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Pereira AR, Assis NVD, Paranhos AGDO, Lima DRS, Baeta BEL, Aquino SFD, Silva SDQ. Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse. ENVIRONMENTAL TECHNOLOGY 2024; 45:2205-2217. [PMID: 36632771 DOI: 10.1080/09593330.2023.2166877] [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: 08/24/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Nathália Vercelli de Assis
- Graduate Program in Biotechnology, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Diego Roberto Sousa Lima
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Bruno Eduardo Lobo Baeta
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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A study comparing the healthy and diseased equine glandular gastric microbiota sampled with sheathed transendoscopic cytology brushes. J Equine Vet Sci 2022; 116:104002. [PMID: 35490972 DOI: 10.1016/j.jevs.2022.104002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The role of the equine gastrointestinal microbiota in the pathogenesis of equine glandular gastric disease (EGGD) is poorly understood. OBJECTIVES To investigate whether the glandular gastric microbiota is altered in horses with EGGD. STUDY DESIGN Prospective longitudinal study METHODS: Five Thoroughbred racehorses from one training centre underwent gastroscopy as part of poor performance investigation. Samples were taken from EGGD lesions and adjacent normal mucosa using sheathed transendoscopic cytology brushes and frozen at -80 °C. DNA was extracted for 16S rRNA sequencing, and sequences compared against a database to generate taxonomic classification of the microbiota. The same horses were sampled six months later. RESULTS Normal glandular mucosal samples were characterised by a higher proportion of Proteobacteria (46.3 %) than EGGD lesions (18.9 %). Relative abundance of Firmicutes was lower in samples from normal mucosa (20.0 %) than EGGD lesions (41.2 %). Linear discriminant analysis effect size (LEfSe) confirmed a greater proportion of Firmicutes species was characteristic of samples collected from EGGD lesions due to a very high relative abundance of Sarcina (up to 92.4 %) in two horses with EGGD. We were unable to comment on the stability of the glandular gastric microbiota over time. MAIN LIMITATIONS Small sample population. None of the horses examined had grossly normal gastric mucosa. CONCLUSIONS The gastric microbiota appears altered in EGGD, although we are unable to demonstrate a causative effect. Sarcina was particularly increased in abundance in EGGD and may be a useful biomarker of disease. Sheathed cytology brushes were an effective method for sampling the gastric mucosa.
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Sarcina ventriculi in an Endoscopic Ultrasound-Guided Fine Needle Aspiration of a Perigastric Lymph Node with Metastatic Pancreatic Adenocarcinoma: A Carry-Through Contaminant Bacterial Microorganism from the Stomach. Case Rep Pathol 2022; 2021:4933279. [PMID: 35003818 PMCID: PMC8731288 DOI: 10.1155/2021/4933279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/10/2021] [Indexed: 11/18/2022] Open
Abstract
Sarcina ventriculi is a rare gram-positive coccus increasingly reported in patients with a history of delayed gastric emptying or gastric outlet obstruction and is sometimes seen in association with emphysematous gastritis and perforation. We report a case of a 67-year-old male who presented with epigastric pain. CT imaging and cholangiopancreatography were concerning for pancreatic neoplasia. Upper endoscopic ultrasound-guided fine needle aspiration cytology of a perigastric lymph node confirmed metastatic adenocarcinoma of pancreatic origin, and cocci arranged in a tetrad fashions characteristic of Sarcina ventriculi were noted. To our knowledge, this is the first reported case of Sarcina ventriculi in an FNA of metastatic pancreatic carcinoma in a perigastric lymph node. These organisms likely represent carry-through contaminants from the transgastric approach of the endoscopic FNA.
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Dumitru A, Aliuş C, Nica AE, Antoniac I, Gheorghiță D, Grădinaru S. Fatal outcome of gastric perforation due to infection with Sarcina spp. A case report. IDCases 2020; 19:e00711. [PMID: 32099809 PMCID: PMC7031000 DOI: 10.1016/j.idcr.2020.e00711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Sarcina ventriculi is an extremely rare pathogen. These gram-positive cocci bacteria are rarely identified in gastric biopsies and usually described in the scientific literature as an incidental finding, particularly in patients with delayed gastric emptying, gastroparesis, emphysematous gastritis or gastric perforation. It occurs most commonly in adult women and can be identified easily by its distinctive morphologic features, such as basophilic staining, cuboidal shape, tetrad arrangement, red blood cell-sized packets, flattened cell walls, and refractile nature in bright field microscopy. Although the pathogenesis of the microorganism is highly debated in humans, this bacterium is a well-known pathogen in livestock. Fewer than 30 cases of human infection have been described in the scientific literature so far, but none mentioned this micro-organism as a potential cause of death. We report the case of a 76-year-old patient with gastric perforation due to massive infection with Sarcina ventriculi. To date, this is the first report of human infection with Sarcina ventriculi in Romania.
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Affiliation(s)
- Adrian Dumitru
- Pathology Department, University Emergency Hospital Bucharest, Romania.,Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Cătălin Aliuş
- 4th Surgical Department, University Emergency Hospital Bucharest, Romania
| | - Adriana Elena Nica
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Anesthesiology Department, University Emergency Hospital Bucharest, Bucharest, Romania
| | - Iulian Antoniac
- Politehnica University of Bucharest, Faculty of Materials Science and Engineering, Romania
| | - Daniela Gheorghiță
- Politehnica University of Bucharest, Faculty of Materials Science and Engineering, Romania
| | - Sebastian Grădinaru
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,4th Surgical Department, University Emergency Hospital Bucharest, Romania
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Oliver A, Kay M, Cooper KK. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics 2018; 19:310. [PMID: 29716534 PMCID: PMC5930826 DOI: 10.1186/s12864-018-4635-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. Results For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4635-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Oliver
- Department of Biology, California State University Northridge, Northridge, CA, USA.,Present Address: Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Matthew Kay
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
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Abstract
Sarcina ventriculi is an increasingly common gram-positive coccus, recognized in gastric biopsies, particularly of patients with delayed gastric emptying. It occurs most commonly in adult women and can be identified easily by its characteristic morphologic features, such as basophilic staining, cuboid shape, tetrad arrangement, red blood cell–sized packets, flattened cell walls, and refractile nature on light microscopy. Although the pathogenesis of the organism is debated, it has been implicated in cases of gastric perforation, emphysematous gastritis, and peritonitis as well as occurring in the background of gastric adenocarcinomas. This review of the literature discusses the clinical features, endoscopy findings, histopathology, ancillary studies, microbiology, pathogenesis, differential diagnosis, treatment, and prognosis of this bacterium based on 19 published cases.
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Affiliation(s)
- Mohamed Rizwan Haroon Al Rasheed
- From the Department of Pathology, University of Illinois, Chicago (Dr Haroon Al Rasheed); and the Department of Pathology, John H. Stroger Jr Hospital of Cook County, Chicago (Dr Senseng)
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Haroon Al Rasheed MR, Kim GJ, Senseng C. A Rare Case of Sarcina ventriculi of the Stomach in an Asymptomatic Patient. Int J Surg Pathol 2015; 24:142-5. [DOI: 10.1177/1066896915610196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sarcina ventriculi is a gram-positive coccus that grows in a tetrad arrangement in the stomach. In the past 35 years, less than 20 cases have been reported in the literature, and it has been associated with life-threatening complications such as emphysematous gastritis and perforation. Treatment of S ventriculi generally consists of proton pump inhibitors with or without adjuvant antibiotic therapy. We report the first ever case of S ventriculi, including the morphological and immunohistochemical features, occurring in an asymptomatic patient with a history of Helicobacter pylori gastric ulcers.
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Affiliation(s)
| | - George J. Kim
- Department of Pathology, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, USA
| | - Carmencita Senseng
- Department of Pathology, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, USA
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Ratuapli SK, Lam-Himlin DM, Heigh RI. Sarcina ventriculi of the stomach: A case report. World J Gastroenterol 2013; 19:2282-2285. [PMID: 23599657 PMCID: PMC3627895 DOI: 10.3748/wjg.v19.i14.2282] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/16/2013] [Accepted: 01/24/2013] [Indexed: 02/06/2023] Open
Abstract
Sarcina ventriculi is a Gram positive organism, which has been reported to be found rarely, in the gastric specimens of patients with gastroparesis. Only eight cases of Sarcina, isolated from gastric specimens have been reported so far. Sarcina has been implicated in the development of gastric ulcers, emphysematous gastritis and gastric perforation. We report a case of 73-year-old male, with history of prior Billroth II surgery and truncal vagotomy, who presented for further evaluation of iron deficiency anemia. An upper endoscopy revealed diffuse gastric erythema, along with retained food. Biopsies revealed marked inflammation with ulcer bed formation and presence of Sarcina organisms. The patient was treated with ciprofloxacin and metronidazole for 1 wk, and a repeat endoscopy showed improvement of erythema, along with clearance of Sarcina organisms. Review of reported cases including ours suggests that Sarcina is more frequently an innocent bystander rather than a pathogenic organism. However, given its association with life threatening illness in two reported cases, it may be prudent to treat with antibiotics and anti-ulcer therapy, until further understanding is achieved.
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