Variations in Gut Microbiome Are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis
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Gut Microbiota and Inflammation
Nutrients 2011, 3, 637-682; doi:10.3390/nu3060637 OPEN ACCESS nutrients ISSN 2072-6643 www.mdpi.com/journal/nutrients Review Gut Microbiota and Inflammation Asa Hakansson and Goran Molin * Food Hygiene, Division of Applied Nutrition, Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-22100 Lund, Sweden; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +46-46-222-8327; Fax: +46-46-222-4532. Received: 15 April 2011; in revised form: 19 May 2011 / Accepted: 24 May 2011 / Published: 3 June 2011 Abstract: Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI) tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics. Keywords: probiotics; inflammation; gut microbiota 1. Inflammation Inflammation is a defence reaction of the body against injury. The word inflammation originates from the Latin word ―inflammatio‖ which means fire, and traditionally inflammation is characterised by redness, swelling, pain, heat and impaired body functions. -
Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
Diarrhea Predominant-Irritable Bowel Syndrome (IBS-D): Effects of Different Nutritional Patterns on Intestinal Dysbiosis and Symptoms
nutrients Review Diarrhea Predominant-Irritable Bowel Syndrome (IBS-D): Effects of Different Nutritional Patterns on Intestinal Dysbiosis and Symptoms Annamaria Altomare 1,2 , Claudia Di Rosa 2,*, Elena Imperia 2, Sara Emerenziani 1, Michele Cicala 1 and Michele Pier Luca Guarino 1 1 Gastroenterology Unit, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; [email protected] (A.A.); [email protected] (S.E.); [email protected] (M.C.); [email protected] (M.P.L.G.) 2 Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; [email protected] * Correspondence: [email protected] Abstract: Irritable Bowel Syndrome (IBS) is a chronic functional gastrointestinal disorder charac- terized by abdominal pain associated with defecation or a change in bowel habits. Gut microbiota, which acts as a real organ with well-defined functions, is in a mutualistic relationship with the host, harvesting additional energy and nutrients from the diet and protecting the host from pathogens; specific alterations in its composition seem to play a crucial role in IBS pathophysiology. It is well known that diet can significantly modulate the intestinal microbiota profile but it is less known how different nutritional approach effective in IBS patients, such as the low-FODMAP diet, could be Citation: Altomare, A.; Di Rosa, C.; responsible of intestinal microbiota changes, thus influencing the presence of gastrointestinal (GI) Imperia, E.; Emerenziani, S.; Cicala, symptoms. The aim of this review was to explore the effects of different nutritional protocols (e.g., M.; Guarino, M.P.L. -
Product Sheet Info
Product Information Sheet for HM-300 Dorea formicigenerans, Strain Atmosphere: Anaerobic Propagation: 4_6_53AFAA 1. Keep vial frozen until ready for use, then thaw. 2. Transfer the entire thawed aliquot into a single tube of Catalog No. HM-300 broth. 3. Incubate the tube at 37°C for 1 to 2 days. For research use only. Not for human use. Citation: Contributor: Acknowledgment for publications should read “The following Emma Allen-Vercoe, Assistant Professor, Department of reagent was obtained through BEI Resources, NIAID, NIH as Molecular and Cellular Biology, University of Guelph, Guelph, part of the Human Microbiome Project: Dorea Ontario, Canada formicigenerans, Strain 4_6_53AFAA, HM-300.” Manufacturer: Biosafety Level: 1 BEI Resources Appropriate safety procedures should always be used with this material. Laboratory safety is discussed in the following Product Description: publication: U.S. Department of Health and Human Services, Bacteria Classification: Lachnospiraceae, Dorea Public Health Service, Centers for Disease Control and Species: Dorea formicigenerans Prevention, and National Institutes of Health. Biosafety in Microbiological and Biomedical Laboratories. 5th ed. Strain: 4_6_53AFAA Washington, DC: U.S. Government Printing Office, 2009; see Original Source: Dorea formicigenerans (D. formicigenerans), www.cdc.gov/biosafety/publications/bmbl5/index.htm. strain 4_6_53AFAA was isolated from human gastrointestinal tract biopsy sample.1,2 Comments: D. formicigenerans, strain 4_6_53AFAA (HMP ID Disclaimers: 9457) is a reference genome for The Human Microbiome You are authorized to use this product for research use only. Project (HMP). HMP is an initiative to identify and It is not intended for human use. characterize human microbial flora. The complete genome of D. formicigenerans, strain 4_6_53AFAA was sequenced Use of this product is subject to the terms and conditions of at the Broad Institute (GenBank: ADLU00000000). -
Specific Substrate-Driven Changes in Human Faecal Microbiota Composition Contrast with Functional Redundancy in Short-Chain Fatty Acid Production
The ISME Journal (2018) 12, 610–622 © 2018 International Society for Microbial Ecology All rights reserved 1751-7362/18 www.nature.com/ismej ORIGINAL ARTICLE Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production Nicole Reichardt1,2, Maren Vollmer1, Grietje Holtrop3, Freda M Farquharson1, Daniel Wefers4, Mirko Bunzel4, Sylvia H Duncan1, Janice E Drew1, Lynda M Williams1, Graeme Milligan2, Thomas Preston5, Douglas Morrison5, Harry J Flint1 and Petra Louis1 1The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK; 2Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; 3Biomathematics and Statistics Scotland, Foresterhill, Aberdeen, UK; 4Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Adenauerring 20A, Karlsruhe, Germany and 5Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue, East Kilbride, UK The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors. To investigate temporal stability and reproducibility, a further experiment was performed 1 year later with four of the carbohydrates. The lower pH (5.5) led to higher butyrate and the higher pH (6.5) to more propionate production. -
Annotations of the Otus with the Lowest P-Values for SR Samples at 0 and 4H Fermentation Time Points
Electronic Supplementary Material (ESI) for Food & Function. This journal is © The Royal Society of Chemistry 2016 Table S1. Taxonomic annotations: Annotations of the OTUs with the lowest p-values for SR samples at 0 and 4h fermentation time points. TAXA ID PHYLUM CLASS ORDER FAMILY GENUS SPECIES 4452633 Firmicutes Clostridia Clostridiales Clostridiaceae unclassified unclassified 191399 Firmicutes Clostridia Clostridiales Ruminococcaceae unclassified unclassified 4256470 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 97otu97833 179291 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 192046 Firmicutes Clostridia Clostridiales unclassified unclassified unclassified 4315974 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus 97otu66887 4343627 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 760967 Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella 97otu12794 4475758 Firmicutes Clostridia Clostridiales Veillonellaceae Veillonella unclassified 566976 Bacteroidetes Gammapro Bacteroidales Bacteroidaceae Bacteroides unclassified teobacteria 328617 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides uniformis 16054 Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus 97otu97520 SR: sun-dried raisins. Table S2. Taxonomic annotations: Annotations of the OTUs with the lowest p-values for SR samples at 0 and 8h fermentation time points. TAXA ID PHYLUM CLASS ORDER FAMILY GENUS SPECIES 194443 Firmicutes Clostridia Clostridiales -
Gut Microbiota Differs in Composition and Functionality Between Children
Diabetes Care Volume 41, November 2018 2385 Gut Microbiota Differs in Isabel Leiva-Gea,1 Lidia Sanchez-Alcoholado,´ 2 Composition and Functionality Beatriz Mart´ın-Tejedor,1 Daniel Castellano-Castillo,2,3 Between Children With Type 1 Isabel Moreno-Indias,2,3 Antonio Urda-Cardona,1 Diabetes and MODY2 and Healthy Francisco J. Tinahones,2,3 Jose´ Carlos Fernandez-Garc´ ´ıa,2,3 and Control Subjects: A Case-Control Mar´ıa Isabel Queipo-Ortuno~ 2,3 Study Diabetes Care 2018;41:2385–2395 | https://doi.org/10.2337/dc18-0253 OBJECTIVE Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared. PATHOPHYSIOLOGY/COMPLICATIONS RESEARCH DESIGN AND METHODS This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors mod- ifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing. 1Pediatric Endocrinology, Hospital Materno- Infantil, Malaga,´ Spain RESULTS 2Clinical Management Unit of Endocrinology and Compared with healthy control subjects, type 1 diabetes was associated with a Nutrition, Laboratory of the Biomedical Research significantly lower microbiota diversity, a significantly higher relative abundance of Institute of Malaga,´ Virgen de la Victoria Uni- Bacteroides Ruminococcus Veillonella Blautia Streptococcus versityHospital,Universidad de Malaga,M´ alaga,´ , , , , and genera, and a Spain lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and 3Centro de Investigacion´ BiomedicaenRed(CIBER)´ Lachnospira. -
Bacteroides Gingivalis, and Bacteroides Endodontalis in a New Genus, Porphyromonas H
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1988, p. 128-131 Vol. 38, No. 1 0020-7713/88/010128-04$02.00/0 Copyright 0 1988, International Union of Microbiological Societies Proposal for Reclassification of Bacteroides asaccharolyticus , Bacteroides gingivalis, and Bacteroides endodontalis in a New Genus, Porphyromonas H. N. SHAH1* AND M. D. COLLINS’ Department of Oral Microbiology, London Hospital Medical College, London El 2AD,l and Division of Microbiology, AFRC Institute of Food Research, Shinfeld, Reading RG2 9AT,= United Kingdom The asaccharolytic, pigmented Bacteroides, Bacteroides asaccharolyticus, Bacteroides gingivalis, and Bacte- roides endodontalis, form a group of relatively homogeneous species which differ markedly in biochemical and chemical properties from the type species of Bacteroides, Bacteroides fragilis (Castellani and Chalmers), such that they should not be retained within this genus. Therefore, we propose that Bacteroides asaccharolyticus (Holdeman and Moore) Finegold and Barnes, Bacteroides gingivalis Coykendhll, Kaczmarek and Slots, and Bacteroides endodontalis van Steenbergen, van Winkelhoff, Mayrand, Grenier and de Graaff be reclassified in a new genus, Porphyromonas, as Porphyromonas asaccharolytica comb. nov., Porphyromonas gingivalis comb. nov., and Porphyromonas endodontalis comb. nov., respectively. In Bergey ’s Manual of Determinative Bacteriology, 8th quite unrelated to the type species of the genus Bacteroides, ed. (12), the asaccharolytic, pigmented Bacteroides were Bacteroides fragilis. All of the asaccharolytic, pigmented regarded as a single homogeneous taxon, Bacteroides mela- bacteroides accumulate major levels of protoheme rather ninogenicus subsp. asaccharolyticus. As the clinical signif- than protoporphyrin when cells are cultured on blood agar icance of these microorganisms in oral cavities was recog- (3,25, 27). The three species are nonfermentative and utilize nized, extensive taxonomic studies were carried out. -
UK Standards for Microbiology Investigations
UK Standards for Microbiology Investigations Identification of Anaerobic Cocci Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 29 © Crown copyright 2015 Identification of Anaerobic Cocci Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 29 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Anaerobic Cocci Contents ACKNOWLEDGMENTS ......................................................................................................... -
Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. -
Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria Zhi Wang, Alexandra S
Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Letisse, Nicolas Terrapon, Pascale Lepercq, Myriam Mercade, Gabrielle Potocki-Veronese To cite this version: Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Letisse, et al.. Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria. mSphere, 2020, 5 (1), 26 p. 10.1128/mSphere.00771-19. hal-02478442 HAL Id: hal-02478442 https://hal.archives-ouvertes.fr/hal-02478442 Submitted on 13 Feb 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Molecular Biology and Physiology Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria a a a a a b,c a Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Létisse, Nicolas Terrapon, Pascale Lepercq, Downloaded from Myriam Mercade,a Gabrielle Potocki-Veronesea aTBI, CNRS, INRA, INSAT, Université de Toulouse, Toulouse, France bAFMB, UMR 7257 CNRS, Aix-Marseille Université, Marseille, France cINRA, USC 1408 AFMB, Marseille, France ABSTRACT Prebiotic oligosaccharides, such as fructooligosaccharides, are increas- ingly being used to modulate the composition and activity of the gut microbiota. -
Human Microbiota Reveals Novel Taxa and Extensive Sporulation Hilary P
OPEN LETTER doi:10.1038/nature17645 Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Hilary P. Browne1*, Samuel C. Forster1,2,3*, Blessing O. Anonye1, Nitin Kumar1, B. Anne Neville1, Mark D. Stares1, David Goulding4 & Trevor D. Lawley1 Our intestinal microbiota harbours a diverse bacterial community original faecal sample and the cultured bacterial community shared required for our health, sustenance and wellbeing1,2. Intestinal an average of 93% of raw reads across the six donors. This overlap was colonization begins at birth and climaxes with the acquisition of 72% after de novo assembly (Extended Data Fig. 2). Comparison to a two dominant groups of strict anaerobic bacteria belonging to the comprehensive gene catalogue that was derived by culture-independent Firmicutes and Bacteroidetes phyla2. Culture-independent, genomic means from the intestinal microbiota of 318 individuals4 found that approaches have transformed our understanding of the role of the 39.4% of the genes in the larger database were represented in our cohort human microbiome in health and many diseases1. However, owing and 73.5% of the 741 computationally derived metagenomic species to the prevailing perception that our indigenous bacteria are largely identified through this analysis were also detectable in the cultured recalcitrant to culture, many of their functions and phenotypes samples. remain unknown3. Here we describe a novel workflow based on Together, these results demonstrate that a considerable proportion of targeted phenotypic culturing linked to large-scale whole-genome the bacteria within the faecal microbiota can be cultured with a single sequencing, phylogenetic analysis and computational modelling that growth medium.