title: High-fat diet alters gut microbiota physiology in mice.
abstract: The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.
authors.affiliation: Molecular Nutrition Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Hannelore
authors.initials: H
authors.lastname: Daniel
authors.affiliation: Proteomics and Bioanalytics, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Amin Moghaddas
authors.initials: AM
authors.lastname: Gholami
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
authors.forename: David
authors.identifier: 000000028997608X
authors.initials: D
authors.lastname: Berry
authors.affiliation: Molecular Nutrition Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Charles
authors.initials: C
authors.lastname: Desmarchelier
authors.affiliation: Proteomics and Bioanalytics, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Hannes
authors.initials: H
authors.lastname: Hahne
authors.affiliation: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Loh
authors.affiliation: 1] INRA/AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France [2] CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Australia.
authors.forename: Stanislas
authors.initials: S
authors.lastname: Mondot
authors.affiliation: INRA/AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Lepage
authors.affiliation: Research Unit Plant-Microbe Interactions, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Rothballer
authors.affiliation: Analytical BioGeoChemistry, Helmoltz Zentrum München, Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Alesia
authors.initials: A
authors.lastname: Walker
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Böhm
authors.affiliation: Microbiology, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Mareike
authors.initials: M
authors.lastname: Wenning
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.affiliation: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Blaut
authors.affiliation: Analytical BioGeoChemistry, Helmoltz Zentrum München, Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Schmitt-Kopplin
authors.affiliation: 1] Proteomics and Bioanalytics, Technische Universität München, Freising-Weihenstephan, Germany [2] Center for Integrated Protein Science Munich, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kuster
authors.affiliation: Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Haller
authors.affiliation: 1] Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany [2] Junior Research Group Intestinal Microbiome, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Clavel
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics; D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D002432:Cecum / Q000382:microbiology; D059305:Diet, High-Fat; D041981:Gastrointestinal Tract / Q000382:microbiology*; D008297:Male; D055442:Metabolome; D051379:Mice; D008810:Mice, Inbred C57BL; D064307:Microbiota / Q000502:physiology*; D009765:Obesity / Q000382:microbiology; D020543:Proteome; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D020543:Proteome; D012336:RNA, Ribosomal, 16S
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