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Sprotte S, Brinks E, Neve H, Franz CM. Complete genome sequence of the novel virulent phage PMBT24 infecting Enterocloster bolteae from the human gut. Heliyon 2024; 10:e28813. [PMID: 38655313 PMCID: PMC11035940 DOI: 10.1016/j.heliyon.2024.e28813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
PMBT24, the first reported virulent bacteriophage infecting the anaerobic human gut bacterium Enterocloster bolteae strain MBT-21, was isolated from a municipal sewage sample and its genome was sequenced and analysed. Transmission electron microscopy revealed a phage with an icosahedral head and a long, non-contractile tail. The circularly permutated, 99,962-bp dsDNA genome of the pac-type phage has a mol% G + C content of 32.1 and comprises 173 putative ORFs. Using amino acid sequence-based phylogeny, phage PMBT24 showed similarity to other, hitherto non-published phage genomes in the databases. Our data suggested phage PMBT24 to present the type phage of a novel genus (proposed name Kielvirus) and novel family of phages (proposed name Kielviridae).
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | | | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
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Gao FZ, He LY, He LX, Bai H, Zhang M, Chen ZY, Qiao LK, Liu YS, Ying GG. Swine farming shifted the gut antibiotic resistome of local people. J Hazard Mater 2024; 465:133082. [PMID: 38016315 DOI: 10.1016/j.jhazmat.2023.133082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China.
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Lu-Kai Qiao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, PR China; School of Environment, South China Normal University, University Town, Guangzhou 510006, PR China.
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Han N, Peng X, Qiang Y, Zhang T, Li X, Zhang W. Genetic characteristics of Blastocystis sp. ST3 at the genome level in the Chinese population. Parasitol Res 2023; 122:2719-2727. [PMID: 37715083 DOI: 10.1007/s00436-023-07973-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023]
Abstract
The gut microbiota comprises the collective genomes of microbial symbionts and is composed of bacteria, fungi, viruses, and protists within the gastrointestinal tract of a host. Although the literature associated with gut microbiota is increasing, studies on eukaryotes in the human gut are just beginning to surface. Blastocystis is one of the most common intestinal parasites of humans and animals and is estimated to colonise more than 1 billion people on a global scale. However, the understanding of the genetic characteristics of Blastocystis subtype (ST) at the genome level and its relationship with other members of the gut microbiota is still limited. In this study, by surveying the prevalence and genome characteristics of Blastocystis sp. ST3 in a Chinese population (prevalence % = 6.09%), the association of Blastocystis sp. ST3 with region and time and the structure of the resident gut bacterial population was clarified. We identified novel sequences (50 mitochondrial and 41 genome sequences) and determined their genetic diversity amongst strains within Blastocystis sp. ST3 (4.14 SNPs/kb). Furthermore, we found that colonisation of Blastocystis was strongly associated with increased bacterial richness and higher abundance of several anaerobes. Finally, we performed time series sampling on two Blastocystis-positive individuals and confirmed that Blastocystis could exist continually in the human gut microbiota and persist for a long time, even for 4 years.
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Affiliation(s)
- Na Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xianhui Peng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yujun Qiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tingting Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiuwen Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wen Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Taha SFM, Bhassu S, Omar H, Raju CS, Rajamanikam A, Govind SKP, Mohamad SB. Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach. 3 Biotech 2023; 13:275. [PMID: 37457869 PMCID: PMC10338424 DOI: 10.1007/s13205-023-03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03671-3.
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Affiliation(s)
- Siti Fatimah Mohd Taha
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chandramati Samudi Raju
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Arutchelvan Rajamanikam
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Suresh Kumar P. Govind
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Qi Y, Yu L, Tian F, Zhao J, Zhai Q. In vitro models to study human gut-microbiota interactions: Applications, advances, and limitations. Microbiol Res 2023; 270:127336. [PMID: 36871313 DOI: 10.1016/j.micres.2023.127336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
In vitro models of the human gut help compensate for the limitations of animal models in studying the human gut-microbiota interaction and are indispensable in the clarification the mechanism of microbial action or in the high-throughput screening and functional evaluation of probiotics. The development of these models constitutes a rapidly developing field of research. From 2D1 to 3D2 and from simple to complex, several in vitro cell and tissue models have been developed and continuously improved. In this review, we categorized and summarized these models and described their development, applications, advances, and limitations by using specific examples. We also highlighted the best ways to select an appropriate in vitro model, and we also discussed which variables to consider when imitating microbial and human gut epithelial interactions.
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Affiliation(s)
- Yuli Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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Magdy Wasfy R, Zoaiter M, Bilen M, Tidjani Alou M, Lo CI, Bellali S, Caputo A, Alibar S, Andrieu C, Raoult D, Fournier PE, Million M. Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis. Antonie Van Leeuwenhoek 2023; 116:541-555. [PMID: 37029880 DOI: 10.1007/s10482-023-01824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
The novel bacterial strain Marseille-P4005T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.
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Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Malak Zoaiter
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Melhem Bilen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Sara Bellali
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Aurelia Caputo
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Stéphane Alibar
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Pierre Edouard Fournier
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France.
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France.
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France.
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Moreira de Gouveia MI, Daniel J, Garrivier A, Bernalier-Donadille A, Jubelin G. Diversity of ethanolamine utilization by human commensal Escherichiacoli. Res Microbiol 2023; 174:103989. [PMID: 35988812 DOI: 10.1016/j.resmic.2022.103989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Ethanolamine (EA) is a substrate naturally present in the human gut and its catabolism by bacteria relies on the presence of eut genes encoding specific metabolic enzymes and accessory proteins. To date, EA utilization has been mostly investigated in gut bacterial pathogens. The aim of this study was to evaluate the ability of human gut commensal Escherichia coli isolates to utilize EA as a nitrogen and/or carbon sources. Although the capacity to consume EA is heterogeneous between the 40 strains of our collection, we determined that most of them could degrade EA to generate ammonia, a useful nitrogen resource for growth. Three isolates were also able to exploit EA as a carbon source. We also revealed that the inability of some strains to catabolize EA is explained either by mutations in the eut locus or by a defect in gene transcription. Finally, we demonstrated the importance of EA utilization for an optimal fitness of commensal E. coli in vivo. Our study provides new insights on the diversity of commensal E. coli strains to utilize EA as a nutrient in the gut and opens the way for new research in the field of interactions between host, gut microbiota and pathogens.
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Affiliation(s)
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
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Musumeci S, Coen M, Leidi A, Schrenzel J. The human gut mycobiome and the specific role of Candida albicans: where do we stand, as clinicians? Clin Microbiol Infect 2021; 28:58-63. [PMID: 34363944 DOI: 10.1016/j.cmi.2021.07.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The so-called 'mycobiome' has progressively acquired interest and increased the complexity of our understanding of the human gut microbiota. Several questions are arising concerning the role of fungi (and in particular of Candida albicans), the so-called 'mycobiome', that has been neglected for a long time and only recently gained interest within the scientific community. There is no consensus on mycobiome normobiosis because of its instability and variability. This review aims to raise awareness about this interesting topic and provide a framework to guide physicians faced with such questions. OBJECTIVES To summarize current knowledge and discuss current and potential implications of the mycobiome in clinical practice. SOURCES We performed a review of the existing literature in Medline Pubmed. CONTENT This review identifies several studies showing associations between specific mycobiome profiles and health. Fungi represent a significant biomass within the microbiota and several factors, such as diet, sex, age, co-morbidities, medications, immune status and inter-kingdom interactions, can influence its structure and population. The human gut mycobiota is indeed a key factor for several physiological processes (e.g. training of the immune system against infections) and pathological processes (e.g. immunological/inflammatory disorders, inflammatory bowel diseases, metabolic syndromes). Moreover, the mycobiome (and C. albicans in particular) could influence an even broader spectrum of conditions such as psychiatric diseases (depression, schizophrenia, bipolar disorder) or chronic viral infections (human immunodeficiency virus, hepatitis B virus); moreover, it could be implicated in tumorigenesis. IMPLICATIONS Candida albicans is a well-known opportunistic pathogen and a major component of the mycobiome but its role in the gastrointestinal tract is still poorly understood. From a potential screening biomarker to a key factor for several pathological processes, its presence could influence or even modify our clinical practice.
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Affiliation(s)
- Stefano Musumeci
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Matteo Coen
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland; Unit of Development and Research in Medical Education (UDREM), Faculty of Medicine, Geneva, Switzerland.
| | - Antonio Leidi
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
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Pergolizzi S, Rizzo G, Favaloro A, Alesci A, Pallio S, Melita G, Cutroneo G, Lauriano ER. Expression of VAChT and 5-HT in Ulcerative colitis dendritic cells. Acta Histochem 2021; 123:151715. [PMID: 33940317 DOI: 10.1016/j.acthis.2021.151715] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis is a chronic inflammatory condition of the gastrointestinal tract that can affect people of worldwide. In contrast with Crohn's disease, that can relate the entire thickness of the bowel wall, the inflammation of ulcerative colitis is limited to the colonic mucosa. Immune cells including activated T cells, plasma cells, mast cells, macrophages, and dendritic cells (DCs) trigger the inflammation. Furthermore, dendritic cells are antigen presenting cells involved in maintaining intestinal immune homeostasis. It has been described an increment of number in DCs colonic mucosa of patients with ulcerative colitis. The immune cells such as antigen-presenting cells can act as autocrine or paracrine modulators. Recent studies showed that dendritic cells synthetized and released classical neurotransmitters as glutamate, dopamine, acetylcholine, and serotonin. Paraformaldehyde-fixed intestinal tissues, obtained from the stricture sites of ten patients with ulcerative colitis were analyzed by immunostaining for Langerin/CD207, serotonin and vesicular acetylcholine transporter. As controls, unaffected (normal) portions of five patients were also investigated. Aim of this study was to characterize for the first time the human gut dendritic cells of ulcerative colitis patients, with Langerin/CD207 that is a c-type lectin expressed by different types of DCs and to colocalize in the same cells the expression of serotonin and vesicular acetylcholine transporter, showing the link between dendritic cells, gut enterochromaffin cells or autonomic nerves in immune activation and generation of intestinal inflammation.
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Kim JY, Whon TW, Lim MY, Kim YB, Kim N, Kwon MS, Kim J, Lee SH, Choi HJ, Nam IH, Chung WH, Kim JH, Bae JW, Roh SW, Nam YD. The human gut archaeome: identification of diverse haloarchaea in Korean subjects. Microbiome 2020; 8:114. [PMID: 32753050 PMCID: PMC7409454 DOI: 10.1186/s40168-020-00894-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/17/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available. RESULTS We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes. CONCLUSIONS The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals. Video Abstract.
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Affiliation(s)
- Joon Yong Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Tae Woong Whon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
| | - Yeon Bee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Namhee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Juseok Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - In-Hyun Nam
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132 Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
| | - Jung-Ha Kim
- Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, 06973 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, 02447 Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
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11
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Huët MAL, Wong LW, Goh CBS, Ong KS, Dwiyanto J, Reidpath D, Lee SM, Rahman S, Tan JBL. First reported case of Gilbertella persicaria in human stool: outcome of a community study from Segamat, Johor, Malaysia. Braz J Microbiol 2020; 51:2067-75. [PMID: 32572838 DOI: 10.1007/s42770-020-00323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 10/24/2022] Open
Abstract
Species of fungi belonging to the order Mucorales can be found everywhere in the environment. Gilbertella persicaria, which belongs to this order, have often been isolated from fruits and in water systems. However, there has been no report of isolation of this fungus from human samples. During a gut mycobiome study, from the Segamat community, Gilbertella persicaria was isolated from a human fecal sample and was characterized through a series of morphological assessment, biochemical tests, and molecular techniques. The isolate produced a white velvety surface that turned grayish after 24 h. Although no biofilm production was observed, the results indicated that the isolate could form calcium oxalate crystals, produced urease, and was resistant to low pH. The isolate was sensitive to amphotericin but resistant to voriconazole and itraconazole. The features of this fungus that could help in its survival in the human gut are also discussed.
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12
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Belkacemi S, Lo CI, Khelaifia S, Raoult D, Fournier PE, Fenollar F. Description of Prevotella rectalis sp. nov., a new bacterium isolated from human rectum. New Microbes New Infect 2020; 36:100703. [PMID: 32566232 DOI: 10.1016/j.nmni.2020.100703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
Using a taxonogenomics method, we describe here a Gram-negative bacterium named Prevotella rectalis sp. nov., strain Marseille-P4334T (= CSUR P4334) isolated from the rectum. Strain Marseille-P4334T has a genome that measure 3.03 Mbp with 43.3 mol% G + C content.
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13
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Kosciow K, Deppenmeier U. Characterization of three novel β-galactosidases from Akkermansia muciniphila involved in mucin degradation. Int J Biol Macromol 2020; 149:331-40. [PMID: 31991210 DOI: 10.1016/j.ijbiomac.2020.01.246] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 01/04/2023]
Abstract
The gut microbe Akkermansia (A.) muciniphila becomes increasingly important as its prevalence is inversely correlated with different human metabolic disorders and diseases. This organism is a highly potent degrader of intestinal mucins and the hydrolyzed glycan compounds can then serve as carbon sources for the organism itself or other members of the gut microbiota via cross-feeding. Despite its importance for the hosts' health and microbiota composition, exact mucin degrading mechanisms are still mostly unclear. In this study, we identified and characterized three extracellular β-galactosidases (Amuc_0771, Amuc_0824, and Amuc_1666) from A. muciniphila ATCC BAA-835. The substrate spectrum of all three enzymes was analyzed and the results indicated a preference for different galactosidic linkages for each hydrolase. All preferred target structures are prevalent within mucins of the colonic habitat of A. muciniphila. To check a potential function of the enzymes for the degradation of mucosal glycan structures, porcine stomach mucin was applied as a model substrate. In summary, we could confirm the involvement of all three β-galactosidases from A. muciniphila in the complex mucin degradation machinery of this important gut microbe. These findings could contribute to the understanding of the molecular interactions between A. muciniphila and its host on a molecular level.
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14
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Bukharin OV, Andryuschenko SV, Perunova NB, Ivanova EV, Chainikova IN, Zdvizhkova IA. Genome sequence data announcement of Bifidobacterium bifidum strain ICIS-202 isolated from a healthy human intestine stimulating active nitrogen oxide production in macrophages. Data Brief 2019; 27:104761. [PMID: 31799343 PMCID: PMC6883332 DOI: 10.1016/j.dib.2019.104761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/22/2019] [Accepted: 10/30/2019] [Indexed: 01/15/2023] Open
Abstract
This report presents the data on the draft genome sequence of Bifidobacterium bifidum strain ICIS-202. The strain, isolated from the intestine of a young healthy woman, was deposited in the State Collection of Microorganisms of Normal Microbiota in Gabrichevsky Institute of Epidemiology and Microbiology, Moscow, Russian Federation as a prospective candidate for probiotic development. The size of the genome was 2,265,060 bp (62,4% G + C content). The annotation revealed 1771 coding sequences, including 1771 proteins, 5 rRNA, 52 tRNA, and 3 ncRNA genes. The draft genome sequence data of B. bifidum strain ICIS-202 is available in DBJ/EMBL/GenBank under the accession nos. SSMS00000000.1, PRJNA412271 and SAMN07709009 for Genome, Bioproject and Biosample databases, respectively.
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15
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Takakura T, Anani H, Fadlane A, Fontanini A, Raoult D, Bou Khalil JY. Enterobacter timonensis sp. nov., a new bacterium isolated from a fresh human stool specimen. New Microbes New Infect 2019; 32:100586. [PMID: 31719992 PMCID: PMC6839016 DOI: 10.1016/j.nmni.2019.100586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen.
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Affiliation(s)
- T Takakura
- Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - H Anani
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - A Fadlane
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - A Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - D Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Developpement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - J Y Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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16
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Mekhalif F, Tidjani Alou M, Zgheib R, Lo C, Fournier PE, Raoult D, Lagier JC. Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child. New Microbes New Infect 2019; 31:100588. [PMID: 31463068 PMCID: PMC6710231 DOI: 10.1016/j.nmni.2019.100588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Based on our phenotypic and genotypic analyses, Brachybacterium massiliense strain Marseille-P2240T (= CSURP2240; = DSM 101766) is a new species isolated from stool of a healthy subject. The strain was stained Gram-positive. It was aerobic, catalase-positive and oxidase-negative. Its optimal growth occurs at 37°C in aerobic condition. The 16S ribosomal RNA sequence analysis revealed that strain Marseille-P2240T shown 98.18% similarity with Brachybacterium saurashtrense strain JG 06, the more closely related species with standing in nomenclature.
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Affiliation(s)
- F. Mekhalif
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - R. Zgheib
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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17
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Ling Y, Watanabe Y, Okuda S. The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks. Comput Struct Biotechnol J 2019; 17:1040-6. [PMID: 31452856 DOI: 10.1016/j.csbj.2019.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/07/2019] [Accepted: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Microbiome studies estimate the functions of bacterial flora in situ on the basis of species composition and gene function; however, estimation of interspecies interaction networks is challenging. This study aimed to develop a method to predict the interaction networks among bacterial species from human gut metagenome data using bioinformatics methods. Our proposed method revealed that adjacent gene pairs involved in bacterial interspecies interactions are localized at boundary regions and encode membrane proteins mediating interactions between the intracellular and extracellular environments, e.g., transporters and channel proteins, and those mediating interactions between metabolic pathways. Actual human gut metagenome data displayed numerous such highly reliable interspecies interaction gene pairs in comparison with random simulated metagenome data sets, suggesting that the species composition of the actual microbiome facilitated more robust interspecific interactions. The present results indicate that molecular interaction networks in human gut flora are organized by a combination of interaction networks common to all individuals and group-specific interaction networks.
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Farhana L, Antaki F, Murshed F, Mahmud H, Judd SL, Nangia-Makker P, Levi E, Yu Y, Majumdar APN. Gut microbiome profiling and colorectal cancer in African Americans and Caucasian Americans. World J Gastrointest Pathophysiol 2018; 9:47-58. [PMID: 30283710 PMCID: PMC6163128 DOI: 10.4291/wjgp.v9.i2.47] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/08/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To determine whether and to what extent the gut microbiome is involved in regulating racial disparity in colorectal cancer (CRC).
METHODS All patients were recruited and experiments were performed in accordance with the relevant guidelines and regulations by the Institutional Review Boards (IRB), committees of the John D. Dingell VAMC and Wayne State University guidelines. African American (AA) and Caucasian American (CA) patients were scheduled for an outpatient screening for colonoscopy, and no active malignancy volunteer patients were doubly consented, initially by the gastroenterologist and later by the study coordinator, for participation in the study. The gut microbial communities in colonic effluents from AAs and CAs were examined using 16sRNA profiling, and bacterial identifications were validated by performing SYBR-based Real Time PCR. For metagenomic analysis to characterize the microbial communities, multiple software/tools were used, including Metastats and R statistical software.
RESULTS It is generally accepted that the incidence and mortality of CRC is higher in AAs than in CAs. However, the reason for this disparity is not well understood. We hypothesize that the gut microbiome plays a role in regulating this disparity. Indeed, we found significant differences in species richness and diversity between AAs and CAs. Bacteroidetes was more abundant in AAs than in CAs. In particular, the pro-inflammatory bacteria Fusobacterium nucleatum and Enterobacter species were significantly higher in AAs, whereas probiotic Akkermansia muciniphila and Bifidobacterium were higher in CAs. The polyphyletic Clostridia class showed a divergent pattern, with Clostridium XI elevated in AAs, and Clostridium IV, known for its beneficial function, higher in CAs. Lastly, the AA group had decreased microbial diversity overall in comparison to the CA group. In summary, there were significant differences in pro-inflammatory bacteria and microbial diversity between AA and CA, which may help explain the CRC disparity between groups.
CONCLUSION Our current investigation, for the first time, demonstrates microbial dysbiosis between AAs and CAs, which could contribute to the racial disparity of CRC.
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Affiliation(s)
- Lulu Farhana
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Fadi Antaki
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Division of Gastroenterology, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Farhan Murshed
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
| | - Hamidah Mahmud
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
| | - Stephanie L Judd
- Division of Gastroenterology, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Pratima Nangia-Makker
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Department of Medicine, Karmanos Cancer Institute, Detroit, MI 48201, United States
| | - Edi Levi
- Department of Pathology Service, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Yingjie Yu
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Adhip PN Majumdar
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Department of Medicine, Karmanos Cancer Institute, Detroit, MI 48201, United States
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Chin SF, Megat Mohd Azlan PIH, Mazlan L, Neoh HM. Identification of Schizosaccharomyces pombe in the guts of healthy individuals and patients with colorectal cancer: preliminary evidence from a gut microbiome secretome study. Gut Pathog 2018; 10:29. [PMID: 30008808 PMCID: PMC6040075 DOI: 10.1186/s13099-018-0258-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/03/2018] [Indexed: 12/01/2022] Open
Abstract
Over the years, genetic profiling of the gut microbiome of patients with colorectal cancer (CRC) using genome sequencing has suggested over-representation of several bacterial taxa. However, little is known about the protein or metabolite secretions from the microbiota that could lead to CRC pathology. Proteomic studies on the role of microbial secretome in CRC are relatively rare. Here, we report the identification of proteins from Schizosaccharomyces pombe found in the stool samples of both healthy individuals and patients with CRC. We found that distinctive sets of S. pombe proteins were present exclusively and in high intensities in each group. Our finding may trigger a new interest in the role of gut mycobiota in carcinogenesis.
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Affiliation(s)
- Siok-Fong Chin
- 1UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | | | - Luqman Mazlan
- 2Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- 1UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
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Beye M, Bakour S, Traore SI, Rathored J, Labas N, Raoult D, Fournier PE. Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut. Stand Genomic Sci 2018; 13:8. [PMID: 29682169 PMCID: PMC5896035 DOI: 10.1186/s40793-018-0310-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy 28-month-old Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid) contains 2354 protein-coding and 46 RNA genes, including four rRNA genes.
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Affiliation(s)
- Mamadou Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Sofiane Bakour
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Sory Ibrahima Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Noémie Labas
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
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21
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Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, Sokhna C, Raoult D, Lagier JC. Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man. Antonie Van Leeuwenhoek 2018; 111:1225-1236. [PMID: 29417358 DOI: 10.1007/s10482-018-1032-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/27/2018] [Indexed: 01/26/2023]
Abstract
A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518T, was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518T can grow in a medium with 0-20% (w/v) sodium chloride (optimally at 5-7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518T (CSUR P3518T, DSM69894).
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Affiliation(s)
- Bruno Senghor
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Hubert Bassène
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Saber Khelaifia
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Catherine Robert
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Raymond Ruimy
- Department of Bacteriology at Nice, Academic Hospital, Nice, France.,Nice Medical University, Nice-Sophia Antipolis University, Nice, France.,INSERM U1065 (C3M), Bacterial Toxins in Host Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Didier Raoult
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jedda, Saudi Arabia
| | - Jean-Christophe Lagier
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 2017. [PMID: 28683828 DOI: 10.1186/s40168-017-0283-285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses. METHODS We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014. RESULTS VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients. CONCLUSIONS This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.
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Affiliation(s)
- Jie Ren
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA.
- Present address: Biology Department, Clark University, 950 Main St, Worcester, MA, 01610, USA.
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Center for Computational Systems Biology, Fudan University, 200433, Shanghai, China.
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Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 2017; 5:69. [PMID: 28683828 PMCID: PMC5501583 DOI: 10.1186/s40168-017-0283-5] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/05/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses. METHODS We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014. RESULTS VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients. CONCLUSIONS This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.
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Affiliation(s)
- Jie Ren
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA.
- Present address: Biology Department, Clark University, 950 Main St, Worcester, MA, 01610, USA.
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Center for Computational Systems Biology, Fudan University, 200433, Shanghai, China.
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24
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Rosing JA, Walker KC, Jensen BA, Heitmann BL. Oral Lactobacillus Counts Predict Weight Gain Susceptibility: A 6-Year Follow-Up Study. Obes Facts 2017; 10:473-482. [PMID: 29020671 PMCID: PMC5741165 DOI: 10.1159/000478095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/07/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Recent studies have shown an association between weight change and the makeup of the intestinal microbiota in humans. Specifically, Lactobacillus, a part of the entire gastrointestinal tract's microbiota, has been shown to contribute to weight regulation. AIM We examined the association between the level of oral Lactobacillus and the subsequent 6-year weight change in a healthy population of 322 Danish adults aged 35-65 years at baseline. DESIGN Prospective observational study. RESULTS In unadjusted analysis the level of oral Lactobacillus was inversely associated with subsequent 6-year change in BMI. A statistically significant interaction between the baseline level of oral Lactobacillus and the consumption of complex carbohydrates was found, e.g. high oral Lactobacillus count predicted weight loss for those with a low intake of complex carbohydrates, while a medium intake of complex carbohydrates predicted diminished weight gain. A closer examination of these relations showed that BMI change and Lactobacillus level was unrelated for those with high complex carbohydrate consumption. CONCLUSION A high level of oral Lactobacillus seems related to weight loss among those with medium and low intakes of complex carbohydrates. Absence, or a low level of oral Lactobacillus, may potentially be a novel marker to identify those at increased risk of weight gain.
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Affiliation(s)
- Johanne Aviaja Rosing
- Department of Public Health, Section for General Practice, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karen Christina Walker
- Department of Public Health, Section for General Practice, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin A.H. Jensen
- Department of Biology, Laboratory for Genomics and Molecular Biomedicine, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Berit L. Heitmann
- Department of Public Health, Section for General Practice, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Research Unit for Dietary Studies, The Parker Institute, Bispebjerg and Frederiksberg Hospital, The Capital Region and University of Copenhagen, Frederiksberg, Denmark
- The Boden Institute of Obesity, Nutrition, Exercise & Eating Disorders Sydney Medical School, The University of Sydney, Sydney, Australia
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- *Prof. Dr. Berit L. Heitmann, Research Unit for Dietary Studies, The Parker Institute, Bispebjerg and Frederiksberg Hospital, The Capital Region, Ndr Fasanvej 57, hovedvejen opg. 5, 1st Floor, 2000 Frederiksberg, Denmark,
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25
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Henriksen EKK, Jørgensen KK, Kaveh F, Holm K, Hamm D, Olweus J, Melum E, Chung BK, Eide TJ, Lundin KEA, Boberg KM, Karlsen TH, Hirschfield GM, Liaskou E. Gut and liver T-cells of common clonal origin in primary sclerosing cholangitis-inflammatory bowel disease. J Hepatol 2017; 66:116-122. [PMID: 27647428 DOI: 10.1016/j.jhep.2016.09.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 09/01/2016] [Accepted: 09/04/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Recruitment of gut-derived memory T-cells to the liver is believed to drive hepatic inflammation in primary sclerosing cholangitis (PSC). However, whether gut-infiltrating and liver-infiltrating T-cells share T cell receptors (TCRs) and antigenic specificities is unknown. We used paired gut and liver samples from PSC patients with concurrent inflammatory bowel disease (PSC-IBD), and normal tissue samples from colon cancer controls, to assess potential T cell clonotype overlap between the two compartments. METHODS High-throughput sequencing of TCRβ repertoires was applied on matched colon, liver and blood samples from patients with PSC-IBD (n=10), and on paired tumor-adjacent normal gut and liver tissue samples from colon cancer patients (n=10). RESULTS An average of 9.7% (range: 4.7-19.9%) memory T cell clonotypes overlapped in paired PSC-IBD affected gut and liver samples, after excluding clonotypes present at similar frequencies in blood. Shared clonotypes constituted on average 16.0% (range: 8.7-32.6%) and 15.0% (range: 5.9-26.3%) of the liver and gut memory T-cells, respectively. A significantly higher overlap was observed between paired PSC-IBD affected samples (8.7%, p=0.0007) compared to paired normal gut and liver samples (3.6%), after downsampling to equal number of reads. CONCLUSION Memory T-cells of common clonal origin were detected in paired gut and liver samples of patients with PSC-IBD. Our data indicate that this is related to PSC-IBD pathogenesis, suggesting that memory T-cells driven by shared antigens are present in the gut and liver of PSC-IBD patients. Our findings support efforts to therapeutically target memory T cell recruitment in PSC-IBD. LAY SUMMARY Primary sclerosing cholangitis (PSC) is a devastating liver disease strongly associated with inflammatory bowel disease (IBD). The cause of PSC is unknown, but it has been suggested that the immune reactions in the gut and the liver are connected. Our data demonstrate for the first time that a proportion of the T-cells in the gut and the liver react to similar triggers, and that this proportion is particularly high in patients with PSC and IBD.
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Affiliation(s)
- Eva Kristine Klemsdal Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristin Kaasen Jørgensen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Fatemeh Kaveh
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital Ullevål, Oslo, Norway
| | - Kristian Holm
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - David Hamm
- Adaptive Biotechnologies Corp., Seattle, WA, USA
| | - Johanna Olweus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Brian K Chung
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Liver Research and NIHR Birmingham Biomedical Research Unit, Institute of Biomedical Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Tor J Eide
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Centre for Immune Regulation, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kirsten Muri Boberg
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Gideon M Hirschfield
- Centre for Liver Research and NIHR Birmingham Biomedical Research Unit, Institute of Biomedical Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Biomedical Research Unit, Institute of Biomedical Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
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26
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Mostafa MM, Nassef M, Badr A. Computational determination of the effects of virulent Escherichia coli and salmonella bacteriophages on human gut. Comput Methods Programs Biomed 2016; 135:27-35. [PMID: 27586477 DOI: 10.1016/j.cmpb.2016.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/15/2016] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Salmonella and Escherichia coli are different types of bacteria that cause food poisoning in humans. In the elderly, infants and people with chronic conditions, it is very dangerous if Salmonella or E. coli gets into the bloodstream and then they must be treated by phage therapy. Treating Salmonella and E. coli by phage therapy affects the gut flora. This research paper presents a system for detecting the effects of virulent E. coli and Salmonella bacteriophages on human gut. METHODS A method based on Domain-Domain Interactions (DDIs) model is implemented in the proposed system to determine the interactions between the proteins of human gut bacteria and the proteins of bacteriophages that infect virulent E. coli and Salmonella. The system helps gastroenterologists to realize the effect of injecting bacteriophages that infect virulent E. coli and Salmonella on the human gut. RESULTS By testing the system over Enterobacteria phage 933W, Enterobacteria phage VT2-Sa and Enterobacteria phage P22, it resulted in four interactions between the proteins of the bacteriophages that infect E. coli O157:H7, E. coli O104:H4 and Salmonella typhimurium and the proteins of human gut bacterium strains. CONCLUSION Several effects were detected such as: antibacterial activity against a number of bacterial species in human gut, regulation of cellular differentiation and organogenesis during gut, lung, and heart development, ammonia assimilation in bacteria, yeasts, and plants, energizing defense system and its function in the detoxification of lipopolysaccharide, and in the prevention of bacterial translocation in human gut.
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Affiliation(s)
- Marwa Mostafa Mostafa
- Department of Computer Science, Faculty of Computers and Information, Cairo University, Egypt.
| | - Mohammad Nassef
- Department of Computer Science, Faculty of Computers and Information, Cairo University, Egypt.
| | - Amr Badr
- Department of Computer Science, Faculty of Computers and Information, Cairo University, Egypt.
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27
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens E, Terrapon N, Henrissat B, White BA, Mosoni P. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics 2016; 17:326. [PMID: 27142817 PMCID: PMC4855328 DOI: 10.1186/s12864-016-2680-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
Background Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1AT. Results Transcriptomic analyses of B. xylanisolvens XB1AT grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. Conclusion This study shows that xylan degradation by B. xylanisolvens XB1AT is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1AT has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2680-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordane Despres
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Evelyne Forano
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Pascale Lepercq
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Sophie Comtet-Marre
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Gregory Jubelin
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRA, Plate-forme d'Exploration du Métabolisme, 63122, Saint-Genès Champanelle, France
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA
| | - Margaret E Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.,INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.,INRA, USC 1408 AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pascale Mosoni
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France.
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28
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Moxon T, Gouseti O, Bakalis S. In silico modelling of mass transfer & absorption in the human gut. J FOOD ENG 2016; 176:110-120. [PMID: 27143811 PMCID: PMC4767037 DOI: 10.1016/j.jfoodeng.2015.10.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 02/08/2023]
Abstract
An in silico model has been developed to investigate the digestion and absorption of starch and glucose in the small intestine. The main question we are aiming to address is the relative effect of gastric empting time and luminal viscosity on the rate of glucose absorption. The results indicate that all factors have a significant effect on the amount of glucose absorbed. For low luminal viscosities (e.g. lower than 0.1 Pas) the rate of absorption is controlled by the gastric emptying time. For viscosities higher than 0.1 Pas a 10 fold increase in viscosity can result in a 4 fold decrease of glucose absorbed. Our model, with the simplifications used to develop it, indicate that for high viscosity luminal phases, gastric emptying rate is not the controlling mechanism for nutrient availability. Developing a mechanistic model could help elucidate the rate limiting steps that control the digestion process.
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Affiliation(s)
- T.E. Moxon
- Chemical Engineering, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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29
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Gorvitovskaia A, Holmes SP, Huse SM. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 2016; 4:15. [PMID: 27068581 PMCID: PMC4828855 DOI: 10.1186/s40168-016-0160-7] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/02/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND In a series of studies of the gut microbiome, "enterotypes" have been used to classify gut microbiome samples that cluster together in ordination analyses. Initially, three distinct enterotypes were described, although later studies reduced this to two clusters, one dominated by Bacteroides or Clostridiales species found more commonly in Western (American and Western European) subjects and the other dominated by Prevotella more often associated with non-Western subjects. The two taxa, Bacteroides and Prevotella, have been presumed to represent consistent underlying microbial communities, but no one has demonstrated the presence of additional microbial taxa across studies that can define these communities. RESULTS We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides- or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the "enterotypes" hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples' Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the "enterotypes" and is not associated with other taxa across studies. The projections we see are consistent with a continuum of values created from a simple mixture of Bacteroides and Prevotella; these two biomarkers are significantly correlated to the projection axes. We suggest that previous findings citing Bacteroides- and Prevotella-dominated clusters are the result of an artifact caused by the greater relative abundance of these two taxa over other taxa in the human gut and the sparsity of Prevotella abundant samples. CONCLUSIONS We believe that the term "enterotypes" is misleading because it implies both an underlying consistency of community taxa and a clear separation of sets of human gut samples, neither of which is supported by the broader data. We propose the use of "biomarker" as a more accurate description of these and other taxa that correlate with diet, lifestyle, and disease state.
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Abstract
The gut microbiome contributes approximately 2kg of the whole body weight, and recent studies suggest that gut microbiota has a profound effect on human metabolism, potentially contributing to several features of the metabolic syndrome. Metabolic syndrome is defined by a clustering of metabolic disorders that include central adiposity with visceral fat accumulation, dyslipidemia, insulin resistance, dysglycemia and non-optimal blood pressure levels. Metabolic syndrome is associated with an increased risk of cardiovascular diseases and type 2 diabetes. It is estimated that around 20-25 percent of the world's adult population has metabolic syndrome. In this manuscript, we have reviewed the existing data linking gut microbiome with metabolic syndrome. Existing evidence from studies both in animals and humans support a link between gut microbiome and various components of metabolic syndrome. Possible pathways include involvement with energy homeostasis and metabolic processes, modulation of inflammatory signaling pathways, interferences with the immune system, and interference with the renin-angiotensin system. Modification of gut microbiota via prebiotics, probiotics or other dietary interventions has provided evidence to support a possible beneficial effect of interventions targeting gut microbiota modulation to treat components or complications of metabolic syndrome.
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Affiliation(s)
- Mohsen Mazidi
- Key State Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang, Beijing, China; Institute of Genetics and Developmental Biology, International College, University of Chinese Academy of Science (IC-UCAS), West Beichen Road, Chaoyang, China
| | - Peyman Rezaie
- Biochemistry and Nutrition Research Center, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Andre Pascal Kengne
- Non-Communicable Disease Research Unit, South African Medical Research Council and University of Cape Town, Cape Town, South Africa
| | - Majid Ghayour Mobarhan
- Biochemistry and Nutrition Research Center, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Cardiovascular Research Center, Mashhad University of Medical Sciences (MUMS), Mashhad, Iran.
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Rm 342, Mayfield House, University of Brighton, BN1 9PH, UK
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Lagier JC, Khelaifia S, Azhar EI, Croce O, Bibi F, Jiman-Fatani AA, Yasir M, Helaby HB, Robert C, Fournier PE, Raoult D. Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut. Stand Genomic Sci 2015; 10:91. [PMID: 26523201 PMCID: PMC4627390 DOI: 10.1186/s40793-015-0081-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100 g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175 bp long genome exhibits a G + C content of 39.15 % and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.
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Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olivier Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huda Ben Helaby
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S. A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation. Data Brief 2015; 4:559-62. [PMID: 26306325 PMCID: PMC4536287 DOI: 10.1016/j.dib.2015.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 01/01/2023] Open
Abstract
We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573. Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5) or not centrifuged (NC; N=5). Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled "Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota" published in Proteomics (Tanca et al., 2015), [1].
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Affiliation(s)
| | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Tramariglio, Alghero, Italy ; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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Abstract
The human oro-gastrointestinal (GI) tract is a complex system, consisting of oral cavity, pharynx, oesophagus, stomach, small intestine, large intestine, rectum and anus, which all together with the accessory digestive organs constitute the digestive system. The function of the digestive system is to break down dietary constituents into small molecules and then absorb these for subsequent distribution throughout the body. Besides digestion and carbohydrate metabolism, the indigenous microbiota has an important influence on host physiological, nutritional and immunological processes, and commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. The main external factors that can affect the composition of the microbial community in generally healthy adults include major dietary changes and antibiotic therapy. Changes in some selected bacterial groups have been observed due to controlled changes to the normal diet e.g. high-protein diet, high-fat diet, prebiotics, probiotics and polyphenols. More specifically, changes in the type and quantity of non-digestible carbohydrates in the human diet influence both the metabolic products formed in the lower regions of the GI tract and the bacterial populations detected in faeces. The interactions between dietary factors, gut microbiota and host metabolism are increasingly demonstrated to be important for maintaining homeostasis and health. Therefore the aim of this review is to summarise the effect of diet, and especially dietary interventions, on the human gut microbiota. Furthermore, the most important confounding factors (methodologies used and intrinsic human factors) in relation to gut microbiota analyses are elucidated.
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