cotton swabs were used to retrieve samples on days 0, 14, and 28, and high-throughput sequencing of 16 S rRNA was used to determine the changes in bacterial community composition. RESULTS Facial application of HA can reduce the abundance of pathogenic bacteria, such as Cutibacterium and S. aureus, and increase the colonization of beneficial bacteria. CONCLUSION This is the first intuitive report to demonstrate the effect of hyaluronic acid on facial microflora in healthy people. Accordingly, sodium hyaluronate was found to have a positive effect on facial skin health.
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Affiliation(s)
- Chen He
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - YingXue Yue
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ruilong Li
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yiping Huang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Luan Shu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huixia Lv
- Special Cosmetics R&D Joint laboratory of China Pharmaceutical University & Bloomage Biotechnology Corporation Limited, Nanjing, China
| | - Jing Wang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhenhai Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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29
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Haertl T, Owsienko D, Schwinn L, Hirsch C, Eskofier BM, Lang R, Wirtz S, Loos HM. Exploring the interrelationship between the skin microbiome and skin volatiles: A pilot study. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Unravelling the interplay between a human’s microbiome and physiology is a relevant task for understanding the principles underlying human health and disease. With regard to human chemical communication, it is of interest to elucidate the role of the microbiome in shaping or generating volatiles emitted from the human body. In this study, we characterized the microbiome and volatile organic compounds (VOCs) sampled from the neck and axilla of ten participants (five male, five female) on two sampling days, by applying different methodological approaches. Volatiles emitted from the respective skin site were collected for 20 min using textile sampling material and analyzed on two analytical columns with varying polarity of the stationary phase. Microbiome samples were analyzed by a culture approach coupled with MALDI-TOF-MS analysis and a 16S ribosomal RNA gene (16S RNA) sequencing approach. Statistical and advanced data analysis methods revealed that classification of body sites was possible by using VOC and microbiome data sets. Higher classification accuracy was achieved by combination of both data pools. Cutibacterium, Staphylococcus, Micrococcus, Streptococcus, Lawsonella, Anaerococcus, and Corynebacterium species were found to contribute to classification of the body sites by the microbiome. Alkanes, esters, ethers, ketones, aldehydes and cyclic structures were used by the classifier when VOC data were considered. The interdisciplinary methodological platform developed here will enable further investigations of skin microbiome and skin VOCs alterations in physiological and pathological conditions.
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30
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Amin H, Marshall IPG, Bertelsen RJ, Wouters IM, Schlünssen V, Sigsgaard T, Šantl-Temkiv T. Optimization of bacterial DNA and endotoxin extraction from settled airborne dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159455. [PMID: 36252657 DOI: 10.1016/j.scitotenv.2022.159455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.
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Affiliation(s)
- Hesham Amin
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Ian P G Marshall
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Randi J Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torben Sigsgaard
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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31
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Robert C, Cascella F, Mellai M, Barizzone N, Mignone F, Massa N, Nobile V, Bona E. Influence of Sex on the Microbiota of the Human Face. Microorganisms 2022; 10:microorganisms10122470. [PMID: 36557723 PMCID: PMC9786802 DOI: 10.3390/microorganisms10122470] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.
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Affiliation(s)
- Clémence Robert
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Correspondence: (C.R.); (E.B.)
| | - Federica Cascella
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
| | - Marta Mellai
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Nadia Barizzone
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Flavio Mignone
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
- SmartSeq s.r.l., 28100 Novara, Italy
| | - Nadia Massa
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
| | - Vincenzo Nobile
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
| | - Elisa Bona
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department for Sustainable Development and Ecological Transition, University of Eastern Piedmont, 13100 Vercelli, Italy
- Correspondence: (C.R.); (E.B.)
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32
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Dityen K, Soonthornchai W, Kueanjinda P, Kullapanich C, Tunsakul N, Somboonna N, Wongpiyabovorn J. Analysis of cutaneous bacterial microbiota of Thai patients with seborrheic dermatitis. Exp Dermatol 2022; 31:1949-1955. [PMID: 36076320 DOI: 10.1111/exd.14674] [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: 01/30/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 12/14/2022]
Abstract
Seborrheic dermatitis (SD) is a chronic inflammatory skin condition that occurs in body areas that contain profuse sebaceous glands. Skin microbiota are diverse across ethnic groups and its dysbiosis has been implicated in the pathogenesis of SD. Here, we reported the contribution of cutaneous bacterial microbiota to SD in the Thai population. Healthy individuals and patients with scalp SD were recruited into the study. Normal skin, scalp skin lesion (SL) and non-lesion sites (SNL) samples were collected using a tape stripping method and next-generation sequencing of 16S rRNA for microbiome analysis. Although bacterial diversity in all sample groups was not statistically different, a population of bacteria commonly found on skin of scalp showed signs of dysbiosis. Apart from the reduction of Corynebacterium spp., SD-specific microbiota was dominated by Firmicutes at taxa level and Pseudomonas spp., Staphylococcus spp. and Micrococcus spp. at genus level. The dysbiosis of the skin microbiota in SD was specifically described as an alteration of bacteria populations commonly found on scalp skin, implying that managing and controlling the cutaneous bacterial microbiome can alleviate and prevent SD and pave the way for the development of new SD treatments.
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Affiliation(s)
- Kanthaporn Dityen
- Division of Immunology, Department of Microbiology, Center of Excellence in Immunology and Immune-Mediated Diseases, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wipasiri Soonthornchai
- Division of Immunology, Department of Microbiology, Center of Excellence in Immunology and Immune-Mediated Diseases, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,School of Science, University of Phayao, Phayao, Thailand
| | - Patipark Kueanjinda
- Division of Immunology, Department of Microbiology, Center of Excellence in Immunology and Immune-Mediated Diseases, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chitrasak Kullapanich
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, Thailand
| | - Naruemon Tunsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, Thailand
| | - Jongkonnee Wongpiyabovorn
- Division of Immunology, Department of Microbiology, Center of Excellence in Immunology and Immune-Mediated Diseases, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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33
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He J, Shen X, Zhang N, Sun C, Shao Y. Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens. Microbiol Spectr 2022; 10:e0150822. [PMID: 36040152 PMCID: PMC9603676 DOI: 10.1128/spectrum.01508-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022] Open
Abstract
Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 106 bacteria (2.24 × 104/cm2) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 106 bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Beijing, China
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34
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Kaur M, Li J, Zhang P, Yang HF, Wang L, Xu M. Agricultural soil physico-chemical parameters and microbial abundance and diversity under long-run farming practices: A greenhouse study. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1026771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The growth of agriculture led to indiscriminate use of synthetic pesticides or fertilizers and unsustainable crop management farming practices which can aggravate harmful impacts on the microbial population and physical and chemical characteristics of soil ecosystem. Based on this fact, the present study was planned to evaluate the effect of long run farming practices on different soil physico-chemical parameters and soil microbial abundance and diversity within different soil depth (0–20 cm and 20–40 cm) at Quzhou Experimental Station of China Agricultural University, Hebei, China during October and December, 2016. The effect of farming practices on soil microbial abundance and diversity was studied by phospho-lipid fatty acid (PLFA) and DNA high-throughput sequencing methods. The findings revealed that soil is neutral to slightly alkaline in nature with highest water content under organic farming (ORF) at 0–20 cm and least under conventional farming at 20–40 cm depth. It was found that the ORF significantly increased the contents of total organic carbon (TOC), total carbon (TC), ammonium nitrogen, available nitrogen (AN), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) followed by low input and conventional farming modes in both October and December soil samples. The correlation analysis showed significantly (at p ≤ 0.05 and 0.01) strong positive relationship within different physical and chemical properties of the soil under study. ANOVA and MANOVA analysis indicated significant effect of interaction between soil depth and farming modes on soil parameters. PCA analysis showed the most significant correlation between most of the bacterial types (G + bacteria, G− bacteria, actinomycetes) and soil AP, total available nitrogen, TOC and soil WC. Pearson correlation analysis revealed a significant correlation between microbial phylum groups (Proteobacteria, Bacteroidetes, and Latescibacteria) and microbial class group (Alphaproteobacteria, Sphingobacteriia, Flavobacteriia) with most of the soil physicochemical properties.
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Olunoiki E, Rehner J, Bischoff M, Koshel E, Vogt T, Reichrath J, Becker SL. Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review. Life (Basel) 2022; 12:life12091420. [PMID: 36143456 PMCID: PMC9503882 DOI: 10.3390/life12091420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future.
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Affiliation(s)
- Esther Olunoiki
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
- “Solution Chemistry of Advanced Materials and Technologies” (SCAMT) Institute, ITMO University, 191002 St. Petersburg, Russia
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Elena Koshel
- “Solution Chemistry of Advanced Materials and Technologies” (SCAMT) Institute, ITMO University, 191002 St. Petersburg, Russia
| | - Thomas Vogt
- Department of Dermatology, Venereology, Allergology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Jörg Reichrath
- Department of Dermatology, Venereology, Allergology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Sören L. Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
- Correspondence: ; Tel.: +49-6841-16-23900
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36
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Prat M, Guenezan J, Drugeon B, Burucoa C, Mimoz O, Pichon M. Impact of Skin Disinfection on Cutaneous Microbiota, before and after Peripheral Venous Catheter Insertion. Antibiotics (Basel) 2022; 11:antibiotics11091209. [PMID: 36139988 PMCID: PMC9495181 DOI: 10.3390/antibiotics11091209] [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: 07/20/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction. Patients with invasive medical devices are at high risk for infection. Skin colonization is the initial stage of these infections, leading to the recommendation of practices requiring disinfection using antiseptics. Microbial communities playing a major role in skin health could be impacted by antiseptic procedures. Aim. To characterize and compare the bacterial communities of skin samples from patients before an antisepsis procedure, and after removal of the medical device itself, according to the nature of the antiseptic molecule (povidone iodine or chlorhexidine). Methods. The study focused on alterations in bacterial communities depending on the nature of the antiseptic procedure and type of intravascular device. After amplification of 16S rDNA, libraries (n = 498 samples) were sequenced using MiSeq platform. Results. Using an in-house pipeline (QIIME2 modules), while no alteration in skin microbiota diversity was associated with antiseptic procedure or PVC type, according to culture results (p < 0.05), alterations were at times associated with restricted diversity and higher dissimilarity (p < 0.05). Antiseptic procedures and PVC types were associated with the modification of specific bacterial representations with modulation of the Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio (modulation of C. acnes, Prevotella, Lagierella, and Actinomyces spp.) (p < 0.05). At baseline, the microbiota shows certain bacteria that are significantly associated with future PVC colonization and/or bacteremia (p < 0.05). All of these modulations were associated with altered expression of metabolic pathways (p < 0.05). Discussion. Finally, this work highlights the need to optimize the management of patients requiring intravascular devices, possibly by modulating the skin microbiota.
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Affiliation(s)
- Manon Prat
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Jeremy Guenezan
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Bertrand Drugeon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Christophe Burucoa
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Olivier Mimoz
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Maxime Pichon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
- Correspondence: ; Tel.: +33-(0)5-4944-4143
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Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
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Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
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Optimization of microbial DNA extraction from human skin samples for CRISPR typing. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Li X, Yang F, Yan H, Shi Y, Chang X, Zhang M, Zhang Y, Zhang M. Microbiota profiling on itchy scalp with undetermined origin. Arch Microbiol 2022; 204:446. [PMID: 35778621 DOI: 10.1007/s00203-022-03077-4] [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: 03/01/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022]
Abstract
Scalp pruritus is a common skin problem that remains therapeutic challenge. The relationships between the dysbiosis of microbiota and skin diseases have caught attention recently. However, there are few reports about microbiota on itchy scalp. This study investigated scalp microbial characteristics of subjects with mild scalp pruritus of undetermined origin and preliminarily screened physiological factors and bacteria potentially related to pruritus. The pruritus severity of 17 qualified females was evaluated by Visual Analogue Scale (VAS). Microbiota collection was done at both itchy (n = 20) and non-itchy sites (n = 27) at occiput and crown of the same subject and Illumina sequencing was performed at the V3-V4 hypervariable regions of 16S rRNA. The corresponding sebum content, hydration, pH, trans-epidermal water loss, erythema index and porphyrin numbers were also measured by skin tester. We identified 3044 amplicon sequence variants from 821 genera. The itchy and non-itchy sites had different microbiota structures (p = 0.045, by multivariate analysis of variance), while there were large inter- and intra-individual variations. Both sites had Staphylococcus, Cutibacterium and Lawsonella as predominant genera, which were not significantly related to pruritus. The use of three genera Lactobacillus, Morganella and Pseudomonas, could well distinguish non-itchy from itchy groups, whereas different composition patterns existed inside each group. Our investigation indicated that though the bacterial community structure on itchy scalp was individual specific, there was difference between itchy and non-itchy sites. The study provides new insights into microbiota profiling on itchy scalp, which will help microbiota-targeted therapeutic experiment or products design for scalp pruritus.
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Affiliation(s)
- Xuejing Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fang Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haosong Yan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Shi
- Henkel (China) Investment Co., Ltd, Shanghai, 200438, China
| | - Xiaowei Chang
- Henkel (China) Investment Co., Ltd, Shanghai, 200438, China
| | - Mengmeng Zhang
- Henkel (China) Investment Co., Ltd, Shanghai, 200438, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Yang J, Shin TS, Kim JS, Jee YK, Kim YK. A new horizon of precision medicine: combination of the microbiome and extracellular vesicles. Exp Mol Med 2022; 54:466-482. [PMID: 35459887 PMCID: PMC9028892 DOI: 10.1038/s12276-022-00748-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
Over several decades, the disease pattern of intractable disease has changed from acute infection to chronic disease accompanied by immune and metabolic dysfunction. In addition, scientific evidence has shown that humans are holobionts; of the DNA in humans, 1% is derived from the human genome, and 99% is derived from microbial genomes (the microbiome). Extracellular vesicles (EVs) are lipid bilayer-delimited nanoparticles and key messengers in cell-to-cell communication. Many publications indicate that microbial EVs are both positively and negatively involved in the pathogenesis of various intractable diseases, including inflammatory diseases, metabolic disorders, and cancers. Microbial EVs in feces, blood, and urine show significant differences in their profiles between patients with a particular disease and healthy subjects, demonstrating the potential of microbial EVs as biomarkers for disease diagnosis, especially for assessing disease risk. Furthermore, microbial EV therapy offers a variety of advantages over live biotherapeutics and human cell EV (or exosome) therapy for the treatment of intractable diseases. In summary, microbial EVs are a new tool in medicine, and microbial EV technology might provide us with innovative diagnostic and therapeutic solutions in precision medicine. The tiny membrane-bound vesicles containing various biomolecules that the organisms comprising our microbiome release could offer a powerful tool for precision medicine. Our bodies are home to trillions of microbes, which interact closely with our tissues to maintain a healthy physiological environment. Yoon-Keun Kim of the Institute of MD Healthcare, Seoul, South Korea, and colleagues have reviewed current research into the extracellular vesicles that these microbes use to communicate with other microbes and their human hosts. The authors note that these vesicles affect tissues throughout the body, and their activities have been linked to various disorders including asthma, Crohn’s disease and cancer. A deeper understanding of how these vesicles prevent or accelerate various conditions in different individuals could yield useful new diagnostic biomarkers and provide the foundation for interventions that are optimized for each patient.
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Affiliation(s)
- Jinho Yang
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Tae-Seop Shin
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Jong Seong Kim
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Young-Koo Jee
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Republic of Korea
| | - Yoon-Keun Kim
- Institute of MD Healthcare Inc., Seoul, Republic of Korea.
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Potbhare R, RaviKumar A, Munukka E, Lahti L, Ashma R. Skin microbiota diversity among genetically unrelated individuals of Indian origin. PeerJ 2022; 10:e13075. [PMID: 35313523 PMCID: PMC8934042 DOI: 10.7717/peerj.13075] [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: 04/17/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography. Methods Axillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3-V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location. Results Our study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal-Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district. Conclusion Our work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals.
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Affiliation(s)
- Renuka Potbhare
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Eveliina Munukka
- Microbiome Biobank, Institute of Biomedicine, University of Turku, Turku, Finland,Biocodex Nordics, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
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Abstract
Cognitive impairment (CI) is among the most common non-motor symptoms of Parkinson’s disease (PD), with a substantially negative impact on patient management and outcome. The development and progression of CI exhibits high interindividual variability, which requires better diagnostic and monitoring strategies. PD patients often display sweating disorders resulting from autonomic dysfunction, which has been associated with CI. Because the axillary microbiota is known to change with humidity level and sweat composition, we hypothesized that the axillary microbiota of PD patients shifts in association with CI progression, and thus can be used as a proxy for classification of CI stages in PD. We compared the axillary microbiota compositions of 103 PD patients (55 PD patients with dementia [PDD] and 48 PD patients with mild cognitive impairment [PD-MCI]) and 26 cognitively normal healthy controls (HC). We found that axillary microbiota profiles differentiate HC, PD-MCI, and PDD groups based on differential ranking analysis, and detected an increasing trend in the log ratio of Corynebacterium to Anaerococcus in progression from HC to PDD. In addition, phylogenetic factorization revealed that the depletion of the Anaerococcus, Peptoniphilus, and W5053 genera is associated with PD-MCI and PDD. Moreover, functional predictions suggested significant increases in myo-inositol degradation, ergothioneine biosynthesis, propionate biosynthesis, menaquinone biosynthesis, and the proportion of aerobic bacteria and biofilm formation capacity, in parallel to increasing CI. Our results suggest that alterations in axillary microbiota are associated with CI in PD. Thus, axillary microbiota has the potential to be exploited as a noninvasive tool in the development of novel strategies. IMPORTANCE Parkinson's disease (PD) is the second most common neurodegenerative disease. Cognitive impairment (CI) in PD has significant negative impacts on life quality of patients. The emergence and progression of cognitive impairment shows high variability among PD patients, and thus requires better diagnostic and monitoring strategies. Recent findings indicate a close link between autonomic dysfunction and cognitive impairment. Since thermoregulatory dysfunction and skin changes are among the main manifestations of autonomic dysfunction in PD, we hypothesized that alterations in the axillary microbiota may be useful for tracking cognitive impairment stages in PD. To our knowledge, this the first study characterizing the axillary microbiota of PD patients and exploring its association with cognitive impairment stages in PD. Future studies should include larger cohorts and multicenter studies to validate our results and investigate potential biological mechanisms.
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Gao C, Guo Y, Chen F. Cross-Cohort Microbiome Analysis of Salivary Biomarkers in Patients With Type 2 Diabetes Mellitus. Front Cell Infect Microbiol 2022; 12:816526. [PMID: 35145929 PMCID: PMC8821939 DOI: 10.3389/fcimb.2022.816526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/10/2022] [Indexed: 01/22/2023] Open
Abstract
Several studies have ascertained differences in salivary microbiota between patients with type 2 diabetes mellitus (T2DM) and healthy populations. However, the predictive accuracy and reproducibility of these 16S rRNA sequencing analyses when applied to other cohorts remain enigmatic. A comprehensive analysis was conducted on the included 470 samples from five researches in publicly available databases. The discrepancy and predictive accuracy of salivary microbiota between T2DM patients and healthy populations were evaluated from multiple perspectives, followed by the identification of salivary biomarkers for DM. Next, a classification model (areas under the curves = 0.92) was developed based on a large sample. The model could be used for clinical diagnosis and prognostic monitoring and as a basis for hypothesis-driven mechanistic researches. Furthermore, the research heterogeneity across geographic regions suggested that microbiological markers might not become a uniform clinical standard in human beings. They rather identify abnormal alterations under the microbiological characteristics of a specific population.
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Affiliation(s)
- Chuqi Gao
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Ying Guo
- Department of Stomatology, General Hospital of Shenzhen University, Shenzhen, China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
- *Correspondence: Feng Chen,
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Ogai K, Nana BC, Lloyd YM, Arios JP, Jiyarom B, Awanakam H, Esemu LF, Hori A, Matsuoka A, Nainu F, Megnekou R, Leke RGF, Ekali GL, Okamoto S, Kuraishi T. Skin microbiome profile of healthy Cameroonians and Japanese. Sci Rep 2022; 12:1364. [PMID: 35079063 PMCID: PMC8789912 DOI: 10.1038/s41598-022-05244-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
The commensal microbes of the skin have a significant impact on dermal physiology and pathophysiology. Racial and geographical differences in the skin microbiome are suggested and may play a role in the sensitivity to dermatological disorders, including infectious diseases. However, little is known about the skin microbiome profiles of people living in Central Africa, where severe tropical infectious diseases impose a burden on the inhabitants. This study provided the skin profiles of healthy Cameroonians in different body sites and compared them to healthy Japanese participants. The skin microbiome of Cameroonians was distinguishable from that of Japanese in all skin sites examined in this study. For example, Micrococcus was predominantly found in skin samples of Cameroonians but mostly absent in Japanese skin samples. Instead, the relative abundance of Cutibacterium species was significantly higher in healthy Japanese. Principal coordinate analysis of beta diversity showed that the skin microbiome of Cameroonians formed different clusters from Japanese, suggesting a substantial difference in the microbiome profiles between participants of both countries. In addition, the alpha diversity in skin microbes was higher in Cameroonians than Japanese participants. These data may offer insights into the determinant factors responsible for the distinctness of the skin microbiome of people living in Central Africa and Asia.
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Affiliation(s)
- Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center (ai@ku), Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Benderli Christine Nana
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Yukie Michelle Lloyd
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - John Paul Arios
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Boonyanudh Jiyarom
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Honore Awanakam
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
| | - Livo Forgu Esemu
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Aki Hori
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Ayaka Matsuoka
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Firzan Nainu
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Rosette Megnekou
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rose Gana Fomban Leke
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | | | - Shigefumi Okamoto
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa, 920-0942, Japan.
| | - Takayuki Kuraishi
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
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Fritz B, Paschko E, Young W, Böhringer D, Wahl S, Ziemssen F, Egert M. Comprehensive Compositional Analysis of the Slit Lamp Bacteriota. Front Cell Infect Microbiol 2021; 11:745653. [PMID: 34869057 PMCID: PMC8635730 DOI: 10.3389/fcimb.2021.745653] [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: 07/29/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022] Open
Abstract
Slit lamps are routinely used to examine large numbers of patients every day due to high throughput. Previous, cultivation-based results suggested slit lamps to be contaminated with bacteria, mostly coagulase-negative staphylococci, followed by micrococci, bacilli, but also Staphylococcus aureus. Our study aimed at obtaining a much more comprehensive, cultivation-independent view of the slit lamp bacteriota and its hygienic relevance, as regularly touched surfaces usually represent fomites, particularly if used by different persons. We performed extensive 16S rRNA gene sequencing to analyse the bacteriota, of 46 slit lamps from two tertiary care centers at two sampling sites, respectively. 82 samples yielded enough sequences for downstream analyses and revealed contamination with bacteria of mostly human skin, mucosa and probably eye origin, predominantly cutibacteria, staphylococci and corynebacteria. The taxonomic assignment of 3369 ASVs (amplicon sequence variants) revealed 19 bacterial phyla and 468 genera across all samples. As antibiotic resistances are of major concern, we screened all samples for methicillin-resistant Staphylococcus aureus (MRSA) using qPCR, however, no signals above the detection limit were detected. Our study provides first comprehensive insight into the slit lamp microbiota. It underlines that slit lamps carry a highly diverse, skin-like bacterial microbiota and that thorough cleaning and disinfection after use is highly recommendable to prevent eye and skin infections.
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Affiliation(s)
- Birgit Fritz
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Edita Paschko
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Wayne Young
- Food Informatics Team, AgResearch Ltd., Palmerston North, New Zealand
| | - Daniel Böhringer
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Siegfried Wahl
- Carl Zeiss Vision International GmbH, Aalen, Germany.,Institute for Ophthalmic Research, Eberhard-Karls University, Tuebingen, Germany
| | - Focke Ziemssen
- Center for Ophthalmology, Eberhard-Karls University, Tuebingen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
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Jayasena Kaluarachchi TD, Campbell PM, Wickremasinghe R, Ranasinghe S, Wickremasinghe R, Yasawardene S, De Silva H, Menike C, Jayarathne MCK, Jayathilake S, Dilhari A, McBain AJ, Weerasekera MM. Distinct microbiome profiles and biofilms in Leishmania donovani-driven cutaneous leishmaniasis wounds. Sci Rep 2021; 11:23181. [PMID: 34848752 PMCID: PMC8633208 DOI: 10.1038/s41598-021-02388-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
The endemic strain of Leishmania donovani in Sri Lanka causes cutaneous leishmaniasis (CL) rather than more common visceral form. We have visualized biofilms and profiled the microbiome of lesions and unaffected skin in thirty-nine CL patients. Twenty-four lesions (61.5%) were biofilm-positive according to fluorescence in situ hybridization. Biopsies of biofilm-positive lesions were dominated by Pseudomonas, class Bacilli and Enterobacteriaceae and distinguished by significantly lower community evenness. Higher relative abundance of a class Bacilli OTU was detected in wound swabs versus contralateral skin. Wound swabs and biopsies had significantly distinct microbiome profiles and lower diversity compared to unaffected skin. Greater abundances of potentially pathogenic organisms were observed in wet ulcers, lesions with high parasite loads and large wounds. In summary, more than half of L. donovani associated CL wounds harboured biofilms and the wounds exhibited a distinct, less diverse, microbiome than unaffected skin.
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Affiliation(s)
- T D Jayasena Kaluarachchi
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
| | - Paul M Campbell
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Rajitha Wickremasinghe
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - Shalindra Ranasinghe
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Renu Wickremasinghe
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Surangi Yasawardene
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | | | - Chandrani Menike
- Department of Parasitology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - M C K Jayarathne
- Department of Family Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Subodha Jayathilake
- Department of Pathology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Ayomi Dilhari
- Department of Basic Sciences, Faculty of Allied Health Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - Andrew J McBain
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Manjula M Weerasekera
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka
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Sulo P, Šipková B. DNA diagnostics for reliable and universal identification of Helicobacter pylori. World J Gastroenterol 2021; 27:7100-7112. [PMID: 34887630 PMCID: PMC8613642 DOI: 10.3748/wjg.v27.i41.7100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/11/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reliable diagnostics are a major challenge for the detection and treatment of Helicobacter pylori (H. pylori) infection. Currently at the forefront are non-invasive urea breath test (UBT) and stool antigen test (SAT). Polymerase chain reaction (PCR) is not endorsed due to nonspecific primers and the threat of false-positives. The specificity of DNA amplification can be achieved by nested PCR (NPCR), which involves two rounds of PCR. If the primers are properly designed for the variable regions of the 16S rRNA gene, it is not difficult to develop an NPCR assay for the unambiguous identification of H. pylori. Elaborate NPCR for a 454 bp amplicon was validated on 81 clinical biopsy, stool, and saliva samples, each from the same individuals, and compared with available H. pylori assays, namely histology, rapid urease test, SAT, and 13C-UBT. The assay was much more sensitive than simple PCR, and it was equally sensitive in biopsy samples as the 13C-UBT test, which is considered the gold standard. In addition, it is sufficiently specific because sequencing of the PCR products exclusively confirmed the presence of H. pylori-specific DNA. However, due to the threshold and lower abundance, the sensitivity was much lower in amplifications from stool or saliva. Reliable detection in saliva also complicates the ability of H. pylori to survive in the oral cavity aside from and independent of the stomach. The reason for the lower sensitivity in stool is DNA degradation; therefore, a new NPCR assay was developed to obtain a shorter 148 bp 16S rRNA amplicon. The assay was validated on stool samples from 208 gastroenterological patients and compared to SAT results. Surprisingly, this NPCR revealed the presence of H. pylori in twice the number of samples as SAT, indicating that many patients are misdiagnosed, not treated by antibiotics, and their problems are interpreted as chronic. Thus, it is unclear how to properly diagnose H. pylori in practice. In the first approach, SAT or UBT is sufficient. If samples are negative, the 148 bp amplicon NPCR assay should be performed. If problems persist, patients should not be considered negative, but due to threshold H. pylori abundance, they should be periodically tested. The advantage of NPCR over UBT is that it can be used universally, including questionable samples taken from patients with achlorhydria, receiving proton pump inhibitors, antibiotics, bismuth compound, intestinal metaplasia, or gastric ulcer bleeding.
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Affiliation(s)
- Pavol Sulo
- Department of Biochemistry, Comenius University, Bratislava 842 15, Slovakia
| | - Barbora Šipková
- Department of Biochemistry, Comenius University, Bratislava 842 15, Slovakia
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Pistone D, Meroni G, Panelli S, D’Auria E, Acunzo M, Pasala AR, Zuccotti GV, Bandi C, Drago L. A Journey on the Skin Microbiome: Pitfalls and Opportunities. Int J Mol Sci 2021; 22:9846. [PMID: 34576010 PMCID: PMC8469928 DOI: 10.3390/ijms22189846] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
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Affiliation(s)
- Dario Pistone
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Gabriele Meroni
- Department of Biomedical Surgical and Dental Sciences-One Health Unit, University of Milan, 20133 Milan, Italy;
| | - Simona Panelli
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Enza D’Auria
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Miriam Acunzo
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Ajay Ratan Pasala
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Claudio Bandi
- Pediatric Clinical Research Center “Invernizzi”, Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
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Endophytic and rhizospheric bacterial communities are affected differently by the host plant species and environmental contamination. Symbiosis 2021. [DOI: 10.1007/s13199-021-00804-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Okamoto S, Ogai K, Mukai K, Sugama J. Association of Skin Microbiome with the Onset and Recurrence of Pressure Injury in Bedridden Elderly People. Microorganisms 2021; 9:microorganisms9081603. [PMID: 34442680 PMCID: PMC8400065 DOI: 10.3390/microorganisms9081603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 01/01/2023] Open
Abstract
Pressure injuries have been identified as one of the main health hazards among bedridden elderly people. Bedridden elderly people often stay in the same position for a long time, because they cannot switch positions; thus, the blood flow in the part of the body that is being compressed between the bed and their own weight is continuously blocked. As a result, redness and ulcers occur due to lacking oxygen and nutrients in the skin tissues, and these sites are often infected with microorganisms and, thus, become suppurative wounds, a condition commonly determined as pressure injuries. If left untreated, the pressure injury will recur with microbial infections, often resulting in cellulitis, osteomyelitis, and sepsis. The skin microbiome, in which many types of bacteria coexist, is formed on the skin surface. However, it remains unclear what characteristic of the skin microbiome among the bedridden elderly constitutes the development and severity of pressure injuries and the development of post-pressure injury infections. Thus, in this review article, we outlined the changes in the skin microbiome among the bedridden elderly people and their potential involvement in the onset and recurrence of pressure injuries.
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Affiliation(s)
- Shigefumi Okamoto
- Advanced Health Care Science Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-0942, Japan;
- Department of Clinical Laboratory Sciences, Faculty of Health Sciences, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kanazawa 920-0942, Japan
- Correspondence:
| | - Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kanazawa 920-0942, Japan;
| | - Kanae Mukai
- Department of Clinical Nursing, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-0942, Japan;
| | - Junko Sugama
- Advanced Health Care Science Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-0942, Japan;
- Research Center for Implementation Nursing Science Initiative, Fujita Health University, Toyoake 470-1192, Japan
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