title: Diet rapidly and reproducibly alters the human gut microbiome.
abstract: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
authors: 1] FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.
authors: Lawrence A
authors: LA
authors: David
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Corinne F
authors: CF
authors: Maurice
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Rachel N
authors: RN
authors: Carmody
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: David B
authors: DB
authors: Gootenberg
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Julie E
authors: JE
authors: Button
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Benjamin E
authors: BE
authors: Wolfe
authors: Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors: Alisha V
authors: AV
authors: Ling
authors: Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA.
authors: A Sloan
authors: AS
authors: Devlin
authors: Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA.
authors: Yug
authors: Y
authors: Varma
authors: Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA.
authors: Michael A
authors: MA
authors: Fischbach
authors: Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors: Sudha B
authors: SB
authors: Biddinger
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Rachel J
authors: RJ
authors: Dutton
authors: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors: Peter J
authors: PJ
authors: Turnbaugh
mesh_terms: D000328:Adult; D001419:Bacteria / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification*; D001439:Bacteroides / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D001647:Bile Acids and Salts / Q000032:analysis / Q000378:metabolism; D045282:Bilophila / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D060435:Carnivory; D004032:Diet / Q000009:adverse effects; D014676:Diet, Vegetarian; D004041:Dietary Fats / Q000009:adverse effects / Q000494:pharmacology; D005243:Feces / Q000737:chemistry / Q000382:microbiology; D005260:Female; D005285:Fermentation / Q000187:drug effects; D005516:Food Microbiology; D041981:Gastrointestinal Tract / Q000187:drug effects / Q000382:microbiology* / Q000821:virology; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D060434:Herbivory; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D008297:Male; D054892:Metagenome / Q000187:drug effects / Q000235:genetics; D064307:Microbiota / Q000187:drug effects / Q000235:genetics; D013997:Time Factors; D055815:Young Adult
chemical_list: D001647:Bile Acids and Salts; D004041:Dietary Fats