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Li T, Ding N, Guo H, Hua R, Lin Z, Tian H, Yu Y, Fan D, Yuan Z, Gonzalez FJ, Wu Y. A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage. Cell Host Microbe 2024; 32:191-208.e9. [PMID: 38237593 PMCID: PMC10922796 DOI: 10.1016/j.chom.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/18/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024]
Abstract
Aspirin-related gastrointestinal damage is of growing concern. Aspirin use modulates the gut microbiota and associated metabolites, such as bile acids (BAs), but how this impacts intestinal homeostasis remains unclear. Herein, using clinical cohorts and aspirin-treated mice, we identified an intestinal microbe, Parabacteroides goldsteinii, whose growth is suppressed by aspirin. Mice supplemented with P. goldsteinii or its BA metabolite, 7-keto-lithocholic acid (7-keto-LCA), showed reduced aspirin-mediated damage of the intestinal niche and gut barrier, effects that were lost with a P. goldsteinii hdhA mutant unable to generate 7-keto-LCA. Specifically, 7-keto-LCA promotes repair of the intestinal epithelium by suppressing signaling by the intestinal BA receptor, farnesoid X receptor (FXR). 7-Keto-LCA was confirmed to be an FXR antagonist that facilitates Wnt signaling and thus self-renewal of intestinal stem cells. These results reveal the impact of oral aspirin on the gut microbiota and intestinal BA metabolism that in turn modulates gastrointestinal homeostasis.
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Affiliation(s)
- Ting Li
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China
| | - Ning Ding
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China
| | - Hanqing Guo
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Rui Hua
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zehao Lin
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huohuan Tian
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yue Yu
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Daiming Fan
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China.
| | - Frank J Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Yue Wu
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China.
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Byun JH, Cho HW, Lee H, Lee WK, Yong D. Parabacteroides leei sp. nov., isolated from human blood. Int J Syst Evol Microbiol 2023; 73. [PMID: 37999940 DOI: 10.1099/ijsem.0.006187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
An obligate anaerobic, Gram-negative, rod-shaped and non-spore-forming bacterium, designated as strain GYB001T, was isolated from the blood of a patient with a sigmoid colon perforation. Taxonomic characterization of the novel isolate was performed using a polyphasic approach. A phylogenetic analysis based on 16S rRNA gene and whole genome sequences revealed that GYB001T represented a member of the genus Parabacteroides, in the family Tannerellaceae. The closest species, based on 16S rRNA sequence, was Parabacteroides gordonii DSM 23371T with 97.4 % similarity. Average nucleotide identity and digital DNA-DNA hybridization values between strain GYB001T and P. gordonii DSM 23371T were 86.7 and 28.7% and between GYB001T and Parabacteroides faecis JCM 18682T were 86.6 and 27.7 %, respectively. The genome was 6.57 Mbp long with 43.3 mol% G+C content. Colonies on Brucella blood agar (BBA) were circular, convex, smooth, grey and small in size. Growth was observed on trypticase soy agar (TSA), TSA +5 % sheep blood and Euglena gracilis agar. Growth occurred at 18-42 °C on BBA in the presence of 0-3 % NaCl (w/v) and at pH 6.0-8.5. The major polar lipids were phosphatidylethanolamine and phospholipids. The major fatty acids in strain GYB001T were anteiso-C15 : 0 and iso-C17 : 0 3-OH, and the predominant respiratory quinones were menaquinone-10 (MK-10) and MK-9. The cell wall contained meso-diaminopimelic acid. Considering these phenotypic features and comparative genome analyses, we propose strain GYB001T as the type strain of Parabacteroides leei sp. nov. (=KCTC 25738T=KBN12P06525T=LMG 32797T).
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Affiliation(s)
- Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Hae Weon Cho
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Myongji Hospital, Goyang, Republic of Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
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Magzal F, Turroni S, Fabbrini M, Barone M, Vitman Schorr A, Ofran A, Tamir S. A personalized diet intervention improves depression symptoms and changes microbiota and metabolite profiles among community-dwelling older adults. Front Nutr 2023; 10:1234549. [PMID: 37794974 PMCID: PMC10547149 DOI: 10.3389/fnut.2023.1234549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/21/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction The impact of diet on mental well-being and gut microorganisms in humans is well recognized. However, research on the connections between food nutrients, gut microbiota, and mental health remains limited. To address this, the present study aimed to assess the effects of a personalized diet, based on individual needs and aligned with the Mediterranean diet principles, on depression symptoms, quality of life, nutritional intake, and gut microbiota changes among older adults living in the community. Methods The intervention involved regular visits from a registered dietitian, who provided tailored dietary recommendations. During the 6-month study, participants completed questionnaires to evaluate their depression levels, quality of life, and dietary habits. Additionally, they provided stool samples for analysis of gut microbiota and metabolites. Results The results demonstrated that the personalized dietary intervention reduced depression symptoms and improved the quality of life among older adults. Furthermore, significant changes in the intake of certain nutrients, such as folate, lutein, zeaxanthin, EPA, and DHA, were observed following the intervention. Moreover, the intervention was associated with increased diversity in the gut microbiome and reduced total short-chain fatty acids, the main metabolites produced by gut microorganisms. The study also revealed correlations between food nutrients, gut microbiota, and mental health parameters. Discussion In conclusion, this research highlights the potential advantages of personalized dietary interventions in managing depression and enhancing overall well-being among older populations. It also sheds light on the role of gut microbiota and its metabolites in these effects. The findings offer valuable insights into the significance of nutrition and gut health for mental well-being in older adults.
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Affiliation(s)
- Faiga Magzal
- Laboratory of Human Health and Nutrition Sciences, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
- Department of Nutrition, Tel Hai College, Upper Galilee, Israel
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | | | - Snait Tamir
- Laboratory of Human Health and Nutrition Sciences, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
- Department of Nutrition, Tel Hai College, Upper Galilee, Israel
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Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiol Lett 2022; 369:6659190. [PMID: 35945336 DOI: 10.1093/femsle/fnac072] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The stability of gut microbiota is essential for the host health. Parabacteroides spp., core members of the human gut microbiota, have average abundance of 1.27% in the human of 12 populations. Parabacteroides has been recently reported to have a close relationship with host health (E.g., metabolic syndrome, inflammatory bowel disease and obesity). Parabacteroides have the physiological characteristics of carbohydrate metabolism and secreting SCFAs. However, antimicrobial resistance of Parabacteroides to antibiotic (such as clindamycin, moxifloxacin and cefoxitin) should not be ignored. In this review, we primarily focused on Parabacteroides distasoniss, Parabacteroides goldsteinii, Parabacteroides johnsonii and Parabacteroides merdae and discussed their relationships with host disease, diet and the prevention or induction of diseases. P. distasonis and P. goldsteinii may be viewed as the potential next generation probiotics (NGP) candidate due to their protective effects on inflammation and obesity in mice. We also discussed the potential therapeutic application of Parabacteroides spp. in maintaining host-intestine homeostasis.
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Affiliation(s)
- Yanlong Cui
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Leshan Zhang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
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El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crépin A. Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics. Front Microbiol 2022; 13:828359. [PMID: 35495704 PMCID: PMC9042397 DOI: 10.3389/fmicb.2022.828359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
Altering the gut microbiota can negatively affect human health. Efforts may be sustained to predict the intended or unintended effects of molecules not naturally produced or expected to be present within the organism on the gut microbiota. Here, culture-dependent and DNA-based approaches were combined to UHPLC-MS/MS analyses in order to investigate the reciprocal interactions between a constructed Human Gut Microbiota Model (HGMM) and molecules including antibiotics, drugs, and xenobiotics. Our HGMM was composed of strains from the five phyla commonly described in human gut microbiota and belonging to Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria. Relevantly, the bacterial diversity was conserved in our constructed human gut model through subcultures. Uneven richness distribution was revealed and the sensitivity of the HGMM was mainly affected by antibiotic exposure rather than by drugs or xenobiotics. Interestingly, the constructed model and the individual cultured strains respond with the same sensitivity to the different molecules. UHPLC-MS/MS analyses revealed the disappearance of some native molecules in the supernatants of the HGMM as well as in those of the individual strains. These results suggest that biotransformation of molecules occurred in the presence of our gut microbiota model and the coupled approaches performed on the individual cultures may emphasize new bacterial strains active in these metabolic processes. From this study, the new HGMM appears as a simple, fast, stable, and inexpensive model for screening the reciprocal interactions between the intestinal microbiota and molecules of interest.
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Affiliation(s)
- Abdelaziz El Houari
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Florine Ecale
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Anne Mercier
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Stéphanie Crapart
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | | | | | | | - Jean-Marc Berjeaud
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Marie-Hélène Rodier
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France.,Laboratoire de Parasitologie et Mycologie, CHU de Poitiers, Poitiers, France
| | - Alexandre Crépin
- UMR CNRS 7267, Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
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6
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Fan G, Song W, Guan Z, Zhang W, Lu X. Some novel features of strong promoters discovered in Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2022; 106:2529-2540. [PMID: 35318522 DOI: 10.1007/s00253-022-11869-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Cytophaga hutchinsonii is an important Gram-negative bacterium belonging to the Bacteroides phylum that can efficiently degrade cellulose. But the promoter that mediates the initiation of gene transcription has been unknown for a long time. In this study, we determined the transcription start site (TSS) of C. hutchinsonii by 5' rapid amplification of cDNA ends (5'RACE). The promoter structure was first identified as TAAT and TATTG which are located -5 and -31 bp upstream of TSS, respectively. The function of -5 and -31 regions and the spacer length of the promoter Pchu_1284 were explored by site directed ligase-independent mutagenesis (SLIM). The results showed that the promoter activities were sharply decreased when the TTG motif was mutated into guanine (G) or cytosine (C). Interestingly, we found that the strong promoter was accompanied with many TTTG motifs which could enhance the promoter activities within certain copies. These characteristics were different from other promoters of Bacteriodes species. Furthermore, we carried out genome scanning analysis for C. hutchinsonii and another Bacteroides species by Perl6.0. The results indicated that the promoter structure of C. hutchinsonii possessed more unique features than other species. Also, the screened inducible promoter Pchu_2268 was used to overexpress protein CHU_2196 with a molecular weight of 120 kDa in C. hutchinsonii. The present study enriched the promoter structure of Bacteroidetes species and also provided a novel method for the highly expressed large protein (cellulase) in vivo, which was helpful to elucidate the unique cellulose degradation mechanism of C. hutchinsonii.Key points• The conserved structure of strong promoter of C. hutchinsonii was elucidated.• Two novel regulation motifs of TTTG and AATTATG in the promoter were discovered.• A new method for induced expression of cellulase in vivo was established.• Helpful for explained the unique cellulose degradation mechanism of C. hutchinsonii.
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Affiliation(s)
- Guoqing Fan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Wenxia Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.
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7
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Ezeji JC, Sarikonda DK, Hopperton A, Erkkila HL, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE, Jacobs MR, Khoretonenko M, Veloo A, Rodriguez-Palacios A. Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes 2022; 13:1922241. [PMID: 34196581 PMCID: PMC8253142 DOI: 10.1080/19490976.2021.1922241] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.
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Affiliation(s)
- Jessica C. Ezeji
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daven K. Sarikonda
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Austin Hopperton
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Hailey L. Erkkila
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel E. Cohen
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Fabio Cominelli
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
| | - Armand E. K. Dichosa
- B-10 Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Caryn E. Good
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael R. Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | | | - Alida Veloo
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Rodriguez-Palacios
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,CONTACT Alexander Rodriguez-Palacios Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Cobo F, Pérez-Carrasco V, Gómez-Vicente E, Martín-Hita L, García-Salcedo JA, Navarro-Marí JM. Parabacteroides goldsteinii abdominal infection in a patient with lymphoma. Infect Dis Now 2021; 52:117-119. [PMID: 33965678 DOI: 10.1016/j.idnow.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs, GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Esther Gómez-Vicente
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs, GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - Lina Martín-Hita
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs, GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José A García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs, GRANADA, University Hospital Virgen de las Nieves, Granada, Spain; GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs, GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay. mSphere 2021; 6:6/2/e01325-20. [PMID: 33827913 PMCID: PMC8546724 DOI: 10.1128/msphere.01325-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Current sequencing-based methods for profiling microbial communities rely on marker gene (e.g., 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. We present an approach based on a single-primer extension reaction using a highly multiplexed oligonucleotide probe pool. This approach, termed MA-GenTA (microbial abundances from genome tagged analysis), enables quantitative, straightforward, cost-effective microbiome profiling that combines desirable features of both 16S rRNA and mWGS strategies. The use of multiple probes per target genome and rigorous probe design criteria enabled robust determination of relative abundance. To test the utility of the MA-GenTA assay, probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, nonmetric multidimensional scaling (NMDS) clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS, and 16S rRNA data sets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes. IMPORTANCE New methods for profiling the microbial communities can create new approaches to understanding the composition and function of those communities. In this study, we combined bacterial genome-specific probe design with a highly multiplexed single primer extension reaction as a new method to profile microbial communities, using stool from various mouse strains as a test case. This method, termed MA-GenTA, was benchmarked against 16S rRNA gene sequencing and metagenome sequencing methods and delivered similar relative abundance and clustering data. Since the probes were generated from reference genomes, MA-GenTA was also able to provide functional pathway data for the stool microbiome in the assayed samples. The method is more informative than 16S rRNA analysis while being less costly than metagenome shotgun sequencing.
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10
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Andrade JC, Almeida D, Domingos M, Seabra CL, Machado D, Freitas AC, Gomes AM. Commensal Obligate Anaerobic Bacteria and Health: Production, Storage, and Delivery Strategies. Front Bioeng Biotechnol 2020; 8:550. [PMID: 32582673 PMCID: PMC7291883 DOI: 10.3389/fbioe.2020.00550] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
In the last years several human commensals have emerged from the gut microbiota studies as potential probiotics or therapeutic agents. Strains of human gut inhabitants such as Akkermansia, Bacteroides, or Faecalibacterium have shown several interesting bioactivities and are thus currently being considered as food supplements or as live biotherapeutics, as is already the case with other human commensals such as bifidobacteria. The large-scale use of these bacteria will pose many challenges and drawbacks mainly because they are quite sensitive to oxygen and/or very difficult to cultivate. This review highlights the properties of some of the most promising human commensals bacteria and summarizes the most up-to-date knowledge on their potential health effects. A comprehensive outlook on the potential strategies currently employed and/or available to produce, stabilize, and deliver these microorganisms is also presented.
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Affiliation(s)
- José Carlos Andrade
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, Portugal
| | - Diana Almeida
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Melany Domingos
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Catarina Leal Seabra
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Daniela Machado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Cristina Freitas
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Maria Gomes
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
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You JS, Yong JH, Kim GH, Moon S, Nam KT, Ryu JH, Yoon MY, Yoon SS. Commensal-derived metabolites govern Vibrio cholerae pathogenesis in host intestine. MICROBIOME 2019; 7:132. [PMID: 31521198 PMCID: PMC6744661 DOI: 10.1186/s40168-019-0746-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/03/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Recent evidence suggests that the commensal microbes act as a barrier against invading pathogens and enteric infections are the consequences of multi-layered interactions among commensals, pathogens, and the host intestinal tissue. However, it remains unclear how perturbations of the gut microbiota compromise host infection resistance, especially through changes at species and metabolite levels. RESULTS Here, we illustrate how Bacteroides vulgatus, a dominant species of the Bacteroidetes phylum in mouse intestine, suppresses infection by Vibrio cholerae, an important human pathogen. Clindamycin (CL) is an antibiotic that selectively kills anaerobic bacteria, and accordingly Bacteroidetes are completely eradicated from CL-treated mouse intestines. The Bacteroidetes-depleted adult mice developed severe cholera-like symptoms, when infected with V. cholerae. Germ-free mice mono-associated with B. vulgatus became resistant to V. cholerae infection. Levels of V. cholerae growth-inhibitory metabolites including short-chain fatty acids plummeted upon CL treatment, while levels of compounds that enhance V. cholerae proliferation were elevated. Furthermore, the intestinal colonization process of V. cholerae was well-simulated in CL-treated adult mice. CONCLUSIONS Overall, we provide insights into how a symbiotic microbe and a pathogenic intruder interact inside host intestine. We identified B. vulgatus as an indigenous microbial species that can suppress intestinal infection. Our results also demonstrate that commensal-derived metabolites are a critical determinant for host resistance against V. cholerae infection, and that CL pretreatment of adult mice generates a simple yet useful model of cholera infection.
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Affiliation(s)
- Jin Sun You
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu Seoul, Seoul, 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Ji Hyun Yong
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu Seoul, Seoul, 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Gwang Hee Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu Seoul, Seoul, 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Sungmin Moon
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Ki Taek Nam
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Ji Hwan Ryu
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Mi Young Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu Seoul, Seoul, 03722, Korea.
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Korea.
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu Seoul, Seoul, 03722, Korea.
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, 03722, Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Korea.
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12
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Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You X. Parabacteroides acidifaciens sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:761-766. [DOI: 10.1099/ijsem.0.003230] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Yu-Jing Wang
- 1State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- 2University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xin-Jie Xu
- 3Central Research Laboratory, Department of Scientific Research, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Nan Zhou
- 1State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yutong Sun
- 1State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chang Liu
- 1State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- 1State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- 2University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xin You
- 4Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing 100730, PR China
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13
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Kim H, Im WT, Kim M, Kim D, Seo YH, Yong D, Jeong SH, Lee K. Parabacteroides chongii sp. nov., isolated from blood of a patient with peritonitis. J Microbiol 2018; 56:722-726. [PMID: 30267315 DOI: 10.1007/s12275-018-8122-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 11/28/2022]
Abstract
An obligate anaerobic, Gram-reaction-negative, non-sporeforming, non-motile, rod shaped bacterium designated YMC B3181T was isolated from the blood of a patient with peritonitis. Strain B3181T grew at 20 to 40°C with optimum growth at 37°C. 16S rRNA gene sequence similarity showed strain B3181T belongs to the genus Parabacteroides and is closely related to Parabacteroides faecis 157T (97.3%), Parabacteroides gordonii MS-1T (96.6%), and Parabacteroides goldsteinii DSM 19448T (95.7%). The G + C content of the genomic DNA was 42.3 mol%. The major cellular fatty acids were anteiso-C15:0 and iso-C17:0 3-OH, and the predominant respiratory quinones were MK-9 and MK-10 menaquinones. Genomic and chemotaxonomic data supported affiliation of B3181T with the genus Parabacteroides. Strain B3181T was phylogenetically and phenotypically different from recognized species of the genus Parabacteroides. Accordingly, this isolate belongs to a novel species for which the name Parabacteroides chongii sp. nov. (type strain YMC B3181T = LMG 30065T = KACC 19034T) is proposed.
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Affiliation(s)
- Hyunsoo Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Laboratory Medicine, National police hospital, Seoul, 05715, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology and Genomic Informatics Center, Hankyong National University, Anseong, 17579, Republic of Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Young Hee Seo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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14
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Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA. Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota. Cell Syst 2018; 7:245-257.e7. [PMID: 30195437 PMCID: PMC6166237 DOI: 10.1016/j.cels.2018.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/15/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
Abstract
The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.
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Affiliation(s)
- Gregory L Medlock
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Dennis G McDuffie
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Michael B Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Natasa Giallourou
- Department of Surgery and Cancer, Division of Integrative Systems Medicine and Digestive Diseases, Faculty of Medicine, Imperial College London, South Kensington, London, UK
| | - Jonathan R Swann
- Department of Surgery and Cancer, Division of Integrative Systems Medicine and Digestive Diseases, Faculty of Medicine, Imperial College London, South Kensington, London, UK
| | - Glynis L Kolling
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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15
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Jiang L, Lv J, Liu J, Hao X, Ren F, Guo H. Donkey milk lysozyme ameliorates dextran sulfate sodium-induced colitis by improving intestinal barrier function and gut microbiota composition. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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16
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Yin D, Yin X, Wang X, Lei Z, Wang M, Guo Y, Aggrey SE, Nie W, Yuan J. Supplementation of amylase combined with glucoamylase or protease changes intestinal microbiota diversity and benefits for broilers fed a diet of newly harvested corn. J Anim Sci Biotechnol 2018; 9:24. [PMID: 29545946 PMCID: PMC5846306 DOI: 10.1186/s40104-018-0238-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/22/2018] [Indexed: 01/05/2023] Open
Abstract
Background The effect of amylases combined with exogenous carbohydrase and protease in a newly harvested corn diet on starch digestibility, intestine health and cecal microbiota was investigated in broiler chickens. Methods Two hunderd and eighty-eight 5-day-old female chickens were randomly divided into six treatments: a newly harvested corn-soybean meal diet (control); control supplemented with 1,500 U/g α-amylase (Enzyme A); Enzyme A + 300 U/g amylopectase + 20,000 U/g glucoamylase (Enzyme B); Enzyme B + protease 10,000 U/g (Enzyme C); Enzyme C + xylanase 15,000 U/g (Enzyme D); and Enzyme D + cellulase 200 U/g + pectinase 1,000 U/g (Enzyme E). Growth performance, starch digestibility, digestive organ morphology, and intestinal microbiota were evaluated in the birds at 16 and 23 d of age. Results Compared with the control diet, supplementation with Enzyme A significantly decreased ileum lesion scoring at 16 d of age (P < 0.05); supplementation with Enzyme B or Enzyme C showed positive effects on ileal amylopectin and total starch digestibility (P < 0.05); Broilers fed with a diet supplemented with Enzyme D had a tendency to decrease body weight gain at 23 d. Enzyme E supplementation improved lesion scoring of jejunum and ileum at 16 d (P < 0.05), and increased ileal amylopectin or total starch digestibility at 23 d (P < 0.05). Supplementation of enzymes changed cecal microbiota diversity. High numbers of Campylobacter, Helicobacter and Butyricicoccus, Anaerostipes and Bifidobacterium, Sutterella and Odoribacter were the main genera detected in supplementations with Enzymes B, C, D, and E respectively. Conclusions Supplementation with amylase combined with glucoamylase or protease showed a beneficial effect on starch digestibility and intestinal microbiota diversity, and increased growth of broilers fed with newly harvested corn.
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Affiliation(s)
- Dafei Yin
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaonan Yin
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingyu Wang
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhao Lei
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Maofei Wang
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuming Guo
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Samuel E Aggrey
- 2NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA USA
| | - Wei Nie
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianmin Yuan
- 1State key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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17
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Oberli M, Douard V, Beaumont M, Jaoui D, Devime F, Laurent S, Chaumontet C, Mat D, Le Feunteun S, Michon C, Davila AM, Fromentin G, Tomé D, Souchon I, Leclerc M, Gaudichon C, Blachier F. Lipo-Protein Emulsion Structure in the Diet Affects Protein Digestion Kinetics, Intestinal Mucosa Parameters and Microbiota Composition. Mol Nutr Food Res 2018; 62. [DOI: 10.1002/mnfr.201700570] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/04/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Marion Oberli
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - Véronique Douard
- Micalis Institute; AgroParisTech; INRA; Université Paris-Saclay; Jouy-en-Josas France
| | - Martin Beaumont
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - Daphné Jaoui
- Micalis Institute; AgroParisTech; INRA; Université Paris-Saclay; Jouy-en-Josas France
| | - Fabienne Devime
- Micalis Institute; AgroParisTech; INRA; Université Paris-Saclay; Jouy-en-Josas France
| | - Sandy Laurent
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | | | - Damien Mat
- UMR GMPA, AgroParisTech, INRA; Université Paris-Saclay; Thiverval-Grignon France
| | - Steven Le Feunteun
- UMR GMPA, AgroParisTech, INRA; Université Paris-Saclay; Thiverval-Grignon France
| | - Camille Michon
- UMR GENIAL, AgroParisTech, INRA; Université Paris-Saclay; Massy France
| | - Anne-Marie Davila
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - Gilles Fromentin
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - Daniel Tomé
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - Isabelle Souchon
- UMR GMPA, AgroParisTech, INRA; Université Paris-Saclay; Thiverval-Grignon France
| | - Marion Leclerc
- Micalis Institute; AgroParisTech; INRA; Université Paris-Saclay; Jouy-en-Josas France
| | - Claire Gaudichon
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
| | - François Blachier
- UMR PNCA, INRA; AgroParisTech; Université Paris-Saclay; Paris France
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18
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Daniluk J, Daniluk U, Rusak M, Dabrowska M, Reszec J, Garbowicz M, Huminska K, Dabrowski A. The effect of penicillin administration in early life on murine gut microbiota and blood lymphocyte subsets. Anaerobe 2017; 47:18-24. [PMID: 28323133 DOI: 10.1016/j.anaerobe.2017.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/04/2017] [Accepted: 03/15/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIM Antibiotics have many beneficial effects but their uncontrolled use may lead to increased risk of serious diseases in the future. Our hypothesis is that an early antibiotic exposition may affect immune system by altering gut microbiota. Therefore, the aim of the study was to determine the effect of penicillin treatment on gut microorganisms and immune system of mice. METHODS 21-days old C57BL6/J/cmdb male mice were treated with low-dose of penicillin (study group) or water only (control group) for 4 weeks. Tissue and stool samples for histology or microbiome assessment and peripheral blood for CBC and flow cytometry evaluation were collected. RESULTS We found high variability in microbiota composition at different taxonomic levels between littermate mice kept in the same conditions, independently of treatment regimen. Interestingly, low-dose of penicillin caused significant increase of Parabacteroides goldsteinii in stool and in colon tissue in comparison to control group (9.5% vs. 4.9%, p = 0.008 and 10.7% vs. 6.1%, p = 0.008, respectively). Moreover, mice treated with penicillin demonstrated significantly elevated percentage of B cells (median 10.5% vs 8.0%, p = 0.01) and decrease in the percentage of total CD4+ cell (median 75.4% vs 82.5%, p = 0.0039) with subsequent changes among subsets - increased percentage of regulatory T cells (Treg), T helper 1 (Th1) and T helper 2 (Th2) cells. CONCLUSION Our study showed significant effect of penicillin on B and T cells in peripheral blood of young mice. This effect may be mediated through changes in gut microbiota represented by the expansion of Parabacteroides goldsteinii.
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Affiliation(s)
- Jaroslaw Daniluk
- Department of Gastroenterology and Internal Medicine, Medical University of Bialystok ul, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
| | - Urszula Daniluk
- Department of Pediatrics, Gastroenterology and Allergology, Medical University of Bialystok ul, J. Waszyngtona 17, 15-274 Bialystok, Poland
| | - Malgorzata Rusak
- Department of Haematological Diagnostics, Medical University of Bialystok ul, J. Waszyngtona 15A, 15-269 Bialystok, Poland
| | - Milena Dabrowska
- Department of Haematological Diagnostics, Medical University of Bialystok ul, J. Waszyngtona 15A, 15-269 Bialystok, Poland
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok ul, J. Waszyngtona 13, 15-269 Bialystok, Poland
| | - Magdalena Garbowicz
- Genomic Laboratory, DNA Research Center ul, Mickiewicza 31, 60-385 Poznan, Poland
| | - Kinga Huminska
- Genomic Laboratory, DNA Research Center ul, Mickiewicza 31, 60-385 Poznan, Poland
| | - Andrzej Dabrowski
- Department of Gastroenterology and Internal Medicine, Medical University of Bialystok ul, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
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Hwang OH, Cho SB, Han DW, Lee SR, Kwag JH, Park SK. Effect of Storage Period on the Changes of Odorous Compound Concentrations and Bacterial Ecology for Identifying the Cause of Odor Production from Pig Slurry. PLoS One 2016; 11:e0162714. [PMID: 27642752 PMCID: PMC5028028 DOI: 10.1371/journal.pone.0162714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/26/2016] [Indexed: 11/19/2022] Open
Abstract
Odor from buildings where pigs are housed is generated by anaerobic fermentation of undigested materials in pig slurry stored for several weeks in pit. The objective of this study was to investigate the effect of storage period on the level of odorous compounds in pig slurry and on its bacterial community. A slurry sample (15 L) was taken from the pit of a finisher pig building and incubated in acryl chambers for six- weeks. Slurry for analysis was sampled every two-week. Levels of odorous compounds in the slurry sample were drastically changed after two weeks of storage period; levels of phenols and short chain fatty acids (SCFAs) were decreased (P<0.05), whereas indoles and branched-chain fatty acids (BCFAs) were increased (P<0.05). Among dominant bacteria, Bacteroides and Porphyromonadacese_uc_g revealed a strong positive correlation with the levels of phenols and SCFAs. Populations of AC160630_g, Acholeplasmatales_uc_g, Mollicutes_uc_g and Cloacamonas_f_uc_g positively correlated with indole and BCFAs content. Taken together, levels of odorous compounds were increased after two weeks of storage, possibly because of changes in the predominant bacterial groups to those that use protein as a carbon source in the hypo-carbohydrate conditions.
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Affiliation(s)
- Ok Hwa Hwang
- National Institute of Animal Science, Rural Development Administration, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Sung Back Cho
- National Institute of Animal Science, Rural Development Administration, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Deug Woo Han
- National Institute of Animal Science, Rural Development Administration, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Sang Ryoung Lee
- National Institute of Animal Science, Rural Development Administration, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Jeong Hoon Kwag
- National Institute of Animal Science, Rural Development Administration, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Sung Kwon Park
- Department of Food Science and Technology, Sejong University, Seoul, Republic of Korea
- * E-mail:
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Jabari L, Gannoun H, Khelifi E, Cayol JL, Godon JJ, Hamdi M, Fardeau ML. Bacterial ecology of abattoir wastewater treated by an anaerobic digestor. Braz J Microbiol 2016; 47:73-84. [PMID: 26887229 PMCID: PMC4822766 DOI: 10.1016/j.bjm.2015.11.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 07/06/2015] [Indexed: 01/15/2023] Open
Abstract
Wastewater from an anaerobic treatment plant at a slaughterhouse was analysed to determine the bacterial biodiversity present. Molecular analysis of the anaerobic sludge obtained from the treatment plant showed significant diversity, as 27 different phyla were identified. Firmicutes, Proteobacteria, Bacteroidetes, Thermotogae, Euryarchaeota (methanogens), and msbl6 (candidate division) were the dominant phyla of the anaerobic treatment plant and represented 21.7%, 18.5%, 11.5%, 9.4%, 8.9%, and 8.8% of the total bacteria identified, respectively. The dominant bacteria isolated were Clostridium, Bacteroides, Desulfobulbus, Desulfomicrobium, Desulfovibrio and Desulfotomaculum. Our results revealed the presence of new species, genera and families of microorganisms. The most interesting strains were characterised. Three new bacteria involved in anaerobic digestion of abattoir wastewater were published.
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Affiliation(s)
- Linda Jabari
- Université de Carthage, Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie (INSAT), 2 Boulevard de la terre, B.P. 676, 1080 Tunis, Tunisia; Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MOI, UM 110, 13288 Marseille cedex 9, France
| | - Hana Gannoun
- Université de Carthage, Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie (INSAT), 2 Boulevard de la terre, B.P. 676, 1080 Tunis, Tunisia; Université Tunis El Manar, Institut Supérieur des Sciences Biologiques Appliquées de Tunis (ISSBAT) 9, avenue Zouhaïer Essafi, 1006 Tunis, Tunisia
| | - Eltaief Khelifi
- Université de Carthage, Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie (INSAT), 2 Boulevard de la terre, B.P. 676, 1080 Tunis, Tunisia
| | - Jean-Luc Cayol
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MOI, UM 110, 13288 Marseille cedex 9, France
| | - Jean-Jacques Godon
- INRA U050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Étangs, F-11100 Narbonne, France
| | - Moktar Hamdi
- Université de Carthage, Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie (INSAT), 2 Boulevard de la terre, B.P. 676, 1080 Tunis, Tunisia
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MOI, UM 110, 13288 Marseille cedex 9, France.
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Bindels LB, Neyrinck AM, Claus SP, Le Roy CI, Grangette C, Pot B, Martinez I, Walter J, Cani PD, Delzenne NM. Synbiotic approach restores intestinal homeostasis and prolongs survival in leukaemic mice with cachexia. ISME JOURNAL 2015; 10:1456-70. [PMID: 26613342 PMCID: PMC5029183 DOI: 10.1038/ismej.2015.209] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/20/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023]
Abstract
Cancer cachexia is a multifactorial syndrome that includes muscle wasting and inflammation. As gut microbes influence host immunity and metabolism, we investigated the role of the gut microbiota in the therapeutic management of cancer and associated cachexia. A community-wide analysis of the caecal microbiome in two mouse models of cancer cachexia (acute leukaemia or subcutaneous transplantation of colon cancer cells) identified common microbial signatures, including decreased Lactobacillus spp. and increased Enterobacteriaceae and Parabacteroides goldsteinii/ASF 519. Building on this information, we administered a synbiotic containing inulin-type fructans and live Lactobacillus reuteri 100-23 to leukaemic mice. This treatment restored the Lactobacillus population and reduced the Enterobacteriaceae levels. It also reduced hepatic cancer cell proliferation, muscle wasting and morbidity, and prolonged survival. Administration of the synbiotic was associated with restoration of the expression of antimicrobial proteins controlling intestinal barrier function and gut immunity markers, but did not impact the portal metabolomics imprinting of energy demand. In summary, this study provided evidence that the development of cancer outside the gut can impact intestinal homeostasis and the gut microbial ecosystem and that a synbiotic intervention, by targeting some alterations of the gut microbiota, confers benefits to the host, prolonging survival and reducing cancer proliferation and cachexia.
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Affiliation(s)
- Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sandrine P Claus
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Caroline I Le Roy
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Corinne Grangette
- Lactic Acid Bacteria and Mucosal Immunity, Centre for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Bruno Pot
- Lactic Acid Bacteria and Mucosal Immunity, Centre for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Inés Martinez
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium.,Walloon Excellence in Life sciences and BIOtechnology (WELBIO), Louvain Drug Research Institute, UCL, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
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22
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Draft Genome Sequence of Parabacteroides goldsteinii with Putative Novel Metallo-β-Lactamases Isolated from a Blood Culture from a Human Patient. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00937-15. [PMID: 26294633 PMCID: PMC4543511 DOI: 10.1128/genomea.00937-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Parabacteroides goldsteinii was isolated from a blood culture. Genomic DNA was sequenced using a MiSeq sequencer and assembled using the SPAdes genome assembler. The draft genome sequence was 6,851,868 bp, spanning 282 contigs of 5,253 coding sequences, 66 tRNAs, and 5 rRNAs. Several putative novel metallo-β-lactamases were discovered.
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23
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Qiu YL, Kuang XZ, Shi XS, Yuan XZ, Guo RB. Paludibacter jiangxiensis sp. nov., a strictly anaerobic, propionate-producing bacterium isolated from rice paddy field. Arch Microbiol 2014; 196:149-55. [DOI: 10.1007/s00203-013-0951-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/20/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
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24
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Jabari L, Gannoun H, Cayol JL, Hedi A, Sakamoto M, Falsen E, Ohkuma M, Hamdi M, Fauque G, Ollivier B, Fardeau ML. Macellibacteroides fermentans gen. nov., sp. nov., a member of the family
Porphyromonadaceae
isolated from an upflow anaerobic filter treating abattoir wastewaters. Int J Syst Evol Microbiol 2012; 62:2522-2527. [DOI: 10.1099/ijs.0.032508-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 °C (optimum 35–40 °C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain LIND7HT used cellobiose, glucose, lactose, mannose, maltose, peptone, rhamnose, raffinose, sucrose and xylose as electron donors. The main fermentation products from glucose metabolism were lactate, acetate, butyrate and isobutyrate. The predominant cellular fatty acids were anteiso-C15 : 0, C15 : 0, C17 : 0 2-OH and a summed feature consisting of C18 : 2ω6,9c and/or anteiso-C18 : 0, and the major menaquinones were MK-9, MK-9(H2) and MK-10. The G+C content of the genomic DNA was 41.4 mol%. Although the closest phylogenetic relatives of strain LIND7HT were
Parabacteroides merdae
,
Parabacteroides goldsteinii
and
Parabacteroides gordonii
, analysis of the hsp60 gene sequence showed that strain LIND7HT was not a member of the genus
Parabacteroides
. On the basis of phylogenetic inference and phenotypic properties, strain LIND7HT ( = CCUG 60892T = DSM 23697T = JCM 16313T) is proposed as the type strain of a novel species in a new genus within the family
Porphyromonadaceae
, Macellibacteroides fermentans gen. nov., sp. nov.
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Affiliation(s)
- Linda Jabari
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Hana Gannoun
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia
| | - Jean-Luc Cayol
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Abdeljabbar Hedi
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Enevold Falsen
- CCUG, Culture Collection, Department of Clinical Bacteriology, University of Göteborg, 41346 Göteborg, Sweden
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moktar Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia
| | - Guy Fauque
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Bernard Ollivier
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Marie-Laure Fardeau
- Aix-Marseille Universit� du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
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25
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Rapid identification of microorganisms isolated from throat swab specimens of community-acquired pneumonia patients by two MALDI-TOF MS systems. Diagn Microbiol Infect Dis 2012; 73:301-7. [DOI: 10.1016/j.diagmicrobio.2012.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/05/2012] [Accepted: 04/16/2012] [Indexed: 11/18/2022]
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26
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Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M, Zhu XF. Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill. Int J Syst Evol Microbiol 2011; 62:2613-2617. [PMID: 22199215 DOI: 10.1099/ijs.0.038000-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated NS31-3(T), was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7-1.0 × 1.4-2.5 µm). The isolate was able to grow on media containing 20% bile salts. API 20A tests showed that acid was produced from glucose, lactose, sucrose, maltose, D-xylose, L-arabinose, cellobiose, D-mannose, D-melezitose, D-raffinose, D-trehalose, D-mannitol, salicin and D-sorbitol. The main fermentation products from PYG broth were lactic acid, propionic acid, formic acid and acetic acid. Chemotaxonomic analysis showed that the major fatty acids were anteiso-C(15:0), C(15:0) and iso-C(17:0) 3-OH and the predominant respiratory quinones were MK-9 and MK-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS31-3(T) was related to members of genus Parabacteroides (91.2-93.2% sequence similarity); the isolate had the closest affinity with Parabacteroides merdae JCM 9497(T). The G+C content of the genomic DNA was 37.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain NS31-3(T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides chartae sp. nov. is proposed. The type strain is NS31-3(T) (=JCM 17797(T) =DSM 24967(T)).
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Affiliation(s)
- Hai-Qin Tan
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
| | - Tian-Tian Li
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
| | - Chu Zhu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
| | - Xin-Qi Zhang
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province 310058, PR China
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27
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Garcia SL, Jangid K, Whitman WB, Das KC. Transition of microbial communities during the adaption to anaerobic digestion of carrot waste. BIORESOURCE TECHNOLOGY 2011; 102:7249-7256. [PMID: 21620691 DOI: 10.1016/j.biortech.2011.04.098] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/28/2011] [Accepted: 04/29/2011] [Indexed: 05/30/2023]
Abstract
In this study a microbial community suitable for anaerobic digestion of carrot pomace was developed from inocula obtained from natural environmental sources. The changes along the process were monitored using pyrosequencing of the 16S rRNA gene. As the community adapted from a diverse natural community to a community with a definite function, diversity decreased drastically. Major bacterial groups remaining after enrichment were Bacilli (31-45.3%), Porphyromonadaceae (12.1-24.8%) and Spirochaetes (12.5-18.5%). The archaeal population was even less diverse and mainly represented by a single OTU that was 99.7% similar to Methanosarcina mazei. One enrichment which failed to produce large amounts of methane had shifts in the bacterial populations and loss of methanogenic archaea.
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Affiliation(s)
- Sarahi L Garcia
- University of Georgia, Biorefining and Carbon Cycling Program, Department of Biological and Agricultural Engineering, Athens, GA 30602-4435, USA
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28
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Zhang J, Wei Y, Xiao W, Zhou Z, Yan X. Performance and spatial community succession of an anaerobic baffled reactor treating acetone-butanol-ethanol fermentation wastewater. BIORESOURCE TECHNOLOGY 2011; 102:7407-7414. [PMID: 21664129 DOI: 10.1016/j.biortech.2011.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 05/10/2011] [Accepted: 05/10/2011] [Indexed: 05/30/2023]
Abstract
An anaerobic baffled reactor with four compartments (C1-C4) was successfully used for treatment of acetone-butanol-ethanol fermentation wastewater and methane production. The chemical oxygen demand (COD) removal efficiency was 88.2% with a CH(4) yield of 0.25L/(g COD(removed)) when organic loading rate (OLR) was 5.4kg CODm(-3)d(-1). C1 played the most important role in solvents (acetone, butanol and ethanol) and COD removal. Community structure of C2 was similar to that in C1 at stage 3 with higher OLR, but was similar to those in C3 and C4 at stages 1-2 with lower OLR. This community variation in C2 was consistent with its increased role in COD and solvent removal at stage 3. During community succession from C1 to C4 at stage 3, abundance of Firmicutes (especially OTUs ABRB07 and ABRB10) and Methanoculleus decreased, while Bacteroidetes and Methanocorpusculum became dominant. Thus, ABRB07 coupled with Methanoculleus and/or acetogen (ABRB10) may be key species for solvents degradation.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd., Shanghai 200032, China
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29
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Nagy E, Becker S, Sóki J, Urbán E, Kostrzewa M. Differentiation of division I (cfiA-negative) and division II (cfiA-positive) Bacteroides fragilis strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Med Microbiol 2011; 60:1584-1590. [PMID: 21680764 DOI: 10.1099/jmm.0.031336-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used in clinical microbiological laboratories to identify bacteria and fungi at a species level and to subtype them. The cfiA gene encoding the unique carbapenemases found in Bacteroides is restricted to division II Bacteroides fragilis strains. The aim of this study was to evaluate whether MALDI-TOF MS is suitable for differentiating B. fragilis strains which harbour the cfiA gene from those that do not. A well-defined collection of 40 B. fragilis isolates with known imipenem MICs (0.062->32 mg l(-1)) were selected for this study. Twelve B. fragilis strains with known cfiA status, including NCTC 9343 (division I) and TAL3636 (division II), were measured by means of microflex LT MALDI-TOF MS and well-defined differences in mass spectra between the cfiA-positive and cfiA-negative strains were found in the interval 4000-5500 Da. A further 28 strains were selected for the blind measurements: 9 cfiA-positive clinical isolates with different imipenem MICs ranging between 0.06 and >32 mg l(-1) (different expressions of the metallo-β-lactamase gene) were clearly separated from the 19 cfiA-negative isolates. The presence or absence of the selected peaks in all tested strains clearly differentiated the strains belonging to B. fragilis division I (cfiA-negative) or division II (cfiA-positive). These results suggest a realistic method for differentiating division II B. fragilis strains (harbouring the cfiA gene) and to determine them at a species level at the same time. Although not all cfiA-positive B. fragilis strains are resistant to carbapenems, they all have the possibility of becoming resistant to this group of antibiotics by acquisition of an appropriate IS element for full expression of the cfiA gene, leading to possible treatment failure.
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Affiliation(s)
- Elisabeth Nagy
- Hungarian Anaerobe Reference Laboratory, Institute of Clinical Microbiology, University of Szeged, Hungary
| | | | - József Sóki
- Hungarian Anaerobe Reference Laboratory, Institute of Clinical Microbiology, University of Szeged, Hungary
| | - Edit Urbán
- Hungarian Anaerobe Reference Laboratory, Institute of Clinical Microbiology, University of Szeged, Hungary
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30
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Awadel-Kariem FM, Patel P, Kapoor J, Brazier JS, Goldstein EJ. First report of Parabacteroides goldsteinii bacteraemia in a patient with complicated intra-abdominal infection. Anaerobe 2010; 16:223-5. [DOI: 10.1016/j.anaerobe.2010.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/05/2010] [Accepted: 01/28/2010] [Indexed: 11/29/2022]
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31
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Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M, Komiya H, Benno Y. Parabacteroides gordonii sp. nov., isolated from human blood cultures. Int J Syst Evol Microbiol 2009; 59:2843-7. [DOI: 10.1099/ijs.0.010611-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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García-Sánchez JE, José Fresnadillo M, García-Sánchez E. [New anaerobic bacterial species in human infections]. Enferm Infecc Microbiol Clin 2009; 28:173-84. [PMID: 19477040 DOI: 10.1016/j.eimc.2008.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 10/20/2022]
Abstract
This review offers succinct, precise, and complete information based on the available data concerning new anaerobic bacterial species involved in infectious diseases in humans. All hitherto undescribed species, those not previously implicated in clinical conditions, those with confirmed implication in human disease that have not been characterized, and those that have undergone taxonomic changes are considered to be "new".
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33
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Nagy E, Maier T, Urban E, Terhes G, Kostrzewa M. Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Clin Microbiol Infect 2009; 15:796-802. [PMID: 19438622 DOI: 10.1111/j.1469-0691.2009.02788.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteroides fragilis and related species are important human pathogens involved in mixed infections of different origins. The B. fragilis group isolates are phenotypically very similar, grow more slowly than aerobic bacteria and, accordingly, are frequently misidentifed with classical or automated phenotypical identification methods. Recent taxonomic changes and new species accepted as members of the Bacteroides genus are not included in the different databases of commercially available identification kits. The use of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was therefore evaluated for the species identification of 277 clinical isolates of the Bacteroides genus. Species identification was carried out with MALDI Bruker Daltonik Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) by comparing the mass spectrum of each strain with the mass spectra of the 3260 reference strains currently available. The results of conventional phenotypical identification of the isolates were used as a reference. 16S rRNA gene sequencing was performed for a selection of the strains that gave discrepant results and for all those inconclusively identified by MALDI-TOF MS; 270 isolates (97.5%) were unequivocally identified [log(score) >/=2.0] by comparison with the reference strains present in the MALDI Biotyper database. Of the 23 isolates for which the MALDI-TOF MS species identification differed from the conventional phenotypical identification, 11 were sequenced. The sequencing data confirmed the MALDI-TOF MS result in ten cases and, for the remaining isolate, the sequencing data did not lead to the determination of the species, but only to that of the genus (Bacteroides sp.). The discriminating power and identification accuracy of MALDI-TOF MS proved to be superior to that of biochemical testing for Bacteroides thetaiotaomicron, Bacteroides ovatus and Bacteroides uniformis.
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Affiliation(s)
- E Nagy
- Institute of Clinical Microbiology, University of Szeged, H-6701 Szeged, Hungary.
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34
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Woo P, Lau S, Teng J, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008; 14:908-34. [DOI: 10.1111/j.1469-0691.2008.02070.x] [Citation(s) in RCA: 524] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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35
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Abstract
SUMMARY Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites. Genomic and proteomic analyses have vastly added to our understanding of the manner in which Bacteroides species adapt to, and thrive in, the human gut. A few examples are (i) complex systems to sense and adapt to nutrient availability, (ii) multiple pump systems to expel toxic substances, and (iii) the ability to influence the host immune system so that it controls other (competing) pathogens. B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics, including cefoxitin, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin).
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36
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Abstract
Knowledge of the composition of the colonic microbiota is important for our understanding of how the balance of these microbes is influenced by diet and the environment, and which bacterial groups are important in maintaining gut health or promoting disease. Molecular methodologies have advanced our understanding of the composition and diversity of the colonic microbiota. Importantly, however, it is the continued isolation of bacterial representatives of key groups that offers the best opportunity to conduct detailed metabolic and functional studies. This also permits bacterial genome sequencing which will accelerate the linkage to functionality. Obtaining new human colonic bacterial isolates can be challenging, because most of these are strict anaerobes and many have rather exact nutritional and physical requirements. Despite this many new species are being isolated and described that occupy distinct niches in the colonic microbial community. This review focuses on these under-studied yet important gut anaerobes.
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Affiliation(s)
- S H Duncan
- Rowett Research Institute, Microbial Ecology Group, Aberdeen, UK.
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37
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Sakamoto M, Kitahara M, Benno Y. Parabacteroides johnsonii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007; 57:293-296. [PMID: 17267966 DOI: 10.1099/ijs.0.64588-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genusParabacteroides. Strain M-165Twas closely related toParabacteroides merdaestrains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165Twere similar to those ofP. merdae, the isolate could be differentiated fromP. merdaeby means of API 20A tests forl-arabinose andl-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect toP. merdaeJCM 9497T(⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165Trepresents a novel species of the genusParabacteroides, for which the nameParabacteroides johnsoniisp. nov. is proposed. The type strain is M-165T(=JCM 13406T=DSM 18315T).
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MESH Headings
- Anaerobiosis
- Bacterial Typing Techniques
- Bacteroidetes/classification
- Bacteroidetes/cytology
- Bacteroidetes/isolation & purification
- Bacteroidetes/physiology
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Feces/microbiology
- Genes, rRNA
- Humans
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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Sakamoto M, Benno Y. Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 2006; 56:1599-1605. [PMID: 16825636 DOI: 10.1099/ijs.0.64192-0] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, Parabacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, Parabacteroides distasonis gen. nov., comb. nov. (the type species), Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.
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MESH Headings
- Bacterial Typing Techniques
- Bacteroides/chemistry
- Bacteroides/classification
- Bacteroides/genetics
- Bacteroides/physiology
- Bacteroidetes/chemistry
- Bacteroidetes/classification
- Bacteroidetes/genetics
- Bacteroidetes/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Vitamin K 2/analysis
- Vitamin K 2/chemistry
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006. [DOI: 10.1099/ijs.0.64289-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in theBacteriological Code(1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should sendthree copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Officefor confirmation that all of the other requirements for valid publication have been met.It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries(i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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