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Guo L, Liu Q, Yin X. Clostridiales in the Gut Against Listeria monocytogenes Infection Through Growth Inhibition. Foodborne Pathog Dis 2024; 21:248-256. [PMID: 38150235 DOI: 10.1089/fpd.2023.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Listeria monocytogenes (Lm) mainly infect pregnant women, children, the elderly, and other populations with low immunity causing septicemia and meningitis. Healthy people can tolerate higher doses of Lm and only cause gastrointestinal symptoms such as abdominal pain and diarrhea after infection. Compared to the above population, healthy people have a richer and more diverse gut microbiota. In this study, we show that the microbiota in the large intestine and the feces of mice can significantly inhibit the growth of Lm compared to the microbiota in the small intestine. Bacteria larger than 1 μm in the gut microbiota play an important role in inhibiting Lm growth. 16s rRNA sequencing results show that these bacteria are mainly composed of Clostridiales under the phylum Firmicutes, including Ruminiclostridium, Butyricicoccus, Lachnoclostridium, Roseburia, Coprooccus, and Blautia. Thus, we demonstrate that there are some potential functional bacteria in the gut microbiota that can increase resistance against Lm.
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Affiliation(s)
- Liang Guo
- Zaozhuang University, Shandong, China
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Bear T, Roy N, Dalziel J, Butts C, Coad J, Young W, Parkar SG, Hedderley D, Dinnan H, Martell S, Middlemiss-Kraak S, Gopal P. Anxiety-like Behavior in Female Sprague Dawley Rats Associated with Cecal Clostridiales. Microorganisms 2023; 11:1773. [PMID: 37512945 PMCID: PMC10386170 DOI: 10.3390/microorganisms11071773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
The relationship between the microbiota profile and exposure to stress is not well understood. Therefore, we used a rat model of unpredictable chronic mild stress (UCMS) to investigate this relationship. Depressive-like behaviors were measured in Female Sprague Dawley rats using the sucrose preference test and the Porsolt swim test. Anxiety-like behaviors were measured with the light-dark box test. Fecal corticosterone, cecal microbiota (composition and organic acids), plasma gut permeability (lipopolysaccharide-binding protein, LBP) and plasma inflammation (12 cytokines) markers were measured. Atypical behaviors were observed in female rats following UCMS, but no depressive-like behaviors were observed. Circulating concentrations of cytokines granulocyte-macrophage colony-stimulating factor and cytokine-induced neutrophil chemoattractant 1 were higher in UCMS-exposed female rats; plasma LBP and cecal organic acid levels remained unchanged. Our results reflect a resilient and adaptive phenotype for female SD rats. The relative abundance of taxa from the Clostridiales order and Desulfovibrionaceae family did, however, correlate both positively and negatively with anxiety-like behaviors and plasma cytokine concentrations, regardless of UCMS exposure, supporting the brain-to-gut influence of mild anxiety with a microbiota profile that may involve inflammatory pathways.
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Affiliation(s)
- Tracey Bear
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
- School of Food and Advanced Technology, Massey University, Palmerston North 4442, New Zealand
| | - Nicole Roy
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
- Department of Human Nutrition, Otago University, Dunedin 9016, New Zealand
- High-Value Nutrition National Science Challenge, Auckland 1145, New Zealand
| | - Julie Dalziel
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Chrissie Butts
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Jane Coad
- School of Food and Advanced Technology, Massey University, Palmerston North 4442, New Zealand
| | - Wayne Young
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Shanthi G Parkar
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Duncan Hedderley
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Hannah Dinnan
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Sheridan Martell
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Susanne Middlemiss-Kraak
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Pramod Gopal
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
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3
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Karpinets TV, Wu X, Solley T, El Alam MB, Sims TT, Yoshida-Court K, Lynn E, Ahmed-Kaddar M, Biegert G, Yue J, Song X, Sun H, Petrosino JF, Mezzari MP, Okhuysen P, Eifel PJ, Jhingran A, Lin LL, Schmeler KM, Ramondetta L, Ajami N, Jenq RR, Futreal A, Zhang J, Klopp AH, Colbert LE. Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure. BMC Cancer 2022; 22:945. [PMID: 36050658 PMCID: PMC9438314 DOI: 10.1186/s12885-022-09997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Gut microbiome community composition differs between cervical cancer (CC) patients and healthy controls, and increased gut diversity is associated with improved outcomes after treatment. We proposed that functions of specific microbial species adjoining the mucus layer may directly impact the biology of CC. Method Metagenomes of rectal swabs in 41 CC patients were examined by whole-genome shotgun sequencing to link taxonomic structures, molecular functions, and metabolic pathway to patient’s clinical characteristics. Results Significant association of molecular functions encoded by the metagenomes was found with initial tumor size and stage. Profiling of the molecular function abundances and their distributions identified 2 microbial communities co-existing in each metagenome but having distinct metabolism and taxonomic structures. Community A (Clostridia and Proteobacteria predominant) was characterized by high activity of pathways involved in stress response, mucus glycan degradation and utilization of degradation byproducts. This community was prevalent in patients with larger, advanced stage tumors. Conversely, community B (Bacteroidia predominant) was characterized by fast growth, active oxidative phosphorylation, and production of vitamins. This community was prevalent in patients with smaller, early-stage tumors. Conclusions In this study, enrichment of mucus degrading microbial communities in rectal metagenomes of CC patients was associated with larger, more advanced stage tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09997-0.
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Affiliation(s)
- Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis Solley
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis T Sims
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica Lynn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mustapha Ahmed-Kaddar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Greyson Biegert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jingyan Yue
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huandong Sun
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Melissa P Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Pablo Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patricia J Eifel
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lilie L Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lois Ramondetta
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim Ajami
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Abstract
The Lactobacillaceae are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and other animals. Various studies have shown that specific Lactobacillaceae species produce metabolites that can inhibit the colonization of fungal and bacterial pathogens, but less is known about how Lactobacillaceae affect individual bacterial species in the endogenous animal microbiota. Here, we show that numerous Lactobacillaceae species inhibit the growth of the Lachnospiraceae family and the S24-7 group, two dominant clades of bacteria within the gut. We demonstrate that inhibitory activity is a property common to homofermentative Lactobacillaceae species, but not to species that use heterofermentative metabolism. We observe that homofermentative Lactobacillaceae species robustly acidify their environment, and that acidification alone is sufficient to inhibit growth of Lachnospiraceae and S24-7 growth, but not related species from the Clostridiales or Bacteroidales orders. This study represents one of the first in-depth explorations of the dynamic between Lactobacillaceae species and commensal intestinal bacteria, and contributes valuable insight toward deconvoluting their interactions within the gut microbial ecosystem.
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Affiliation(s)
- Emma J. E. Brownlie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Danica Chaharlangi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Erin Oi-Yan Wong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Deanna Kim
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,CONTACT William Wiley Navarre Department of Molecular Genetics, University of Toronto Faculty of Medicine, 661 University Avenue, Suite 1600, Toronto, ONM5G 1M1, Canada
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Shen R, Ke L, Li Q, Dang X, Shen S, Shen J, Li S, Liang L, Peng B, Kuang M, Ma Y, Yang Z, Hua Y. Abnormal bile acid-microbiota crosstalk promotes the development of hepatocellular carcinoma. Hepatol Int 2022; 16:396-411. [PMID: 35211843 PMCID: PMC9013324 DOI: 10.1007/s12072-022-10299-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/03/2022] [Indexed: 02/07/2023]
Abstract
Background Gut microbiota and microbe-derived metabolites are involved in the development of HCC. Bile acids (BAs) are the most important gut microbiota-modulated endogenous signaling molecules. Methods We tested serum bile acid levels and gut microbiome compositions in patients with HCC, chemical-induced HCC mouse models (DEN-HCC mice) and mouse orthotopic implanted liver tumor models with vancomycin treatment (vancomycin-treated mice). Then, we screened an important kind of HCC-related BAs, and verified its effect on the growth of HCC in vivo and in vitro. Results We found that the remarkably decreasing percentages of serum secondary BAs in the total bile acids of patients and DEN-HCC mice, especially, conjugated deoxycholic acids (DCA). The relative abundance of the bile salt hydrolase (BSH)-rich bacteria (Bifidobacteriales, Lactobacillales, Bacteroidales, and Clostridiales) was decreased in the feces of patients and DEN-HCC mice. Then, in vancomycin-treated mice, vancomycin treatment induced a reduction in the BSH-rich bacteria and promoted the growth of liver tumors. Similarly, the percentage of conjugated DCA after vancomycin treatment was significantly declined. We used a kind of conjugated DCA, Glyco-deoxycholic acid (GDCA), and found that GDCA remarkably inhibited the growth of HCC in vivo and in vitro. Conclusions We conclude that the remarkably decreasing percentages of serum conjugated DCA may be closely associated with HCC, which may be induced by the reducing gut BSH-rich bacteria. The mechanisms may be correlated with conjugated DCA directly inhibiting the growth and migration of HCC cells. Supplementary Information The online version contains supplementary material available at 10.1007/s12072-022-10299-7.
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Affiliation(s)
- Rui Shen
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Lixin Ke
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Qiao Li
- Department of Liver Surgery, Guangdong Provincial People's Hospital, Guangzhou, People's Republic of China
| | - Xi Dang
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Shunli Shen
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Jianming Shen
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Shaoqiang Li
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Lijian Liang
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Baogang Peng
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China.
| | - Ming Kuang
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China.
| | - Yi Ma
- Department of Organ Transplantation, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Zhonghan Yang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
| | - Yunpeng Hua
- Hepatobiliary and Pancreatic Surgery Center, First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China.
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Clark AS, Williams SD, Maxwell K, Rosales SM, Huebner LK, Landsberg JH, Hunt JH, Muller EM. Characterization of the Microbiome of Corals with Stony Coral Tissue Loss Disease along Florida's Coral Reef. Microorganisms 2021; 9:2181. [PMID: 34835306 DOI: 10.3390/microorganisms9112181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Stony coral tissue loss disease (SCTLD) is an emergent and often lethal coral disease that was first reported near Miami, FL (USA) in 2014. Our objective was to determine if coral colonies showing signs of SCTLD possess a specific microbial signature across five susceptible species sampled in Florida’s Coral Reef. Three sample types were collected: lesion tissue and apparently unaffected tissue of diseased colonies, and tissue of apparently healthy colonies. Using 16S rRNA high-throughput gene sequencing, our results show that, for every species, the microbial community composition of lesion tissue was significantly different from healthy colony tissue and from the unaffected tissue of diseased colonies. The lesion tissue of all but one species (Siderastrea siderea) had higher relative abundances of the order Rhodobacterales compared with other types of tissue samples, which may partly explain why S. siderea lesions often differed in appearance compared to other species. The order Clostridiales was also present at relatively high abundances in the lesion tissue of three species compared to healthy and unaffected tissues. Stress often leads to the dysbiosis of coral microbiomes and increases the abundance of opportunistic pathogens. The present study suggests that Rhodobacterales and Clostridiales likely play an important role in SCTLD.
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Montalban-Arques A, Katkeviciute E, Busenhart P, Bircher A, Wirbel J, Zeller G, Morsy Y, Borsig L, Glaus Garzon JF, Müller A, Arnold IC, Artola-Boran M, Krauthammer M, Sintsova A, Zamboni N, Leventhal GE, Berchtold L, de Wouters T, Rogler G, Baebler K, Schwarzfischer M, Hering L, Olivares-Rivas I, Atrott K, Gottier C, Lang S, Boyman O, Fritsch R, Manz MG, Spalinger MR, Scharl M. Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host Microbe 2021; 29:1573-1588.e7. [PMID: 34453895 DOI: 10.1016/j.chom.2021.08.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/16/2021] [Accepted: 08/03/2021] [Indexed: 12/30/2022]
Abstract
Despite overall success, T cell checkpoint inhibitors for cancer treatment are still only efficient in a minority of patients. Recently, intestinal microbiota was found to critically modulate anti-cancer immunity and therapy response. Here, we identify Clostridiales members of the gut microbiota associated with a lower tumor burden in mouse models of colorectal cancer (CRC). Interestingly, these commensal species are also significantly reduced in CRC patients compared with healthy controls. Oral application of a mix of four Clostridiales strains (CC4) in mice prevented and even successfully treated CRC as stand-alone therapy. This effect depended on intratumoral infiltration and activation of CD8+ T cells. Single application of Roseburia intestinalis or Anaerostipes caccae was even more effective than CC4. In a direct comparison, the CC4 mix supplementation outperformed anti-PD-1 therapy in mouse models of CRC and melanoma. Our findings provide a strong preclinical foundation for exploring gut bacteria as novel stand-alone therapy against solid tumors.
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Affiliation(s)
- Ana Montalban-Arques
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Egle Katkeviciute
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Busenhart
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bircher
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yasser Morsy
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lubor Borsig
- Department of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Anne Müller
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Isabelle C Arnold
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mariela Artola-Boran
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Department of Quantitative Biomedicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Federal Institute of Technology Zurich, Zurich, Switzerland
| | - Gabriel E Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Katharina Baebler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marlene Schwarzfischer
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Larissa Hering
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ivan Olivares-Rivas
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kirstin Atrott
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Claudia Gottier
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvia Lang
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Fritsch
- Department of Medical Oncology and Hematology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Baquer F, Ali Sawan A, Auzou M, Grillon A, Jaulhac B, Join-Lambert O, Boyer PH. Broth Microdilution and Gradient Diffusion Strips vs. Reference Agar Dilution Method: First Evaluation for Clostridiales Species Antimicrobial Susceptibility Testing. Antibiotics (Basel) 2021; 10:antibiotics10080975. [PMID: 34439025 PMCID: PMC8388896 DOI: 10.3390/antibiotics10080975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/05/2022] Open
Abstract
Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference method. In this work, we evaluated two broth microdilution kits (MICRONAUT-S Anaerobes® MIC and Sensititre Anaerobe MIC®) and one gradient diffusion strip method (Liofilchem®) for antimicrobial susceptibility testing of 47 Clostridiales isolates (Clostridium, Clostridioides and Hungatella species) using the agar dilution method as a reference. The evaluation focused on comparing six antimicrobial molecules available in both microdilution kits. Analytical performances were evaluated according to the Food and Drug Administration (FDA) recommendations. Essential agreements (EA) and categorical agreements (CA) varied greatly according to the molecule and the evaluated method. Vancomycin had values of essential and categorical agreements above 90% for the three methods. The CA fulfilled the FDA criteria for three major molecules in the treatment of Gram-positive anaerobic infections (metronidazole, piperacillin/tazobactam and vancomycin). The highest rate of error was observed for clindamycin. Multicenter studies are needed to further validate these results.
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Affiliation(s)
- Florian Baquer
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
| | - Asma Ali Sawan
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Michel Auzou
- Research Group on Microbial Adaptation GRAM 2.0, Department of Microbiology and Hygiene, Caen University Hospital of Caen, UniCaen-UniRouen, F-14033 Caen, France; (M.A.); (O.J.-L.)
| | - Antoine Grillon
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Benoît Jaulhac
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Olivier Join-Lambert
- Research Group on Microbial Adaptation GRAM 2.0, Department of Microbiology and Hygiene, Caen University Hospital of Caen, UniCaen-UniRouen, F-14033 Caen, France; (M.A.); (O.J.-L.)
| | - Pierre H. Boyer
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
- Correspondence:
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Usui N, Matsuzaki H, Shimada S. Characterization of Early Life Stress-Affected Gut Microbiota. Brain Sci 2021; 11:brainsci11070913. [PMID: 34356147 PMCID: PMC8306161 DOI: 10.3390/brainsci11070913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Early life stress (ELS), such as neglect and maltreatment, exhibits a strong impact on the mental and brain development of children. However, it is not fully understood how ELS affects the body and behavior of children. Therefore, in this study, we performed social isolation on weaned pre-adolescent mice and investigated how ELS could affect gut microbiota and mouse behavior. Using the metagenomics approach, we detected an overall ELS-related change in the gut microbiota and identified Bacteroidales and Clostridiales as significantly altered bacterial groups. These metagenomic alterations impaired social behavior in ELS mice, which also correlated with the abundance of Bacteroidales and Clostridiales. Our results demonstrate that ELS alters the gut microbiota and reduces social behavior in adolescent mice.
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Affiliation(s)
- Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan;
- United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan;
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka 541-8567, Japan
- Division of Development of Mental Functions, Research Center for Child Mental Development, University of Fukui, Fukui 910-1193, Japan
- Correspondence: ; Tel.: +81-6-6879-3124
| | - Hideo Matsuzaki
- United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan;
- Division of Development of Mental Functions, Research Center for Child Mental Development, University of Fukui, Fukui 910-1193, Japan
- Life Science Innovation Center, University of Fukui, Fukui 910-1193, Japan
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan;
- United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan;
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka 541-8567, Japan
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10
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Galluzzo P, Capri FC, Vecchioni L, Realmuto S, Scalisi L, Cottone S, Nuzzo D, Alduina R. Comparison of the Intestinal Microbiome of Italian Patients with Multiple Sclerosis and Their Household Relatives. Life (Basel) 2021; 11:life11070620. [PMID: 34206853 PMCID: PMC8307959 DOI: 10.3390/life11070620] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system, caused by a combination of genetic and environmental factors. In recent years, a role in MS pathogenesis was assigned to the gut microbiota. However, different signatures of gut dysbiosis have been shown to depend on environmental factors, like diet and lifestyle. In this study, we compared the gut microbiome in MS patients and their household healthy relatives sharing lifestyle and environmental factors. Faecal metagenomic DNA was extracted and the V3–V4 regions of the conserved bacterial 16S ribosomal RNA gene were amplified and sequenced. While overall bacterial communities were similar, specific families differed between healthy and MS subjects. We observed an increase in Ruminococcaceae, Christensenellaceae, Desulfovibrionaceae, Clostridiales, and Family XIII in MS patients, while Bacteroidaceae, Tannerellaceae, Veillonellaceae, and Burkholderiaceae were more abundant in healthy controls. In addition, principle coordinate analysis showed that the gut microbiome of all MS patients formed a cluster being less diverse than the household relatives and that gut microbiota of MS patients with EDSS 4.5–7 formed a distinct cluster in respect to their controls. Overall, our study is consistent with the hypothesis that MS patients have gut microbial dysbiosis and evidenced the importance of environmental factors in shaping the gut microbiome.
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Affiliation(s)
- Paola Galluzzo
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via G. Marinuzzi 3, 90129 Palermo, Italy
| | - Fanny Claire Capri
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
| | - Luca Vecchioni
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
| | - Sabrina Realmuto
- Centro Sclerosi Multipla, UOC Neurologia e Stroke Unit, AOOR Villa Sofia Cervello, 90146 Palermo, Italy;
| | - Luca Scalisi
- Centro Medico di Fisioterapia “Villa Sarina“, Via Porta Palermo 123, 91011 Alcamo, Italy;
| | - Salvatore Cottone
- U.O.C. Neurologia con Stroke Unit A.R.N.A.S. Civico, 90127 Palermo, Italy;
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, CNR, Via U. La Malfa 153, 90146 Palermo, Italy
- Correspondence: (D.N.); (R.A.); Tel.: +39-091-23897306 (R.A.)
| | - Rosa Alduina
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
- Correspondence: (D.N.); (R.A.); Tel.: +39-091-23897306 (R.A.)
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11
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Zhou C, Chen LL, Lu RQ, Ma WW, Xiao R. Alteration of Intestinal Microbiota Composition in Oral Sensitized C3H/HeJ Mice Is Associated With Changes in Dendritic Cells and T Cells in Mesenteric Lymph Nodes. Front Immunol 2021; 12:631494. [PMID: 34177885 PMCID: PMC8222730 DOI: 10.3389/fimmu.2021.631494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
This research aimed to investigate the allergic reaction of C3H/HeJ mice after sensitization with ovalbumin (OVA) without any adjuvant and to analyze the association between intestinal microbiota and allergy-related immune cells in mesenteric lymph nodes (MLN). The allergic responses of C3H/HeJ mice orally sensitized with OVA were evaluated, and immune cell subsets in spleen and MLN and cytokines were also detected. The intestinal bacterial community structure was analyzed, followed by Spearman correlation analysis between changed gut microbiota species and allergic parameters. Sensitization induced a noticeable allergic response to the gavage of OVA without adjuvant. Increased levels of Th2, IL-4, CD103+CD86+ DC, and MHCII+CD86+ DC and decreased levels of Th1, Treg, IFN-γ, TGF-β1, and CD11C+CD103+ DC were observed in allergic mice. Furthermore, families of Lachnospiraceae, Clostridiaceae_1, Ruminococcaceae, and peprostreptococcaceae, all of which belonging to the order Clostridiales, were positively related to Treg and CD11C+CD103+ DC, while they were negatively related to an allergic reaction, levels of Th2, CD103+CD86+ DC, and MHCII+CD86+ DC in MLN. The family of norank_o_Mollicutes_RF39 belonging to the order Mollicutes_RF39 was similarly correlated with allergic reaction and immune cells in MLN of mice. To sum up, allergic reactions and intestinal flora disturbances could be induced by OVA oral administration alone. The orders of Clostridiales and Mollicutes_RF39 in intestinal flora are positively correlated with levels of Treg and CD11C+CD103+ DC in MLN of mice.
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Affiliation(s)
- Cui Zhou
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing, China
| | - Ling-Ling Chen
- Nutritional Department, Handan First Hospital, Handan, China
| | - Rui-Qi Lu
- School of Basic Medicine, Capital Medical University, Beijing, China
| | - Wei-Wei Ma
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing, China
| | - Rong Xiao
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing, China
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12
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Karpat I, Karolyi M, Pawelka E, Seitz T, Thaller F, Wenisch C. Flavonifractor plautii bloodstream infection in an asplenic patient with infectious colitis. Wien Klin Wochenschr 2021; 133:724-6. [PMID: 34046735 DOI: 10.1007/s00508-021-01877-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/13/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Flavonifractor plautii is a gram-positive, strictly anaerobic, rod-shaped bacterium. It belongs to the family of Clostridiales, is frequently found in the human gut microbiome and is rarely isolated in other human specimens. CLINICAL PRESENTATION We report a case of a bloodstream infection with Flavonifractor plautii following infectious colitis in a 24-year-old asplenic woman with beta thalassemia. The patient presented to our department with diarrhea, fever, and lower abdominal pain for over 1 month. F. plautii was the only organism isolated from blood cultures. RESULTS The antimicrobial resistance pattern showed in vitro sensitivity to all antimicrobials used for treatment; however, in vivo treatment with amoxicillin and clavulanic acid failed. After switching to meropenem and metronidazole the patient rapidly recovered. CONCLUSION Asplenia and a damaged intestinal wall might have favored the bloodstream infection. We found similarities in attributes of the affected patients and in treatment patterns between our case and the only three other published case reports.
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13
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David MM, Tataru C, Daniels J, Schwartz J, Keating J, Hampton-Marcell J, Gottel N, Gilbert JA, Wall DP. Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes. mSystems 2021; 6:e00193-20. [PMID: 33824194 DOI: 10.1128/mSystems.00193-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations, efforts to identify microbial biomarkers have been limited due to a lack of appropriately matched controls, stratification of participants within the autism spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of families with age-matched sibling pairs between 2 and 7 years old (within 2 years of each other), where one child had a diagnosis of ASD and the other did not. Parents collected stool samples, provided a home video of their ASD child's natural social behavior, and responded online to diet and behavioral questionnaires. 16S rRNA V4 amplicon sequencing of 117 samples (60 ASD and 57 controls) identified 21 amplicon sequence variants (ASVs) that differed significantly between the two cohorts: 11 were found to be enriched in neurotypical children (six ASVs belonging to the Lachnospiraceae family), while 10 were enriched in children with ASD (including Ruminococcaceae and Bacteroidaceae families). Summarizing the expected KEGG orthologs of each predicted genome, the taxonomic biomarkers associated with children with ASD can use amino acids as precursors for butyragenic pathways, potentially altering the availability of neurotransmitters like glutamate and gamma aminobutyric acid (GABA).IMPORTANCE Autism spectrum disorder (ASD), which now affects 1 in 54 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in humans. This has been due in part to sample size that sufficiently covers the spectrum of phenotypes known to autism (which range from subtle to severe) and a lack of appropriately matched controls. Our original study proposes to overcome these limitations by collecting stool-associated microbiome on 60 sibling pairs of children, one with autism and one neurotypically developing, both 2 to 7 years old and no more than 2 years apart in age. We use exact sequence variant analysis and both permutation and differential abundance procedures to identify 21 taxa with significant enrichment or depletion in the autism cohort compared to their matched sibling controls. Several of these 21 biomarkers have been identified in previous smaller studies; however, some are new to autism and known to be important in gut-brain interactions and/or are associated with specific fatty acid biosynthesis pathways.
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14
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Jung DH, Yong JH, Hwang W, Yoon MY, Yoon SS. An efficient system for intestinal on-site butyrate production using novel microbiome-derived esterases. J Biol Eng 2021; 15:9. [PMID: 33676548 PMCID: PMC7936488 DOI: 10.1186/s13036-021-00259-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/04/2021] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids, especially butyrate, play beneficial roles in sustaining gastrointestinal health. However, due to limitations associated with direct consumption of butyrate, there has been interest in using prodrugs of butyrate. Tributyrin (TB), a triglyceride composed of three butyrate molecules and a glycerol, is a well-studied precursor of butyrate. We screened a metagenome library consisting of 5760 bacterial artificial chromosome clones, with DNA inserts originating from mouse microbiomes, and identified two clones that efficiently hydrolyse TB into butyrate. Nucleotide sequence analysis indicated that inserts in these two clones are derived from unknown microbes. BLASTp analysis, however, revealed that each insert contains a gene homologous to acetylesterase or esterase genes, from Clostridium spp. and Bacteroides spp., respectively. Predicted structures of these two proteins both contain serine-histidine-aspartate catalytic triad, highly conserved in the family of esterases. Escherichia coli host expressing each of the two candidate genes invariably produced greater amounts of butyrate in the presence of TB. Importantly, administration of TB together with cloned E. coli cells alleviated inflammatory symptoms in a mouse model of acute colitis. Based on these results, we established an efficient on-site and real-time butyrate production system that releases butyrate in a controlled manner inside the intestine.
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Affiliation(s)
- Dah Hyun Jung
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hyun Yong
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Wontae Hwang
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mi Young Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea. .,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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15
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Abstract
The steep rise in food allergy (FA) has evoked environmental factors involved in disease pathogenesis, including the gut microbiota, diet, and their metabolites. Early introduction of solid foods synchronizes with the "weaning reaction," a time during which the microbiota imprints durable oral tolerance. Recent work has shown that children with FA manifest an early onset dysbiosis with the loss of Clostridiales species, which promotes the differentiation of ROR-γt+ regulatory T cells to suppress FA. This process can be reversed in pre-clinical mouse models by targeted bacteriotherapy. Here, we review the dominant tolerance mechanisms enforced by the microbiota to suppress FA and discuss therapeutic intervention strategies that act to recapitulate the early life window of opportunity in stemming the FA epidemic.
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Affiliation(s)
- Emmanuel Stephen-Victor
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Crestani
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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16
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Mukorako P, Lopez C, Baraboi ED, Roy MC, Plamondon J, Lemoine N, Biertho L, Varin TV, Marette A, Richard D. Alterations of Gut Microbiota After Biliopancreatic Diversion with Duodenal Switch in Wistar Rats. Obes Surg 2020; 29:2831-2842. [PMID: 31165976 DOI: 10.1007/s11695-019-03911-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The biliopancreatic diversion with duodenal switch (BPD/DS) represents the most effective surgical procedure for the treatment of severe obesity and associated type 2 diabetes. The mechanisms whereby BPD/DS exerts its positive metabolic effects have however yet to be fully delineated. The objective of this study was to distinguish the effects of the two components of BPD/DS, namely the sleeve gastrectomy (SG) and the DS derivation, on gut microbiota, and to appraise whether changes in microbial composition are linked with surgery-induced metabolic benefits. METHODS BPD/DS, DS, and SG were performed in Wistar rats fed a standard chow diet. Body weight and energy intake were measured daily during 8 weeks post-surgery, at which time glucagon-like peptide 1 (GLP-1), peptide tyrosine tyrosine (PYY), insulin, and glucose were measured. Fecal samples were collected prior to surgery and at 2 and 8 weeks post-surgery. Intraluminal contents of the alimentary, biliopancreatic, and common limbs (resulting from BPD/DS) were taken from the proximal portion of each limb. Fecal and small intestinal limb samples were analyzed by 16S ribosomal RNA gene sequencing. RESULTS BPD/DS and DS led to lower digestible energy intake (P = 0.0007 and P = 0.0002, respectively), reduced weight gain (P < 0.0001) and body fat mass (P < 0.0001), improved glucose metabolism, and increased GLP-1 (P = 0.0437, SHAM versus DS) and PYY levels (P < 0.0001). These effects were associated with major alterations of both the fecal and small intestinal microbiota, as revealed by significant decrease in bacterial richness and diversity at 2 (P < 0.0001, Chao1 index; P < 0.0001, Shannon index) and 8 weeks (P = 0.0159, SHAM versus DS, Chao1 index; P = 0.0219, SHAM versus DS, P = 0.0472, SHAM versus BPD/DS, Shannon index) post-surgery in BPD/DS and DS, and increased proportions of Bifidobacteriales (a 60% increase in both groups) but reduced Clostridiales (a 50% decrease and a 90% decrease respectively), which were mostly accounted at the genus level by higher relative abundance of Bifidobacterium in both the fecal and intestinal limb samples, as well as reduced abundance of Peptostreptococcaceae and Clostridiaceae in the small intestine. Those effects were not seen in SG rats. CONCLUSION The metabolic benefits following BPD/DS are seemingly due to the DS component of the surgery. Furthermore, BPD/DS causes marked alterations in fecal and small intestinal microbiota resulting in reduced bacterial diversity and richness. Our data further suggest that increased abundance of Bifidobacterium and reduced level of two Clostridiales species in the gut microbiota might contribute to the positive metabolic outcomes of BPD/DS.
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Affiliation(s)
- Paulette Mukorako
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Carlos Lopez
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Elena-Dana Baraboi
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Marie-Claude Roy
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Julie Plamondon
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Natacha Lemoine
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Laurent Biertho
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Thibault V Varin
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - André Marette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada
| | - Denis Richard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Pavillon Marguerite-d'Youville 2725 chemin Sainte- Foy, Québec, G1V 4G5, Canada.
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17
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Abstract
Sewage overflows, agricultural runoff, and stormwater discharges introduce fecal pollution into surface waters. Distinguishing these sources is critical for evaluating water quality and formulating remediation strategies. With the falling costs of sequencing, microbial community-based water quality assessment tools are under development. However, their application is limited by the need to build reference libraries, which requires extensive sampling of sources and bioinformatic expertise. Here, we introduce FORest Enteric Source IdentifiCation (FORENSIC; https://forensic.sfs.uwm.edu/), an online, library-independent source tracking platform based on random forest classification and 16S rRNA gene amplicon sequences to identify in environmental samples common fecal contamination sources, including humans, domestic pets, and agricultural animals. FORENSIC relies on a broad reference signature database of Bacteroidales and Clostridiales, two predominant bacterial groups that have coevolved with their hosts. As a result, these groups demonstrate cohesive and reliable assemblage patterns within mammalian species or among species sharing the same diet/physiology. We created a scalable and extensible platform that we tested for global applicability using samples collected in distant geographic locations. This Web application offers a fast and intuitive approach for fecal source identification, particularly in sewage-contaminated waters.IMPORTANCE FORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk in polluted waters. To test for fecal contamination sources, the platform only requires paired-end reads targeting the V4 or V6 regions of the 16S rRNA gene. We demonstrated that we could use V4V5 reads trimmed to the V4 positions to generate the reference signature. The systematic workflow we describe to create and validate the signatures could be applied to many disciplines. With the increasing gap between advancing technology and practical applications, this platform makes sequence-based water quality assessments accessible to the public health and water resource communities.
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18
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Schoster A, Kunz T, Lauper M, Graubner C, Schmitt S, Weese JS. Prevalence of Clostridium difficile and Clostridium perfringens in Swiss horses with and without gastrointestinal disease and microbiota composition in relation to Clostridium difficile shedding. Vet Microbiol 2019; 239:108433. [PMID: 31767096 DOI: 10.1016/j.vetmic.2019.108433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/27/2022]
Abstract
Overgrowth of enteric clostridia in dysbiosis in horses with colic is presumed but scarcely investigated. The objective was to provide prevalence data of Clostridium difficile and Clostridium perfringens in horses with and without gastrointestinal disease in Switzerland, and investigate microbiota differences between C. difficile shedders and non-shedders. Fecal samples were taken from healthy horses (n = 103), horses with colic (n = 98) and horses with diarrhea (n = 151). Colic horses were sampled on three days. Selective enrichment culture and molecular typing for C. difficile and C. perfringens was performed. Microbiota differences between horses with colic shedding (n = 7) and not shedding (n = 7) C. difficile were assessed using metagenomic sequencing. The cumulative prevalence (19% C. difficile; 16% C. perfringens) was higher compared to single day samples (1-10% C. difficile; 3-8% C. perfringens, all p < 0.003). Horses with colic shed significantly more C. difficile (p < 0.001) but not C. perfringens (p = 0.09) compared to healthy horses. Prevalence in horses with diarrhea was 8% for both Clostridium species. There were no significant microbiota differences between C. difficile shedders and non-shedders with regards to relative abundance on any phylogenetic level, and alpha diversity. Limited differences were seen on LEfSE analysis and in beta diversity indices. Multiple fecal samples should be taken when investigating shedding of enteric clostridia. As horses with colic shed more enteric clostridia compared to healthy horses special biosecurity protocols for horses with colic should be considered in hospitals. Differences in microbiota composition between C. difficile shedders and non-shedders were limited. Further studies on the role of dysbiosis in C. difficile are needed.
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Affiliation(s)
- A Schoster
- University of Zurich, Vetsuisse Faculty, Equine Department, Winterthurerstrasse 260, 8057 Zurich, Switzerland.
| | - T Kunz
- University of Zurich, Vetsuisse Faculty, Equine Department, Winterthurerstrasse 260, 8057 Zurich, Switzerland.
| | - M Lauper
- University of Berne, Vetsuisse Faculty, Institut Suisse de Médicine Equine, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - C Graubner
- University of Berne, Vetsuisse Faculty, Institut Suisse de Médicine Equine, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - S Schmitt
- University of Zurich, Vetsuisse Faculty, Section of Veterinary Bacteriology, Winterthurerstrasse 270, 8057 Zurich, Switzerland.
| | - J S Weese
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, N1G2W1 Guelph, Canada.
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19
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Hrncirova L, Machova V, Trckova E, Krejsek J, Hrncir T. Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice. Microorganisms 2019; 7:microorganisms7100383. [PMID: 31548508 PMCID: PMC6843281 DOI: 10.3390/microorganisms7100383] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/13/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
The worldwide incidence of many immune-mediated and metabolic diseases, initially affecting only the wealthy Western countries, is increasing rapidly. Many of these diseases are associated with the compositional and functional alterations of gut microbiota, i.e., dysbiosis. The most consistent markers of the dysbiosis are a decrease in microbiota diversity and an expansion of Proteobacteria. The role of food preservatives as potential triggers of gut microbiota dysbiosis has been long overlooked. Using a human microbiota-associated mouse model, we demonstrate that a mixture of common antimicrobial food additives induces dysbiosis characterised by an overgrowth of Proteobacteria phylum and a decrease in the Clostridiales order. Remarkably, human gut microbiota in a Nod2-deficient genetic background is even more susceptible to the induction of Proteobacteria dysbiosis by additives than the microbiota in a wild-type background. To conclude, our data demonstrate that antimicrobial food additives trigger gut microbiota dysbiosis in both wild-type and Nod2-deficient backgrounds and at the exposure levels reached in European populations. Whether this additive-modified gut microbiota plays a significant role in the pathogenesis of immune-mediated and metabolic diseases remains to be elucidated.
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Affiliation(s)
- Lucia Hrncirova
- Charles University in Prague, The Faculty of Medicine in Hradec Kralove, 500 03 Hradec Kralove, Czech Republic.
- The Institute of Microbiology, The Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic.
| | - Vladimira Machova
- The Institute of Microbiology, The Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic.
| | - Eva Trckova
- The Institute of Microbiology, The Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic.
| | - Jan Krejsek
- Charles University in Prague, The Faculty of Medicine in Hradec Kralove, 500 03 Hradec Kralove, Czech Republic.
| | - Tomas Hrncir
- The Institute of Microbiology, The Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic.
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20
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Zegarra-Ruiz DF, El Beidaq A, Iñiguez AJ, Lubrano Di Ricco M, Manfredo Vieira S, Ruff WE, Mubiru D, Fine RL, Sterpka J, Greiling TM, Dehner C, Kriegel MA. A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity. Cell Host Microbe 2018; 25:113-127.e6. [PMID: 30581114 DOI: 10.1016/j.chom.2018.11.009] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/27/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
Western lifestyle is linked to autoimmune and metabolic diseases, driven by changes in diet and gut microbiota composition. Using Toll-like receptor 7 (TLR7)-dependent mouse models of systemic lupus erythematosus (SLE), we dissect dietary effects on the gut microbiota and find that Lactobacillus reuteri can drive autoimmunity but is ameliorated by dietary resistant starch (RS). Culture of internal organs and 16S rDNA sequencing revealed TLR7-dependent translocation of L. reuteri in mice and fecal enrichment of Lactobacillus in a subset of SLE patients. L. reuteri colonization worsened autoimmune manifestations under specific-pathogen-free and gnotobiotic conditions, notably increasing plasmacytoid dendritic cells (pDCs) and interferon signaling. However, RS suppressed the abundance and translocation of L. reuteri via short-chain fatty acids, which inhibited its growth. Additionally, RS decreased pDCs, interferon pathways, organ involvement, and mortality. Thus, RS exerts beneficial effects in lupus-prone hosts through suppressing a pathobiont that promotes interferon pathways implicated in the pathogenesis of human autoimmunity.
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MESH Headings
- Animals
- Autoimmunity
- Clostridiaceae
- DNA, Ribosomal/genetics
- Dendritic Cells/metabolism
- Diet
- Diet Therapy
- Disease Models, Animal
- Fatty Acids, Volatile/antagonists & inhibitors
- Fatty Acids, Volatile/metabolism
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Germ-Free Life
- Glomerulonephritis/pathology
- Humans
- Hypersensitivity
- Interferon Type I/metabolism
- Kidney/pathology
- Lactobacillus/drug effects
- Lactobacillus/genetics
- Lactobacillus/pathogenicity
- Limosilactobacillus reuteri
- Lupus Erythematosus, Systemic/microbiology
- Lupus Erythematosus, Systemic/mortality
- Lupus Erythematosus, Systemic/pathology
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Inbred C57BL
- RNA, Ribosomal, 16S/genetics
- Starch
- Survival Rate
- Toll-Like Receptor 7/metabolism
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Affiliation(s)
- Daniel F Zegarra-Ruiz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Asmaa El Beidaq
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Alonso J Iñiguez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | | | - Silvio Manfredo Vieira
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - William E Ruff
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Derek Mubiru
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Rebecca L Fine
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - John Sterpka
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Teri M Greiling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Carina Dehner
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Martin A Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA.
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21
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Ma B, McComb E, Gajer P, Yang H, Humphrys M, Okogbule-Wonodi AC, Fasano A, Ravel J, Viscardi RM. Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants. Front Microbiol 2018; 9:2755. [PMID: 30487786 PMCID: PMC6246636 DOI: 10.3389/fmicb.2018.02755] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022] Open
Abstract
Intestinal barrier immaturity, or "leaky gut," is the proximate cause of susceptibility to necrotizing enterocolitis in preterm neonates. However, the impact of intestinal microbiota development on intestinal mucosal barrier maturation has not been evaluated in this population. In this study, we investigated a longitudinally sampled cohort of 38 preterm infants < 33 weeks gestation monitored for intestinal permeability (IP) and fecal microbiota during the first 2 weeks of life. Rapid decrease in IP indicating intestinal barrier function maturation correlated with significant increase in community diversity. In particular, members of the Clostridiales and Bifidobacterium were highly transcriptionally active, and progressively increasing abundance in Clostridiales was significantly associated with decreased intestinal permeability. Further, neonatal factors previously identified to promote intestinal barrier maturation, including early exclusive breastmilk feeding and shorter duration antibiotic exposure, associate with the early colonization of the intestinal microbiota by members of the Clostridiales, which altogether are associated with improved intestinal barrier function in preterm infants.
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Affiliation(s)
- Bing Ma
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Elias McComb
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pawel Gajer
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Hongqiu Yang
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mike Humphrys
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Adora C. Okogbule-Wonodi
- Department of Pediatrics and Child Health, Howard University College of Medicine, Washington, DC, United States
| | - Alessio Fasano
- Department of Pediatrics, Basic, Clinical and Translational Research, MassGeneral Hospital for Children, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Rose M Viscardi
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
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22
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Abstract
BACKGROUND Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clostridiales and Bacteroidales are particularly suitable for identifying sources of fecal contamination in environmental samples. However, a comprehensive evaluation of their predictive power and development of computational approaches is lacking. Given the global public health concern for waterborne disease, accurate identification of fecal pollution sources is essential for effective risk assessment and management. Here, we use random forest algorithm and 16S rRNA gene amplicon sequences assigned to Clostridiales and Bacteroidales to identify common fecal pollution sources. We benchmarked the accuracy, consistency, and sensitivity of our classification approach using fecal, environmental, and artificial in silico generated samples. RESULTS Clostridiales and Bacteroidales classifiers were composed mainly of sequences that displayed differential distributions (host-preferred) among sewage, cow, deer, pig, cat, and dog sources. Each classifier correctly identified human and individual animal sources in approximately 90% of the fecal and environmental samples tested. Misclassifications resulted mostly from false-positive identification of cat and dog fecal signatures in host animals not used to build the classifiers, suggesting characterization of additional animals would improve accuracy. Random forest predictions were highly reproducible, reflecting the consistency of the bacterial signatures within each of the animal and sewage sources. Using in silico generated samples, we could detect fecal bacterial signatures when the source dataset accounted for as little as ~ 0.5% of the assemblage, with ~ 0.04% of the sequences matching the classifiers. Finally, we developed a proxy to estimate proportions among sources, which allowed us to determine which sources contribute the most to observed fecal pollution. CONCLUSION Random forest classification with 16S rRNA gene amplicons offers a rapid, sensitive, and accurate solution for identifying host microbial signatures to detect human and animal fecal contamination in environmental samples.
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Affiliation(s)
- Adélaïde Roguet
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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23
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Farowski F, Els G, Tsakmaklis A, Higgins PG, Kahlert CR, Stein-Thoeringer CK, Bobardt JS, Dettmer-Wilde K, Oefner PJ, Vehreschild JJ, Vehreschild MJ. Assessment of urinary 3-indoxyl sulfate as a marker for gut microbiota diversity and abundance of Clostridiales. Gut Microbes 2018; 10:133-141. [PMID: 30118620 PMCID: PMC6546351 DOI: 10.1080/19490976.2018.1502536] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/04/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES After allogeneic hematopoietic stem cell transplantation (allo-HCT), urinary levels of 3-indoxyl sulfate (3-IS) correlate with the relative abundance of bacteria from the class Clostridia (RAC), and antibiotic treatment is considered the major determinant of this outcome. A high RAC has been associated with favorable outcome after allo-HCT and protection from Clostridium difficile infection (CDI). We assessed correlations between alpha diversity, RAC and urinary 3-IS levels in a non-allo-HCT clinical cohort of antibiotic treated patients to further explore 3-IS as a biomarker of reduced diversity and predisposition to CDI. METHODS Fecal and urinary specimens were analyzed from 40 non-allo-HCT hospitalized patients before and 9 ± 2 days after initiation of intravenous antibiotic treatment. Fecal microbiota were analyzed by 16s RNA sequencing and urinary 3-IS was analyzed by liquid chromatography-tandem mass spectrometry. Receiver operating characteristic (ROC) analysis was performed to assess the predictive value of 3-IS. RESULTS At a RAC cutoff of <30%, the binary logarithm of 3-IS (medium 3-IS: ≤2.5; high 3-IS: >2.5) was predictive with an accuracy of 82% (negative predictive value: 87%, positive predictive value 67%). Accuracy was improved by combing antibiotic history with 3-IS levels (accuracy 89%, npv 88%, ppv 92%). CONCLUSION In conjunction with patient antibiotic history, 3-IS is a candidate marker to predict RAC.
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Affiliation(s)
- Fedja Farowski
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Gregor Els
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Christian R. Kahlert
- Clinic of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Christoph K. Stein-Thoeringer
- Clinic und Polyclinic for Internal Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Immunology program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Johanna S. Bobardt
- Clinic und Polyclinic for Internal Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Katja Dettmer-Wilde
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Jörg Janne Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Maria J.G.T. Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
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24
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Herrmann E, Young W, Reichert-Grimm V, Weis S, Riedel CU, Rosendale D, Stoklosinski H, Hunt M, Egert M. In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing-A Proof-of-Principle Study. Nutrients 2018; 10:nu10020179. [PMID: 29415499 PMCID: PMC5852755 DOI: 10.3390/nu10020179] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/19/2018] [Accepted: 01/30/2018] [Indexed: 02/07/2023] Open
Abstract
Resistant starch (RS) is the digestion resistant fraction of complex polysaccharide starch. By reaching the large bowel, RS can function as a prebiotic carbohydrate, i.e., it can shape the structure and activity of bowel bacterial communities towards a profile that confers health benefits. However, knowledge about the fate of RS in complex intestinal communities and the microbial members involved in its degradation is limited. In this study, 16S ribosomal RNA (rRNA)-based stable isotope probing (RNA-SIP) was used to identify mouse bowel bacteria involved in the assimilation of RS or its derivatives directly in their natural gut habitat. Stable-isotope [U13C]-labeled native potato starch was administrated to mice, and caecal contents were collected before 0 h and 2 h and 4 h after administration. 'Heavy', isotope-labeled [13C]RNA species, presumably derived from bacteria that have metabolized the labeled starch, were separated from 'light', unlabeled [12C]RNA species by fractionation of isolated total RNA in isopycnic-density gradients. Inspection of different density gradients showed a continuous increase in 'heavy' 16S rRNA in caecal samples over the course of the experiment. Sequencing analyses of unlabeled and labeled 16S amplicons particularly suggested a group of unclassified Clostridiales, Dorea, and a few other taxa (Bacteroides, Turicibacter) to be most actively involved in starch assimilation in vivo. In addition, metabolic product analyses revealed that the predominant 13C-labeled short chain fatty acid (SCFA) in caecal contents produced from the [U13C] starch was butyrate. For the first time, this study provides insights into the metabolic transformation of RS by intestinal bacterial communities directly within a gut ecosystem, which will finally help to better understand its prebiotic potential and possible applications in human health.
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Affiliation(s)
- Elena Herrmann
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Wayne Young
- AgResearch Limited, Food Nutrition and Health Team, Grasslands Research Centre, Palmerston North 4474, New Zealand;
- Riddet Institute, Massey University, Palmerston North 4474, New Zealand
- High-Value Nutrition, National Science Challenge, University of Auckland, Auckland 1142, New Zealand
| | - Verena Reichert-Grimm
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Severin Weis
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany; (V.R.-G.); (C.U.R.)
| | - Douglas Rosendale
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Halina Stoklosinski
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Martin Hunt
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4474, New Zealand; (D.R.); (H.S.); (M.H.)
| | - Markus Egert
- Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (E.H.); (S.W.)
- Correspondence: ; Tel.: +49-7720-307-4554
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25
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Serrano AE, Escudero LV, Tebes-Cayo C, Acosta M, Encalada O, Fernández-Moroso S, Demergasso C. First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. Stand Genomic Sci 2017; 12:43. [PMID: 28770028 PMCID: PMC5525254 DOI: 10.1186/s40793-017-0252-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum. Here, we describe the first whole draft genome sequence of an arsenic-reducing strain belonging to the Fusibacter genus showing the highest 16S rRNA gene sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%. Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for RNAs. Insights from the genome sequence and some microbiological features of the strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample SAMD00055724. The release of the genome sequence of this strain could contribute to the understanding of the arsenic biogeochemistry in extreme environments.
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Affiliation(s)
- Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Lorena V Escudero
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Cinthya Tebes-Cayo
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mauricio Acosta
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | | | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
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26
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Schoster A, Staempfli H, Guardabassi L, Jalali M, Weese J. Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life. BMC Vet Res 2017; 13:144. [PMID: 28558788 PMCID: PMC5450145 DOI: 10.1186/s12917-017-1064-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/18/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diarrhea in foals affects up to 60% of foals during the first six months of life. The effect of diarrhea on the fecal bacterial microbiota in foals has not been investigated. Little is known on the fecal bacterial microbial richness and diversity of foals at a young age. The objective was to compare the fecal bacterial microbiota of healthy foals to foals with diarrhea at two and four weeks of life. METHODS Fecal samples were collected from foals (n = 20) at 1-14 (T1) and 15-28 (T2) days of age and analyzed using high throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity and beta diversity indices were assessed between age-matched foals with diarrhea (n = 9) and healthy foals (n = 11), and between time points. RESULTS Differences in microbial community composition based on time point and health status were observed on all taxonomic levels. Of 117 enriched species in healthy foals at T2, 50 (48%) were Lachnospiraceae or Ruminococcaceae. The Chao richness index was increased in healthy foals at T2 compared to T1 (p = 0.02). Foals with diarrhea had a significantly lower richness index than non-diarrheic foals at T2 (p = 0.04). Diarrhea had an inconsistent effect, while time point had a consistent effect on microbial community structure. CONCLUSIONS Preventative and therapeutic measures for diarrhea should focus on maintaining bacterial microbiota richness. Lachnospiraceae and Ruminococcaceae were underrepresented in foals with diarrhea. These should be evaluated further as potential therapeutic options.
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Affiliation(s)
- A. Schoster
- Equine Department, University of Zurich, Vetsuisse Faculty, Winterthurerstrasse 260, 8057 Zurich, Zurich Switzerland
- Department of Veterinary Disease Biology, University of Copenhagen, Faculty of Health and Medical Science, Stigbojlen 4, 1870, Copenhagen, Denmark
| | - H.R. Staempfli
- Department of Clinical Studies, University of Guelph, Ontario Veterinary College, Guelph, N1G2W1 Canada
| | - L.G. Guardabassi
- Department of Veterinary Disease Biology, University of Copenhagen, Faculty of Health and Medical Science, Stigbojlen 4, 1870, Copenhagen, Denmark
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St Kitts and Nevis
| | - M. Jalali
- Department of Pathobiology, University of Guelph, Ontario Veterinary College, Guelph, N1G2W1 Canada
| | - J.S. Weese
- Department of Pathobiology, University of Guelph, Ontario Veterinary College, Guelph, N1G2W1 Canada
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27
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Magnusson KR, Hauck L, Jeffrey BM, Elias V, Humphrey A, Nath R, Perrone A, Bermudez LE. Relationships between diet-related changes in the gut microbiome and cognitive flexibility. Neuroscience 2015; 300:128-40. [PMID: 25982560 DOI: 10.1016/j.neuroscience.2015.05.016] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/10/2015] [Accepted: 05/06/2015] [Indexed: 02/06/2023]
Abstract
Western diets are high in fat and sucrose and can influence behavior and gut microbiota. There is growing evidence that altering the microbiome can influence the brain and behavior. This study was designed to determine whether diet-induced changes in the gut microbiota could contribute to alterations in anxiety, memory or cognitive flexibility. Two-month-old, male C57BL/6 mice were randomly assigned high-fat (42% fat, 43% carbohydrate (CHO), high-sucrose (12% fat, 70% CHO (primarily sucrose) or normal chow (13% kcal fat, 62% CHO) diets. Fecal microbiome analysis, step-down latency, novel object and novel location tasks were performed prior to and 2weeks after diet change. Water maze testing for long- and short-term memory and cognitive flexibility was conducted during weeks 5-6 post-diet change. Some similarities in alterations in the microbiome were seen in both the high-fat and high-sucrose diets (e.g., increased Clostridiales), as compared to the normal diet, but the percentage decreases in Bacteroidales were greater in the high-sucrose diet mice. Lactobacillales was only significantly increased in the high-sucrose diet group and Erysipelotrichales was only significantly affected by the high-fat diet. The high-sucrose diet group was significantly impaired in early development of a spatial bias for long-term memory, short-term memory and reversal training, compared to mice on normal diet. An increased focus on the former platform position was seen in both high-sucrose and high-fat groups during the reversal probe trials. There was no significant effect of diet on step-down, exploration or novel recognitions. Higher percentages of Clostridiales and lower expression of Bacteroidales in high-energy diets were related to the poorer cognitive flexibility in the reversal trials. These results suggest that changes in the microbiome may contribute to cognitive changes associated with eating a Western diet.
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Affiliation(s)
- K R Magnusson
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331 USA.
| | - L Hauck
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA.
| | - B M Jeffrey
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA.
| | - V Elias
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331 USA.
| | - A Humphrey
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA.
| | - R Nath
- Department of Human Development and Family Sciences, School of Social and Behavioral Health Sciences, Oregon State University, Corvallis, OR 97331 USA.
| | - A Perrone
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA; Linus Pauling Institute, Oregon State University, Corvallis, OR 97331 USA.
| | - L E Bermudez
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331 USA.
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Tomazetto G, Hahnke S, Maus I, Wibberg D, Pühler A, Schlüter A, Klocke M. Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation. J Biotechnol 2014; 192 Pt A:59-61. [PMID: 25242663 DOI: 10.1016/j.jbiotec.2014.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/01/2023]
Abstract
The bacterium Peptoniphilus sp. strain ING2-D1G (DSM 28672), a mesophilic and obligate anaerobic bacterium belonging to the order Clostridiales was isolated from a biogas-producing lab-scale completely stirred tank reactor (CSTR) optimized for anaerobic digestion of maize silage in co-fermentation with pig and cattle manure. In this study, the whole genome sequence of Peptoniphilus sp. strain ING2-D1G, a new isolate potentially involved in protein breakdown and acidogenesis during biomass degradation, is reported. The chromosome of this strain is 1.6Mb in size and encodes genes predicted to be involved in the production of acetate, lactate and butyrate specifying the acidogenic metabolism of the isolate.
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Affiliation(s)
- Geizecler Tomazetto
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
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29
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Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IAC, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, Chain P, Davenport KW, Rohde M, Spring S, Klenk HP, Stams AJM. Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 2014; 9:821-39. [PMID: 25197466 PMCID: PMC4148979 DOI: 10.4056/sigs.5209235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
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Affiliation(s)
- Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Michael Visser
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Claudia Loeffler
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Matthias Boll
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Petra Worm
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Diana Z Sousa
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Caroline M Plugge
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Peter J Schaap
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ines A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofiya N Parshina
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Moscow, Russia
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Janine Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands ; University of Minho, Centre of Biological Engineering, Braga, Portugal
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30
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Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IAC, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, Stams AJM. Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci 2014; 9:655-75. [PMID: 25197452 PMCID: PMC4149029 DOI: 10.4056/sigs.4718645] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sofiya N Parshina
- Wingradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | | | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Petra Worm
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | | | - Janine C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hans Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
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31
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Visser M, Worm P, Muyzer G, Pereira IAC, Schaap PJ, Plugge CM, Kuever J, Parshina SN, Nazina TN, Ivanova AE, Bernier-Latmani R, Goodwin LA, Kyrpides NC, Woyke T, Chain P, Davenport KW, Spring S, Klenk HP, Stams AJM. Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T). Stand Genomic Sci 2013; 8:69-87. [PMID: 23961313 PMCID: PMC3739171 DOI: 10.4056/sigs.3627141] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3,567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism.
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Affiliation(s)
- Michael Visser
- Wageningen University, Laboratory of Microbiology, Wageningen, the Netherlands
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32
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Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IAC, Parshina SN, Bernier-Latmani R, Stams AJM, Klenk HP. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)). Stand Genomic Sci 2012; 7:304-19. [PMID: 23408247 PMCID: PMC3569383 DOI: 10.4056/sigs.3226659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.
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Affiliation(s)
- Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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33
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Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci 2012; 6:1-13. [PMID: 23407703 PMCID: PMC3558970 DOI: 10.4056/sigs.2736042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
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34
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Han C, Mwirichia R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Stand Genomic Sci 2011; 4:371-80. [PMID: 21886864 PMCID: PMC3156405 DOI: 10.4056/sigs.2004684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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35
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Han C, Gu W, Zhang X, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Schneider S, Rohde M, Göker M, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Stand Genomic Sci 2010; 3:337-45. [PMID: 21304738 PMCID: PMC3035304 DOI: 10.4056/sigs.1373474] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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36
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Spring S, Lapidus A, Schröder M, Gleim D, Sims D, Meincke L, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci 2009; 1:242-53. [PMID: 21304664 PMCID: PMC3035247 DOI: 10.4056/sigs.39508] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575T, isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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37
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Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Han C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci 2009; 1:159-65. [PMID: 21304652 PMCID: PMC3035230 DOI: 10.4056/sigs.24194] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family 'Peptostreptococcaceae'. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family 'Peptostreptococcaceae' for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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