20 results on '"Pascale Lepercq"'
Search Results
2. Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria
- Author
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Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Létisse, Nicolas Terrapon, Pascale Lepercq, Myriam Mercade, and Gabrielle Potocki-Veronese
- Subjects
Dorea ,chronic gut diseases ,fructooligosaccharides ,microbiome ,phosphotransferase system ,Microbiology ,QR1-502 - Abstract
ABSTRACT Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters. IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.
- Published
- 2020
- Full Text
- View/download PDF
3. Procyanidin—Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro
- Author
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Carine Le Bourvellec, Priscilla Bagano Vilas Boas, Pascale Lepercq, Sophie Comtet-Marre, Pauline Auffret, Philippe Ruiz, Romain Bott, Catherine M. G. C. Renard, Claire Dufour, Jean-Marc Chatel, and Pascale Mosoni
- Subjects
in vitro batch fermentation ,polyphenols ,dietary fiber ,16S metabarcoding ,metabotype ,Nutrition. Foods and food supply ,TX341-641 - Abstract
B-type oligomeric procyanidins in apples constitute an important source of polyphenols in the human diet. Their role in health is not known, although it is suggested that they generate beneficial bioactive compounds upon metabolization by the gut microbiota. During apple processing, procyanidins interact with cell-wall polysaccharides and form stable complexes. These interactions need to be taken into consideration in order to better assess the biological effects of fruit constituents. Our objectives were to evaluate the impact of these interactions on the microbial metabolization of cell walls and procyanidins, and to investigate the potential anti-inflammatory activity of the resulting metabolome, in addition to analyzing the taxonomical changes which the microbiota undergo. In vitro fermentation of three model apple matrices with microbiota from 4 healthy donors showed that the binding of procyanidins to cell-wall polysaccharides, whether covalently or non-covalently, substantially reduced procyanidin degradation. Although cell wall-unbound procyanidins negatively affected carbohydrate fermentation, they generated more hydroxyphenylvaleric acid than bound procyanidins, and increased the abundance of Adlercreutzia and Gordonibacter genera. The best results in terms of production of anti-inflammatory bioactive metabolites were observed from the apple matrix with no bonds between procyanidins and cell wall polysaccharides, although the matrix with non-covalent bonds was not far behind.
- Published
- 2019
- Full Text
- View/download PDF
4. The fate of tetrathionate during the development of a biofilm in biogenic sulfuric acid attack on different cementitious materials
- Author
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Amr Aboulela, Matthieu Peyre Lavigne, Tony Pons, Mansour Bounouba, Maud Schiettekatte, Pascale Lepercq, Myriam Mercade, Cédric Patapy, Samuel Meulenyzer, Alexandra Bertron, Laboratoire Matériaux et Durabilité des constructions (LMDC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Holcim, INSA Toulouse, and Holcim Innovation Center
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Environmental Engineering ,Sulfur Compounds ,Sulfates ,Sulfuric acid ,Thiosulfates ,Alkalies ,Sulfuric Acids ,Pollution ,Sulfur cycle ,[SPI.GCIV]Engineering Sciences [physics]/Civil Engineering ,Biodeterioration ,Biofilms ,[SDE]Environmental Sciences ,Cementitious materials ,Environmental Chemistry ,Sewer networks ,Waste Management and Disposal ,Oxidation-Reduction ,Sulfur - Abstract
International audience; The biodeterioration of cement-based materials in sewer environments occurs because of the production of sulfuric acid from the biochemical oxidation of H2S by sulfur-oxidizing bacteria (SOB). In the perspective of determining the possible reaction pathways for the sulfur cycle in such conditions, hydrated ce-mentitious binders were exposed to an accelerated laboratory test (BAC test) to reproduce a biochemical attack similar to the one occurring in the sewer networks. Tetrathionate was used as a reduced sulfur source to naturally develop sulfur-oxidizing activities on the surfaces of materials.The transformation of tetrathionate was investigated on materials made from different binders: Portland cement, calcium aluminate cement, calcium sulfoaluminate cement and alkali-activated slag. The pH and the concentration of the different sulfur species were monitored in the leached solutions during 3 months of exposure. The results showed that the formation of different polythionates was independent of the nature of the material. The main parameter controlling the phenomena was the evolution of the pH of the leached solutions. Moreover, tetrathionate disproportionation was detected with the formation of more reduced forms of sulfur compounds (pentathionate, hexathionate and elemental sulfur) along with thiosulfate and sulfate. The experimental findings allowed numerical models to be developed to estimate the amount of sulfur compounds as a function of the pH evolution. In addition, biomass samples were collected from the exposed surface and from the deteriorated layers to identifythe microbial populations. No clear influence of the cementitious materials on the selected populations was detected, confirming the previous results concerning the impact of the materials on the selected reaction pathways for tetrathionate transformation.
- Published
- 2022
5. In Vivo Competitions between Fibrobacter succinogenes , Ruminococcus flavefaciens , and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
- Author
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Pascale Lepercq, Bryan A. White, Philippe Ruiz, Pascale Mosoni, Evelyne Forano, Carl J. Yeoman, Christopher J. Fields, Montana State University (MSU), Eastern Illinois University, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), MEDIS laboratory (INRAE France) Roy J. Carver Biotechnology Center Montana Agricultural Experiment Station MONB00113National Institute of General Medical Sciences of the National Institutes of Health (NIH-NIGMS) P20GM103474U.S. Beef W4177MONB00195, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Carl R. Woese Institute of Genomic Biology, University of Illinois System-University of Illinois System, University of Illinois College of Medicine, MEDIS laboratory (INRAE France) Roy J. Carver Biotechnology Center Montana Agricultural Experiment Station MONB00113 National Institute of General Medical Sciences of the National Institutes of Health (NIH-NIGMS) P20GM103474 U.S. Beef W4177 MONB00195, and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
animal structures ,[SDV]Life Sciences [q-bio] ,Population ,Cellulase ,Microbiology ,03 medical and health sciences ,Rumen ,fluids and secretions ,cellulose degradation ,Virology ,Metabolome ,Food science ,education ,gnotobiotic animal model ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,education.field_of_study ,rumen ,Fibrobacter succinogenes ,biology ,030306 microbiology ,food and beverages ,biology.organism_classification ,QR1-502 ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,pili IV ,biology.protein ,Xylanase ,Fermentation ,Bacteria ,CAZymes ,outer membrane vesicles ,Research Article - Abstract
Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens, has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production., Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions in vivo have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with F. succinogenes S85 and Methanobrevibacter sp. strain 87.7, and 5 months later, the lambs were inoculated with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that F. succinogenes and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that F. succinogenes relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while R. albus and R. flavefaciens preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of in vivo competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response.
- Published
- 2021
6. Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria
- Author
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Gabrielle Potocki-Véronèse, Elisabeth Laville, Nicolas Terrapon, Pascale Lepercq, Zhi Wang, Pietro Tedesco, Fabien Létisse, Myriam Mercade, Alexandra S. Tauzin, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Provence-Alpes-Cote d'Azur Region Occitanie, Institut National de la Recherche Agronomique (INRA), INSA Toulouse, China Scholarship Council, European Project: 685474,H2020,H2020-LEIT-BIO-2015-1,METAFLUIDICS(2016), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
- Subjects
0301 basic medicine ,Molecular Biology and Physiology ,medicine.medical_treatment ,Dorea ,chronic gut diseases ,fructooligosaccharides ,microbiome ,phosphotransferase system ,prebiotique ,lcsh:QR1-502 ,Oligosaccharides ,Gut flora ,phosphotransférase ,lcsh:Microbiology ,protéine transmembranaire ,Phosphotransferase ,Transporter Classification Database ,biology ,Microbiology and Parasitology ,PEP group translocation ,Microbiologie et Parasitologie ,QR1-502 ,3. Good health ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Biochemistry ,Carbohydrate Metabolism ,Research Article ,Firmicutes ,030106 microbiology ,Microbiology ,03 medical and health sciences ,Metabolomics ,microbiote ,transmembrane protein ,Escherichia coli ,medicine ,Humans ,oligosaccharide ,Microbiome ,Molecular Biology ,ingénierie du génome ,métagénomique ,metagenomics ,Bacteria ,Prebiotic ,Phosphotransferases ,biology.organism_classification ,Gastrointestinal Microbiome ,Prebiotics ,030104 developmental biology ,Fermentation ,genome engineering - Abstract
Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases., Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters. IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.
- Published
- 2020
7. Procyanidin—Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro
- Author
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Claire Dufour, Pascale Lepercq, Pauline Auffret, Pascale Mosoni, Catherine M.G.C. Renard, Philippe Ruiz, Sophie Comtet-Marre, Priscilla Bagano Vilas Boas, Jean-Marc Chatel, Carine Le Bourvellec, Romain Bott, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), UMR 241 EIO, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Département Caractérisation et Elaboration des Produits Issus de l'Agriculture (CEPIA), Institut National de la Recherche Agronomique (INRA), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), and Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
- Subjects
0301 basic medicine ,procédé agroalimentaire ,[SDV]Life Sciences [q-bio] ,Anti-Inflammatory Agents ,in vitro batch fermentation ,polyphenols ,dietary fiber ,16S metabarcoding ,metabotype ,Gut flora ,Cell Wall ,fermentation in vitro ,chemistry.chemical_classification ,Nutrition and Dietetics ,biology ,Chemistry ,solvent free microwave extraction (sfem) ,04 agricultural and veterinary sciences ,040401 food science ,Proanthocyanidin ,Biochemistry ,extraction d'adn ,Malus ,lcsh:Nutrition. Foods and food supply ,paroi cellulaire végétale ,composition phénolique ,pcr quantitative ,lcsh:TX341-641 ,Polysaccharide ,Article ,Cell wall ,03 medical and health sciences ,polyphénol ,0404 agricultural biotechnology ,Metabolome ,Carbohydrate fermentation ,Humans ,procyanidine ,Proanthocyanidins ,030109 nutrition & dietetics ,Bacteria ,purée de fruit ,biology.organism_classification ,Gastrointestinal Microbiome ,Polyphenol ,Fruit ,Fermentation ,extraction ,métabolite microbien ,malus domestica borkh ,Food Science - Abstract
B-type oligomeric procyanidins in apples constitute an important source of polyphenols in the human diet. Their role in health is not known, although it is suggested that they generate beneficial bioactive compounds upon metabolization by the gut microbiota. During apple processing, procyanidins interact with cell-wall polysaccharides and form stable complexes. These interactions need to be taken into consideration in order to better assess the biological effects of fruit constituents. Our objectives were to evaluate the impact of these interactions on the microbial metabolization of cell walls and procyanidins, and to investigate the potential anti-inflammatory activity of the resulting metabolome, in addition to analyzing the taxonomical changes which the microbiota undergo. In vitro fermentation of three model apple matrices with microbiota from 4 healthy donors showed that the binding of procyanidins to cell-wall polysaccharides, whether covalently or non-covalently, substantially reduced procyanidin degradation. Although cell wall-unbound procyanidins negatively affected carbohydrate fermentation, they generated more hydroxyphenylvaleric acid than bound procyanidins, and increased the abundance of Adlercreutzia and Gordonibacter genera. The best results in terms of production of anti-inflammatory bioactive metabolites were observed from the apple matrix with no bonds between procyanidins and cell wall polysaccharides, although the matrix with non-covalent bonds was not far behind.
- Published
- 2019
8. Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
- Author
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Pascale Mosoni, Eric Peyretaillade, Pascale Lepercq, Kevin J. Shingfield, Sophie Comtet-Marre, Pierre Peyret, Ali R. Bayat, Frédérique Chaucheyras-Durand, Evelyne Forano, Nicolas Parisot, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), EA4678 CIDAM, Université d'Auvergne - Clermont-Ferrand I (UdA), Nutritional Physiology, Green Technology, Natural Resources Institute Finland (LUKE), Institute of Biological, Environmental and Rural Sciences, Nutritional Physiology, Green Technology, Region Auvergne (Bourse Innovation et Transfert de Technologie), Lallemand Animal Nutrition (France), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Natural resources institute Finland, and Forano, Evelyne
- Subjects
0301 basic medicine ,Microbiology (medical) ,carbohydrate esterases ,Microorganism ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,microbiote digestif ,Cellulase ,Microbiology ,03 medical and health sciences ,Rumen ,Fibrobacter ,fiber degradation ,glycoside hydrolases ,metatranscriptomics ,polysaccharide lyases ,rumen ,Prevotella ,dairy cows ,dégradation des fibres ,glycoside hydrolase ,Pectinase ,Original Research ,2. Zero hunger ,biology ,Microbiology and Parasitology ,biology.organism_classification ,Microbiologie et Parasitologie ,030104 developmental biology ,Fibrolytic bacterium ,polysaccharide ,vache laitière ,biology.protein ,Protozoa - Abstract
Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community. Functional analysis identified 12,237 CAZymes, accounting for 1% of the transcripts. The CAZyme profile was dominated by families GH94 (cellobiose-phosphorylase), GH13 (amylase), GH43 and GH10 (hemicellulases), GH9 and GH48 (cellulases), PL11 (pectinase) as well as GH2 and GH3 (oligosaccharidases). Our data support the pivotal role of the most characterized fibrolytic bacteria (Prevotella, Ruminocccus and Fibrobacter), and highlight a substantial, although most probably underestimated, contribution of fungi and ciliate protozoa to polysaccharide degradation. Particularly these results may motivate further exploration of the role and the functions of protozoa in the rumen. Moreover, an important part of the fibrolytic bacterial community remains to be characterized since one third of the CAZyme transcripts originated from distantly related strains. These findings are used to highlight limitations of current metatranscriptomics approaches to understand the functional rumen microbial community and opportunities to circumvent them.
- Published
- 2017
- Full Text
- View/download PDF
9. Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis
- Author
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Sophie Comtet-Marre, Pascale Mosoni, Pascale Lepercq, Evelyne Forano, Carl J. Yeoman, Bryan A. White, Catherine M.G.C. Renard, Christopher J. Fields, Carine Le Bourvellec, Jordane Despres, Bernard Henrissat, Nicolas Terrapon, Grégory Jubelin, Margret E. Berg Miller, Microbiologie Equipe Qualité et Sécurité des Aliments (INRA), Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Mosoni, Pascale, SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
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0301 basic medicine ,Dietary Fiber ,MESH: RNA/methods ,Citrus ,Pectin ,Mutant ,Bacteroides xylanisolvens ,RNA-Seq ,Polysaccharide-Utilization Locus ,Bacteroides ,MESH: Substances ,MESH: Mutagenesis ,chemistry.chemical_classification ,Genetics ,2. Zero hunger ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,digestive, oral, and skin physiology ,food and beverages ,Pectin degradation ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,MESH: Malus/chemistry ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,RNA, Bacterial ,Biochemistry ,Malus ,Pectins ,Erratum ,MESH: Bacterial/genetics ,CAZymes ,Research Article ,Biotechnology ,food.ingredient ,030106 microbiology ,Mutagenesis (molecular biology technique) ,MESH: Pectins/metabolism ,Genomics ,Computational biology ,Biology ,Polysaccharide ,Human gut ,MESH: Genetic Loci ,Microbiology ,Cell wall ,03 medical and health sciences ,MESH: Sequence Analysis ,food ,microbiote ,MESH: RNA ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Microbiome ,pectine ,Sequence Analysis, RNA ,MESH: Bacteroides/metabolism ,MESH: Transcriptome ,RNA-seq ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,030104 developmental biology ,chemistry ,MESH: Citrus/chemistry ,Genetic Loci ,Mutagenesis ,MESH: Bacteroides/genetics ,MESH: Dietary Fiber/metabolism ,Transcriptome ,Bacteria ,Function (biology) - Abstract
Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis BMC Genomics 2016 17:426 DOI: 10.1186/s12864-016-2758-3 After publication of the original article [1], it came to the authors’ attention that a funding source received by B. Henrissat had been accidently omitted from the Acknowledgements. The following sentence should have been included in the original article; International audience; BACKGROUND: Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens.RESULTS: Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70%) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation.CONCLUSION: This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem.
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- 2016
10. Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level
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Nicolas Terrapon, Eric C. Martens, Grégory Jubelin, Bryan A. White, Carl J. Yeoman, Margaret E. Berg Miller, Pascale Mosoni, Pascale Lepercq, Sophie Comtet-Marre, Christopher J. Fields, Jordane Despres, Christophe Chambon, Bernard Henrissat, Evelyne Forano, Mosoni, Pascale, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), European Project: 322820,EC:FP7:ERC,ERC-2012-ADG_20120314,HUMAN MICROBIOTA(2013), European Union's Seventh Framework Program (FP)/European Research Council (ERC) Grant 322820, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
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0301 basic medicine ,Proteomics ,bactéroïde ,appareil intestinal ,Operon ,Mutant ,xylan degradation ,human gut ,bacteroide ,polysaccharide-utilization locus ,CAZymes ,RNA-seq ,proteomics ,mutagenesis ,Bacteroides xylanisolvens ,xylan ,Gene expression ,Bacteroides ,Polysaccharide-Utilization Locus ,protéomique ,mutagenèse ,Plant Proteins ,2. Zero hunger ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,food and beverages ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,Biochemistry ,Multigene Family ,dégradation ,Xylans ,Research Article ,Biotechnology ,Biotechnologies ,Human gut ,Microbiology ,Cell wall ,03 medical and health sciences ,Bacterial Proteins ,Genetics ,Humans ,Gene ,Sequence Analysis, RNA ,Gene Expression Profiling ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Gastrointestinal Tract ,030104 developmental biology ,Mutagenesis ,Xylan degradation ,humain ,Bacteria - 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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- 2016
11. Composition and metabolism of the intestinal microbiota in consumers and non-consumers of yogurt
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Pilar Galan, Joël Doré, Catherine Juste, Elise Alvaro, Malène Sutren, Claude Andrieux, Pascale Lepercq, Violaine Rochet, Lionel Rigottier-Gois, and Yvonne Duval
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Adult ,DNA, Bacterial ,Male ,Population ,Colony Count, Microbial ,Medicine (miscellaneous) ,Diet Surveys ,Polymerase Chain Reaction ,law.invention ,Bile Acids and Salts ,Feces ,Probiotic ,law ,Lactobacillus ,Humans ,Food microbiology ,Food science ,education ,In Situ Hybridization, Fluorescence ,Bifidobacterium ,education.field_of_study ,Nutrition and Dietetics ,biology ,Probiotics ,Lactobacillaceae ,Middle Aged ,Fatty Acids, Volatile ,Yogurt ,beta-Galactosidase ,biology.organism_classification ,Intestines ,Lacticaseibacillus casei ,Case-Control Studies ,Food Microbiology ,Electrophoresis, Polyacrylamide Gel ,Female ,Fermentation ,Bacteria - Abstract
The objective of the present study was to evaluate the impact of a regular consumption of yogurt on the composition and metabolism of the human intestinal microbiota. Adult subjects were selected on the basis of daily food records and divided into two groups: yogurt consumers (at least 200 g yogurt consumed per d,n30); non-consumers (no yogurt,n21). Their faecal microbiota was analysed using molecular methods (in situhybridisation and PCR amplification combined with separation by denaturing gel electrophoresis) and its metabolic characteristics were assessed by measuring glycosidase, β-glucuronidase and reductase activities and profiling SCFA, neutral sterols and bile acids. The yogurt starterLactobacillus delbrueckiissp.bulgaricus(identity confirmed by 16S rRNA sequencing) was detected in 73 % of faecal samples from fermented milk consumersv. 28 % from non-consumers (P = 0·003). In yogurt consumers, the level of Enterobacteriaceae was significantly lower (P = 0·006) and β-galactosidase activity was significantly increased (P = 0·048). In addition, within this group, β-galactosidase activity and theBifidobacteriumpopulation were both positively correlated with the amount of fermented milk ingested (r0·66,P r0·43,P = 0·018, respectively). Apart from these effects, which can be considered beneficial to the host, no other major differences could be detected regarding the composition and metabolic activity of intestinal microbiota.
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- 2007
12. Epimerization of chenodeoxycholic acid to ursodeoxycholic acid byClostridium baratiiisolated from human feces
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Pascale Lepercq, Philippe Gérard, Fabienne Béguet, Pierre Raibaud, Jean-Pierre Grill, Purification Relano, Chantal Cayuela, Catherine Juste, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), UR 0910 JOUY LEPSD Laboratoire d'Écologie et Physiologie du Système Digestif, Laboratoire des BioSciences de l’Aliment - Faculté des Sciences et Techniques, Université Henri Poincaré - Nancy 1 (UHP), Groupe Probiotiques et Fonctions Digestives, Groupe Danone, and DANONE, Admin
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Clostridium ,Male ,Bile acid epimerization ,0303 health sciences ,human intestinal microbiota ,030306 microbiology ,[SDV]Life Sciences [q-bio] ,[SDV.MP.PRB] Life Sciences [q-bio]/Microbiology and Parasitology/domain_sdv.mp.prb ,Microbiology ,3. Good health ,[SDV.MP.PRB.BIF] Life Sciences [q-bio]/Microbiology and Parasitology/domain_sdv.mp.prb/domain_sdv.mp.prb.bif ,Feces ,03 medical and health sciences ,Isomerism ,Ursodeoxycholic acid ,Genetics ,Humans ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,Molecular Biology ,Clostridium baratii ,Aged ,Chenodeoxycholic acid ,030304 developmental biology - Abstract
Ursodeoxycholic acid-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. This work reports the first isolation of 7-epimerizing bacteria from feces of a healthy volunteer, on the basis of their capacity to epimerize the primary bile acid, chenodeoxycholic acid, to ursodeoxycholic acid. Five isolates were found to be active starting from unconjugated chenodeoxycholic acid and its tauro-conjugated homologue, but none of these strains could epimerize the glyco-conjugated form. Biochemical testing and 16S ribosomal DNA sequencing converged to show that all five isolates were closely related to Clostridium baratii (99% sequence similarity), suggesting that this bacterial species could be responsible at least partially, for this bioconversion in the human gut.
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- 2004
13. Bacterial protein signals are associated with Crohn's disease
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Harry Sokol, Stanislas Mondot, Pascale Lepercq, Olivier David, Peter Sykacek, Florence Blon, Laurent Beaugerie, Brigitte Schaeffer, Véronique Monnet, David P. Kreil, Catherine Juste, Benoît Valot, S. Dusko Ehrlich, Patrice Martin, Alain Van Dorsselaer, Joël Doré, Wilfrid Carré, Valentin Loux, Christine Carapito, Jean-François Gibrat, Philippe Seksik, Christian Beauvallet, Alain Guillot, Sebastian Vaca, Nicolas Pons, Florence Levenez, Patricia Lepage, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Animale et Biologie Intégrative (GABI), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Service de Gastroentérologie et nutrition [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), La plante et son environnement (PSE), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Espaces et Sociétés (ESO), Le Mans Université (UM)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-AGROCAMPUS OUEST-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN), INRA, UR 0341 Mathématiques et Informatique Appliquées, 1Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, Unité Mathématique Informatique et Génome (MIG), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Le Mans Université (UM)-Université d'Angers (UA)-AGROCAMPUS OUEST-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Unité Commune d'Expérimentation Animale de Vilvert (UCEA), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP], Normandie Université (NU)-Normandie Université (NU)-Le Mans Université (UM)-Université d'Angers (UA)-AGROCAMPUS OUEST-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement (IGARUN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Le Mans Université (UM)
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Adult ,Male ,Firmicutes ,Enteric Bacterial Microflora ,Difference gel electrophoresis ,Organic chemistry ,Crohn's Disease ,Microbiology ,03 medical and health sciences ,0302 clinical medicine ,Bacterial Proteins ,Crohn Disease ,Sequence Analysis, Protein ,Tandem Mass Spectrometry ,protéine bactérienne ,RNA, Ribosomal, 16S ,Prevotella ,Zymogen granule membrane ,Humans ,Electrophoresis, Gel, Two-Dimensional ,030304 developmental biology ,0303 health sciences ,biology ,Bacteria ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,Inflammatory Bowel Disease ,Gastroenterology ,maladie de crohn ,biology.organism_classification ,Mucus ,Intestines ,Chimie organique ,Cross-Sectional Studies ,Biochemistry ,Proteome ,030211 gastroenterology & hepatology ,Female ,Cell envelope ,Biomarkers ,RC ,Chromatography, Liquid - Abstract
International audience; OBJECTIVE: No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. DESIGN: We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. RESULTS: Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. CONCLUSIONS: This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.
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- 2014
14. Isolates from Normal Human Intestinal Flora but not Lactic Acid Bacteria Exhibit 7?- and 7?- Hydroxysteroid Dehydrogenase Activities
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Fabienne Béguet, Catherine Juste, Philippe Gérard, Jean-Pierre Grill, Pascale Lepercq, Chantal Cayuela, and Purification Relano
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0303 health sciences ,Bile acid ,biology ,030306 microbiology ,medicine.drug_class ,General Engineering ,biology.organism_classification ,Ursodeoxycholic acid ,3. Good health ,Lactic acid ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Clostridium ,chemistry ,Biochemistry ,Chenodeoxycholic acid ,Lactobacillus ,medicine ,General Earth and Planetary Sciences ,Bacteria ,030304 developmental biology ,General Environmental Science ,Bifidobacterium ,medicine.drug - Abstract
Ursodeoxycholic acid (UDCA)-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. UDCA is the 7β-OH epimer of the primary (i.e. synthesized by the liver) bile acid chenodeoxycholic acid (CDCA). Epimerization proceeds in two subsequent and reversible steps, catalysed by a 7α- and a 7β-hydroxysteroid dehydrogenase (7α- and 7β- HSDH), with 7oxo-lithocholic acid (7oxo-LCA) as the intermediate product. The aim of this study was to test the 7α- and 7β-HSDH activities of anaerobic whole cell cultures of a number of lactic acid bacteria and human intestinal isolates, using CDCA, UDCA and 7oxo- LCA as the substrates. Among 140 strains tested, 21 exhibited at least one of both 7-HSDH activities. 7α-HSDH activity was detected in six strains, 7β-HSDH in nine strains, and both activities in six other strains. All active strains were isolated from normal human and infant faeces. They belonged to the genera Clostridium , Eubacterium and Ruminococcus, whereas no strain of Lactobacillus, Bifidobacterium or Streptococcus was found to be active under our study conditions. The present study therefore revealed, for the first time, a number of normal human intestinal isolates supporting the epimerization of CDCA to UDCA, and further extended our knowledge of those intestinal bacteria which are responsible for 7α- or 7β-HSDH activity.Key words: screening, bile acids, epimerization, intestinal microflora, lactic acid bacteria, probiotics.
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- 2011
15. Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces
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Françoise Gavini, Pascale Lepercq, Marion Leclerc, Philippe Gérard, Catherine Juste, Pierre Raibaud, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), Unité Matériaux et Transformations - UMR 8207 (UMET), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut National de la Recherche Agronomique (INRA), UR 0910 PSD Écologie et Physiologie du Système Digestif, Gérard, Philippe, and Institut de Chimie du CNRS (INC)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)
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DNA, Bacterial ,Male ,bactéroïde ,[SDV]Life Sciences [q-bio] ,Population ,Molecular Sequence Data ,Applied Microbiology and Biotechnology ,DNA, Ribosomal ,Microbiology ,Microbial Ecology ,03 medical and health sciences ,Feces ,bacteroid ,RNA, Ribosomal, 16S ,Bacteroides ,Humans ,education ,métabolisme du cholestérol ,Bacteroidaceae ,fecès ,030304 developmental biology ,Aged ,Human feces ,0303 health sciences ,education.field_of_study ,Ecology ,biology ,Strain (chemistry) ,030306 microbiology ,poultry droppings ,Bacteroides dorei ,biology.organism_classification ,16S ribosomal RNA ,Bacteroides Infections ,Cholesterol ,Bacteria ,Food Science ,Biotechnology - Abstract
The microbial community in the human colon contains bacteria that reduce cholesterol to coprostanol, but the species responsible for this conversion are still unknown. We describe here the first isolation and characterization of a cholesterol-reducing bacterium of human intestinal origin. Strain D8 was isolated from a 10 −8 dilution of a fresh stool sample provided by a senior male volunteer with a high capacity to reduce luminal cholesterol to coprostanol. Cholesterol-to-coprostanol conversion by strain D8 started on the third day, while cells were in stationary phase, and was almost complete after 7 days. Intermediate products (4-cholesten-3-one and coprostanone) were occasionally observed, suggesting an indirect pathway for cholesterol-to-coprostanol conversion. Resting-cell assays showed that strain D8 could reduce 1.5 μmol of cholesterol/mg bacterial protein/h. Strain D8 was a gram-negative, non-spore-forming, rod-shaped organism identified as a member of the genus Bacteroides closely related to Bacteroides vulgatus , based on its morphological and biochemical characteristics. The 16S rRNA gene sequence of strain D8 was most similar (>99.5%) to those of two isolates of the recently described species Bacteroides dorei . Phylogenetic tree construction confirmed that Bacteroides sp. strain D8 clustered within an independent clade together with these B. dorei strains. Nevertheless, no cholesterol-reducing activity could be detected in cultures of the B. dorei type strain. Based on Bacteroides group-specific PCR-temporal temperature gradient gel electrophoresis, there was no correlation between the presence of a band comigrating with the band of Bacteroides sp. strain D8 and cholesterol conversion in 11 human fecal samples, indicating that this strain is unlikely to be mainly responsible for cholesterol conversion in the human population.
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- 2007
16. Correlation between faecal microbial community structure and cholesterol-to-coprostanol conversion in the human gut
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Catherine Juste, Patrick Veiga, Katiana Saunier, Philippe Gérard, Pascale Lepercq, Fabienne Béguet, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), and UR 0910 PSD Écologie et Physiologie du Système Digestif
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Adult ,DNA, Bacterial ,[SDV]Life Sciences [q-bio] ,Colony Count, Microbial ,DNA, Ribosomal ,Microbiology ,Feces ,03 medical and health sciences ,chemistry.chemical_compound ,Most probable number ,RNA, Ribosomal, 16S ,Genetics ,Cluster Analysis ,Humans ,Food science ,Molecular Biology ,Phylogeny ,030304 developmental biology ,Principal Component Analysis ,0303 health sciences ,Bacteria ,biology ,030306 microbiology ,Dendrogram ,UPGMA ,Genes, rRNA ,Middle Aged ,biology.organism_classification ,DNA Fingerprinting ,Cholestanol ,Gastrointestinal Tract ,Coprostanol ,Cholesterol ,Microbial population biology ,chemistry ,DNA profiling ,Temperature gradient gel electrophoresis - Abstract
Intensity of the cholesterol-to-coprostanol conversion in the intestine, as assessed by the coprostanol-to-cholesterol ratio in faeces, was found highly variable among 15 human volunteers, ranging from absent to almost complete cholesterol conversion. The number of coprostanoligenic bacteria in the same faecal samples, as estimated by the most probable number method, was found to be less than 10(6) cellsg-1 of fresh stools in the low-to-inefficient converters and at least 10(8) cellsg-1 of fresh stools in the highest converters, indicating that the population level of cultivable faecal coprostanoligenic bacteria correlated with the intensity of cholesterol-to-coprostanol conversion in the human gut. Microbial communities of the samples were profiled by temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNA gene amplicons. Dendrogram analysis of the TTGE profiles using the Pearson product moment correlation coefficient and a unweighted pair group method with arithmetic averages (UPGMA) algorithm clearly separated banding patterns from low-to-inefficient and high converters in two different clusters suggesting a relationship between TTGE profiles and coprostanoligenic activity. Principal components analysis further demonstrated that a large subset of bands rather than some individual bands contributed to this clustering.
- Published
- 2005
17. Bifidobacterium animalis strain DN-173 010 hydrolyses bile salts in the gastrointestinal tract of pigs
- Author
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C. Juste, C. Cayuela, Pascale Lepercq, P. Relano, DANONE, Admin, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), DANONE VITAPOLE, and Groupe DANONE
- Subjects
Male ,Time Factors ,medicine.drug_class ,Duodenum ,Swine ,[SDV]Life Sciences [q-bio] ,Colony Count, Microbial ,Bifidobacteriales ,Microbiology ,law.invention ,Taurochenodeoxycholic Acid ,[SDV.MP.PRB.BIF] Life Sciences [q-bio]/Microbiology and Parasitology/domain_sdv.mp.prb/domain_sdv.mp.prb.bif ,Probiotic ,Glycochenodeoxycholic Acid ,In vivo ,law ,medicine ,Animals ,Gastrointestinal Transit ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,ComputingMilieux_MISCELLANEOUS ,Gastrointestinal tract ,Bile acid ,biology ,Portal Vein ,Hydrolysis ,Gastroenterology ,[SDV.MP.PRB] Life Sciences [q-bio]/Microbiology and Parasitology/domain_sdv.mp.prb ,biology.organism_classification ,Small intestine ,Bifidobacterium animalis ,Bifidobacteriaceae ,medicine.anatomical_structure ,Bifidobacterium - Abstract
Background: Bile salt hydrolase (BSH) activity is widespread among ingested bifidobacteria and lactobacilli. It is sometimes considered to be beneficial because of its putative lowering effect on cholesterol absorption and sometimes considered to be deleterious because it may compromise normal fat absorption and even promote the formation of secondary cytotoxic bile acids by the resident intestinal flora. However, the true hydrolysis of bile salts in vivo by ingested living bacteria remains unexplored. The aim of the study was to examine whether or not Bifidobacterium animalis DN-173 010 ( used in fermented milks), which demonstrates a BSH activity in vitro, was also active in vivo during its transit in the intestine of pigs. Methods: Direct measurement of total and unconjugated bile acids reabsorbed into the portal vein was done, before and after the pigs had been treated for 2 weeks with two daily doses of approximate to 3.5 . 10(11) colony-forming units of living (6 pigs) or inactivated B. animalis (6 pigs). Results: None of the treatments modified the portal serum concentration of total bile acids over a 6-h postprandial period. Unconjugated bile acids represented up to 44% and 53% of total bile acids after 1 and 2 weeks of treatment with living bacteria, respectively, compared with only 25% ( P < 0.05) before treatment or after 1 or 2 weeks of treatment with inactivated bacteria. Conclusions: Living B. animalis DN-173 010 exhibited a BSH activity in the gastrointestinal tract of pigs, most probably in the small bowel. There was no sign of increased formation of secondary bile acids beyond the hydrolysis reaction.
- Published
- 2004
18. Isolates from normal human intestinal flora but not lactic acid bacteria exhibit 7α- and 7β-hydroxysteroid dehydrogenase activities
- Author
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Pascale Lepercq, Philippe Gérard, Fabienne Béguet, Jean-pierre Grill, Purification Relano, Chantal Cayuela, Catherine Juste, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), Laboratoire des BioSciences de l’Aliment - Faculté des Sciences et Techniques, Université Henri Poincaré - Nancy 1 (UHP), DANONE VITAPOLE, and Groupe DANONE
- Subjects
0303 health sciences ,03 medical and health sciences ,030306 microbiology ,[SDV]Life Sciences [q-bio] ,General Engineering ,General Earth and Planetary Sciences ,030304 developmental biology ,3. Good health ,General Environmental Science - Abstract
Ursodeoxycholic acid (UDCA)-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. UDCA is the 7 b -OH epimer of the primary (i.e. synthesized by the liver) bile acid chenodeoxycholic acid (CDCA). Epimerization proceeds in two subsequent and reversible steps, catalysed by a 7 a - and a 7 b -hydroxysteroid dehydrogenase (7 a - and 7 b - HSDH), with 7oxo-lithocholic acid (7oxo-LCA) as the intermediate product. The aim of this study was to test the 7 a - and 7 b -HSDH activities of anaerobic whole cell cultures of a number of lactic acid bacteria and human intestinal isolates, using CDCA, UDCA and 7oxo- LCA as the substrates. Among 140 strains tested, 21 exhibited at least one of both 7-HSDH activities. 7 a -HSDH activity was detected in six strains, 7 b -HSDH in nine strains, and both activities in six other strains. All active strains were isolated from normal human and infant faeces. They belonged to the genera Clostridium , Eubacterium and Ruminococcus , whereas no strain of Lactobacillus , Bifidobacterium or Streptococcus was found to be active under our study conditions. The present study therefore revealed, for the first time, a number of normal human intestinal isolates supporting the epimerization of CDCA to UDCA, and further extended our knowledge of those intestinal bacteria which are responsible for 7 a -or7 b -HSDH activity. Key words: screening, bile acids, epimerization, intestinal microflora, lactic acid bacteria, probiotics.
- Published
- 2004
19. Influence of Camembert consumption on the composition and metabolism of intestinal microbiota: a study in human microbiota-associated rats
- Author
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Claude Andrieux, Pascale Le Ruyet, Joël Doré, Catherine Juste, Riwanon Lemée, Lionel Rigottier-Gois, Evelyne F. Lhoste, Malène Sutren, Pascale Lepercq, Christophe Lay, UR 0910 PSD Écologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique (INRA), Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Recherche et Développement, and LACTALIS (LACTALIS NUTRITION)
- Subjects
Male ,intestinal microbiota ,Lactobacillus casei ,medicine.drug_class ,Cultured Milk Products ,[SDV]Life Sciences [q-bio] ,Microbial metabolism ,Colony Count, Microbial ,Medicine (miscellaneous) ,Polymerase Chain Reaction ,Camembert ,law.invention ,Bile Acids and Salts ,cheese ,03 medical and health sciences ,Probiotic ,Eating ,Feces ,law ,medicine ,Animals ,Humans ,Food science ,Cecum ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,Nutrition and Dietetics ,Bile acid ,biology ,030306 microbiology ,Streptococcus ,food and beverages ,biology.organism_classification ,Rats, Inbred F344 ,Diet ,Rats ,Lactobacillus ,human-microbiota-associated rats ,probiotics ,Fermentation ,Electrophoresis, Polyacrylamide Gel ,Female ,Bacteria - Abstract
The objective of the present study was to evaluate the consequence of Camembert consumption on the composition and metabolism of human intestinal microbiota. Camembert cheese was compared with milk fermented by yoghurt starters andLactobacillus caseias a probiotic reference. The experimental model was the human microbiota-associated (HM) rat. HM rats were fed a basal diet (HMB group), a diet containing Camembert made from pasteurised milk (HMCp group) or a diet containing fermented milk (HMfm group). The level of micro-organisms from dairy products was measured in faeces using cultures on a specific medium and PCR–temporal temperature gradient gel electrophoresis. The metabolic characteristics of the caecal microbiota were also studied: SCFA, NH3, glycosidase and reductase activities, and bile acid degradations. The results showed that micro-organisms from cheese comprised 105–108bacteria/g faecal sample in the HMCp group.Lactobacillusspecies from fermented milk were detected in HMfm rats. Consumption of cheese and fermented milk led to similar changes in bacterial metabolism: a decrease in azoreductase activity and NH3concentration and an increase in mucolytic activities. However, specific changes were observed: in HMCp rats, the proportion of ursodeoxycholic resulting from chenodeoxycholic epimerisation was higher; in HMfm rats, α and β-galactosidases were higher than in other groups and both azoreductases and nitrate reductases were lower. The results show that, as for fermented milk, Camembert consumption did not greatly modify the microbiota profile or its major metabolic activities. Ingested micro-organisms were able to survive in part during intestinal transit. These dairy products exert a potentially beneficial influence on intestinal metabolism.
- Published
- 2004
20. Gnotobiotic rats harboring human intestinal microbiota as a model for studying cholesterol-to-coprostanol conversion
- Author
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Philippe Gérard, Pascale Lepercq, Violaine Rochet, Catherine Juste, Claude Andrieux, Lionel Rigottier-Gois, Fabienne Béguet, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), and UR 0910 PSD Écologie et Physiologie du Système Digestif
- Subjects
[SDV]Life Sciences [q-bio] ,Population ,Colony Count, Microbial ,Applied Microbiology and Biotechnology ,Microbiology ,Feces ,03 medical and health sciences ,chemistry.chemical_compound ,Animals ,Germ-Free Life ,Humans ,Microbiome ,education ,Biotransformation ,cholesterol-to-coprostanol conversion ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,human intestinal microbiota ,Bacteria ,Ecology ,biology ,030306 microbiology ,animal model ,Human microbiome ,Biodiversity ,biology.organism_classification ,temporal temperature gradient gel electrophoresis ,DNA Fingerprinting ,Sterol ,Rats ,Cholestanol ,Gastrointestinal Tract ,Coprostanol ,Cholesterol ,Biochemistry ,chemistry ,Microbial population biology ,Models, Animal ,fluorescent in situ hybridization ,Oxidation-Reduction ,Temperature gradient gel electrophoresis - Abstract
The efficiency of microbial reduction of cholesterol to coprostanol in human gut is highly variable among population and mechanisms remain unexplored. In the present study, we investigated whether microbial communities and their cholesterol metabolism characteristics can be transferred to germ-free rats. Two groups of six, initially germ-free rats were associated with two different human microbiota, exhibiting high and low cholesterol-reducing activities. Four months after inoculation, enumeration of coprostanoligenic bacteria, fecal coprostanol levels and composition of the fecal microbial communities were studied in gnotobiotic rats and compared with those of the human donors. Combination of culture (most probable number enumeration of active bacteria) and biochemical approaches (extraction followed by gas chromatography of sterols) showed that gnotobiotic rats harbored a coprostanoligenic bacterial population level and exhibited coprostanoligenic activities similar to those of the corresponding human donor. On the other hand, molecular approaches (whole-cell hybridization with fluorescently labeled 16S rRNA-targeted oligonucleotide probes, and temporal temperature gradient gel electrophoresis of bacterial 16S rRNA gene amplicons) demonstrated that gnotobiotic rats reproduced a stable microbial community, close to the human donor microbiota at the group or genus levels but different at the dominant species level. These results suggest that the gnotobiotic rat model can be used to explore the still unknown human intestinal microbiota involved in luminal cholesterol metabolism, including regulation of expression of its activity and impact on health.
- Published
- 2004
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