A proof of concept infant-microbiota associated rat model for studying the role of gut microbiota and alleviation potential of Cutibacterium avidum in infant colic

Establishing the relationship between gut microbiota and host health has become a main target of research in the last decade. Human gut microbiota-associated animal models represent one alternative to human research, allowing for intervention studies to investigate causality. Recent cohort and in vitro studies proposed an altered gut microbiota and lactate metabolism with excessive H$_{2}$ production as the main causes of infant colic. To evaluate H$_{2}$ production by infant gut microbiota and to test modulation of gut colonizer lactose- and lactate-utilizer non-H$_{2}$-producer, Cutibacterium avidum P279, we established and validated a gnotobiotic model using young germ-free rats inoculated with fecal slurries from infants younger than 3 months. Here, we show that infant microbiota-associated (IMA) rats inoculated with fresh feces from healthy (n = 2) and colic infants (n = 2) and fed infant formula acquired and maintained similar quantitative and qualitative fecal microbiota composition compared to the individual donor's profile. We observed that IMA rats excreted high levels of H$_{2}$, which were linked to a high abundance of lactate-utilizer H$_{2}$-producer Veillonella. Supplementation of C. avidum P279 to colic IMA rats reduced H$_{2}$ levels compared to animals receiving a placebo. Taken together, we report high H$_{2}$ production by infant gut microbiota, which might be a contributing factor for infant colic, and suggest the potential of C. avidum P279 in reducing the abdominal H$_{2}$ production, bloating, and pain associated with excessive crying in colic infants

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

Acknowledgements The Rowett Institute of Nutrition and Health (University of Aberdeen) receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS). POS is a PhD student supported by the Scottish Government (RESAS) and the Science Foundation Ireland, through a centre award to the APC Microbiome Institute, Cork, Ireland. Data Summary The high-quality draft genomes generated in this work were deposited at the European Nucleotide Archive under the following accession numbers: 1. Eubacterium rectale T1-815; CVRQ01000001–CVRQ0100 0090: http://www.ebi.ac.uk/ena/data/view/PRJEB9320 2. Roseburia faecis M72/1; CVRR01000001–CVRR010001 01: http://www.ebi.ac.uk/ena/data/view/PRJEB9321 3. Roseburia inulinivorans L1-83; CVRS01000001–CVRS0 100 0151: http://www.ebi.ac.uk/ena/data/view/PRJEB9322Peer reviewedPublisher PD

Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats

The global prevalence of Fe deficiency is high and a common corrective strategy is oral Fe supplementation, which may affect the commensal gut microbiota and gastrointestinal health. The aim of the present study was to investigate the impact of different dietary Fe concentrations on the gut microbiota and gut health of rats inoculated with human faecal microbiota. Rats (8 weeks old, n 40) were divided into five (n 8 each) groups and fed diets differing only in Fe concentration during an Fe-depletion period (12 weeks) and an Fe-repletion period (4 weeks) as follows: (1) Fe-sufficient diet throughout the study period; (2) Fe-sufficient diet followed by 70mg Fe/kg diet; (3) Fe-depleted diet throughout the study period; (4) Fe-depleted diet followed by 35mg Fe/kg diet; (5) Fe-depleted diet followed by 70mg Fe/kg diet. Faecal and caecal samples were analysed for gut microbiota composition (quantitative PCR and pyrosequencing) and bacterial metabolites (HPLC), and intestinal tissue samples were investigated histologically. Fe depletion did not significantly alter dominant populations of the gut microbiota and did not induce Fe-deficiency anaemia in the studied rats. Provision of the 35mg Fe/kg diet after feeding an Fe-deficient diet significantly increased the abundance of dominant bacterial groups such as Bacteroides spp. and Clostridium cluster IV members compared with that of an Fe-deficient diet. Fe supplementation increased gut microbial butyrate concentration 6-fold compared with Fe depletion and did not affect histological colitis scores. The present results suggest that Fe supplementation enhances the concentration of beneficial gut microbiota metabolites and thus may contribute to gut healt

Ruminococcal cellulosome systems from rumen to human

This article is protected by copyright. All rights reserved. The authors appreciate the kind assistance of Miriam Lerner (ImmunArray Ltd. Company, Rehovot, Israel) with experiments involving the MicroGrid II arrayer. This research was supported by a grant (No. 1349) to EAB also from the Israel Science Foundation (ISF) and a grant (No. 24/11) issued to RL by The Sidney E. Frank Foundation also through the ISF. Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation, from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, by the Weizmann Institute of Science Alternative Energy Research Initiative (AERI) and the Helmsley Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. HF and SHD acknowledge support from the Scottish Government Food Land and People programme and from BBSRC grant no. BB/L009951/1. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic ChemistryPeer reviewedPostprin

Métabolisme des fibres dans le côlon humain (caractérisation de la flore fibrolytique et des mécanismes microbiens impliqués dans la survenue des troubles fonctionnels intestinaux)

Le côlon humain est un écosystème microbien complexe dont l'une des fonctions majeures est d'assurer la dégradation et la fermentation des fibres alimentaires, constituées pour une large part, par les glucides pariétaux (cellulose et hémicelluloses). La dégradation de ces substrats dans le côlon est un processus complexe faisant intervenir de nombreux groupes fonctionnels de microorganismes associés en une chaîne trophique. parmi ces groupes, les bactéries fibrolytiques ont un rôle prépondérant puisqu'elles interviennent dans les 1ères étapes pour assurer la dégradation des polyosides en fragments plus petits, fermentés ensuite par de nombreuses espèces. Bien que la fermentation des fibres alimentaires par la flore intestinale soit aujourd'hui reconnue pour ses effets bénéfiques sur la santé de l'Homme, ce processus peut également être à l'origine de troubles fonctionnels intestinaux (TFI). La prévalence de TFI est élevée dans les pays occidentaux, cette pathologie digestive étant considérée comme un véritable problème de santé publique. L'origine de ces TFI est assez mal connue. Toutefois, la flore colique semble jouer un rôle prépondérant dans la genèse de ces troubles digestifs. Le 1er objectif de ces travaux de thèse a été de poursuivre la caractérisation de la flore fibrolytique du côlon, déjà initiée au laboratoire. Dans un 2nd temps, les travaux ont été focalisés sur l'étude de la composition de la flore fécale de sujets atteints de TFI, avec pour objectif de définir si un déséquilibre microbien existe au sein de la flore intestinale chez ces sujets. La structure des microflores cellulolytique et xylanolytique du côlon est très diversifiée. De nombreuses espèces nouvelles ont été isolées, appartenant à des genres bactériens variés (Bacteroides, Roseburia, Clostridium, Ruminococcus). Ces espèces présentent des caractéristiques physiologiques et métaboliques différentes. Ces travaux ont, en particulier, permis de montrer que certaines de ces espèces (Roseburia, Ruminococcus) pouvaient contribuer de manière importante à la production de gaz (H2) dans le côlon. Les interactions entre espèces fibrolytiques productrices ou non de H2 ont été étudiées lors de la fermentation des fibres. Ces travaux ont démontré qu'une espèce non productrice de H2 pouvait dominer la niche écologique et réduire la production de gaz lors de la fermentation des fibres. En outre, des transferts inter-espèces de H2 ont été mis en évidence entre espèces fibrolytiques productrices de H2 et microorganismes hydrogénotrophes. Ainsi, l'association de Roseburia intestinalis à une espèce acétogène hydrogénotrophe s'est traduite par une homo-fermentation du xylane, avec synthèse de butyrate et absence de production de H2. L'analyse de la flore fécale de sujets atteints de TFI versus celle de sujets sains a permis de démontrer l'existence d'importantes perturbations au sein de la flore intestinale chez les patients TFI. Les principales modifications mises en évidence chez les sujets atteints de TFI concernent les groupes microbiens impliqués dans le métabolisme de l'hydrogène et dans le métabolisme du lactate. Les bactéries sulfato-réductrices semblent jouer un rôle prépondérant au sein de ces 2 métabolismes, leur population étant significativement plus élevée chez les sujets TFI que chez les sujets sains. En parallèle, un modèle animal (rat à flore humaine) reproduisant les principales perturbations microbiologiques caractérisant les TFI a été développé.CLERMONT FD-BCIU-Santé (631132104) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

H2/CO2 metabolism in acetogenic bacteria isolated from the human colon

2 tables 3 graph.International audienc

Le microbiote comme outil thérapeutique dans l’allergie alimentaire

Part of special issue:14ème Congrès Francophone d’Allergologie - 16-19 avril 2019 - Paris, Palais des CongrèsLe microbiote comme outil thérapeutique dans l’allergie alimentair

Microbiote et maladies infectieuses intestinales

International audienc

Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease

International audienceThe human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom