High-fat diet alters gut microbiota physiology in mice

• Published in: The ISME Journal Vol. 8; no. 2; pp. 295 - 308
• Main Authors: Daniel, Hannelore, Gholami, Amin Moghaddas, Berry, David, Desmarchelier, Charles, Hahne, Hannes, Loh, Gunnar, Mondot, Stanislas, Lepage, Patricia, Rothballer, Michael, Walker, Alesia, Böhm, Christoph, Wenning, Mareike, Wagner, Michael, Blaut, Michael, Schmitt-Kopplin, Philippe, Kuster, Bernhard, Haller, Dirk, Clavel, Thomas
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-02-2014; Nature Publishing Group
• Subjects: 631/326/41/1969; 631/45/320; 692/698/2741/2135; Amino acids; Animals; Bacteria; Bacteria - classification; Bacteria - genetics; Bacterial Physiological Phenomena; Biodiversity; Biomedical and Life Sciences; Cecum - microbiology; Chemical composition; Diet; Diet, High-Fat; Ecology; Ecosystems; Evolutionary Biology; Gastrointestinal Tract - microbiology; Infrared spectroscopy; Life Sciences; Male; Mass spectrometry; Metabolites; Metabolome; Mice; Mice, Inbred C57BL; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microbiota - physiology; Obesity - microbiology; Original; original-article; Proteome; RNA, Ribosomal, 16S - genetics; Sugar; intestinal microbiota; metabolomics; spectroscopy; diet-induced obesity; high-fat diet; metaproteome; OLIGONUCLEOTIDE PROBES; CHOLESTEROL; INTESTINAL MICROBIOTA; RAMAN-SPECTROSCOPY; IN-SITU HYBRIDIZATION; WEIGHT-LOSS; DATABASE; INDUCED OBESITY; BACTERIAL-POPULATIONS; REVEALS
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2013.155

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.