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Diet rapidly and reproducibly alters the human gut microbiome
Open accessAbstract
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.
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In the citing paper
“the composition and function of the microbiota shifted over 1–2 days18,20,23”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [18]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Both red meat and animal protein decrease levels of Firmicutes, while high dietary fiber increase them [133].”
From The Pathophysiology of Gestational Diabetes Mellitus (2018) · cites this paper as [133]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Individuals on a Western diet share a similar gut microbiota profile to that observed in obese individuals (David et al., 2014).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as David et al., 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“For instance, individuals on either an animal-or plant-based diet, when switched to the other diet, experienced substantial changes in the gut microbiota composition, within 24 hours (David et al., 2014).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as David et al., 2014
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The microbiota/microbiome in turn plays an important role in extracting and metabolizing dietary ingredients9-14.”
From Persistent gut microbiota immaturity in malnourished Bangladeshi children (2014) · cites this paper as [13]
The cited source says what the claim attributes to it.
In the citing paper
“Nutrient availability significantly impacts the diversity and abundance of the micro-organisms that colonize the intestine [58–63].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [60]
The cited source says what the claim attributes to it.
In the citing paper
“Intake of an animal-based diet showed significant increases in bile-tolerant anaerobes including Alistipes, Bilophila and Bacteroides (Cotillard et al., 2013;David et al., 2014).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as David et al., 2014
In the citing paper
“The secondary BA DCA is known to promote DNA damage and hepatic carcinoma and accumulates significantly on an animal product-based diet in humans [246].”
From Gut-pancreas-liver Axis as a target for treatment of NAFLD/NASH (2020) · cites this paper as [246]
In the citing paper
“The secondary BA DCA is known to promote DNA damage and hepatic carcinoma and accumulates significantly on an animal product-based diet in humans [246].”
From Gut-pancreas-liver Axis as a target for treatment of NAFLD/NASH (2020) · cites this paper as [246]
In the citing paper
“Short-term changes in diet during prospective dietary intervention studies have also been shown to rapidly change the human gut microbiota (David et al., 2014).”
From Gut-microbiota-targeted diets modulate human immune status (2021) · cites this paper as David et al., 2014
In the citing paper
“Similarly, studies from our group (39) and others (71) show that gut microbial communities differ in vegetarians and vegans compared with omnivores.”
From The contributory role of gut microbiota in cardiovascular disease (2014) · cites this paper as [71]
In the citing paper
“The impact of both short23 and long term dietary patterns24 on the gut microbiome cannot be overstated25, 26.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [23]
In the citing paper
“Western-style, high-fat, animal-based diets promote bile-tolerant, pro-inflammatory taxa (e.g., Alistipes, Bilophila wadsworthia, R. torques), reduce diversity, deplete Prevotella, and expand Proteobacteria, driving barrier dysfunction, endotoxemia, and chronic inflammation.77–80”
From Gut dysbiosis in oncology: a risk factor for immunoresistance (2026) · cites this paper as [77]
In the citing paper
“and controlled feeding studies show that the gut microbiota can shift within days of a dietary change.77”
From Gut dysbiosis in oncology: a risk factor for immunoresistance (2026) · cites this paper as [77]
In the citing paper
“Clinical studies have linked deficient SCFA production to conditions such as graft-versus-host disease and poor responses to cancer immunotherapies, spurring interest in SCFA supplementation or diets to restore microbial balance.15,77,88,146,147”
From Gut dysbiosis in oncology: a risk factor for immunoresistance (2026) · cites this paper as [77]
In the citing paper
“Likewise, mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day [5,6,18,19].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [18]
In the citing paper
“Both diets shifted gut microbiota composition [35], with the animal-based diet displaying significantly decreased levels of carbohydrate fermentation faecal metabolites and increased amino acid fermentation faecal metabolites within 24 h, in comparison to baseline and the plant-based diet [18].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [18]
In the citing paper
“However, the microbiota of the participants returned to baseline within 3-day post-dietary intervention [18].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [18]
In the citing paper
“However, the duration of any intervention required to illicit a permanent change to the core microbial profile is still unknown, with most producing only transient fluctuations within the community [18].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [18]
In the citing paper
“Diet has a major impact on gut microbiome biology (85).”
From Health Benefits of the Mediterranean Diet: Metabolic and Molecular Mechanisms (2018) · cites this paper as [85]
In the citing paper
“extreme short-term diets, such as those devoid of any carbohydrates, have been shown to have a more-pronounced effect on the human microbiota31.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [31]
In the citing paper
“Transient diet-induced alterations occur independently of body weight and adiposity and are detectable in humans within 24 to 48 hours after dietary manipulation (4).”
From The gut microbiota at the intersection of diet and human health (2018) · cites this paper as [4]
In the citing paper
“Studies have shown that diet can alter the gut microbiome.48”
From The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids (2015) · cites this paper as [48]
In the citing paper
“an animal-based diet increases the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreases the levels of Firmicutes that metabolise dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii).105 106”
From The gut microbiota and host health: a new clinical frontier (2016) · cites this paper as [105]
In the citing paper
“diet modulates the composition and function of this community of microbes in humans and other mammals18–25”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [18]
In the citing paper
“and accordingly, genes related to succinate production pathway were enriched in subjects receiving an animal-based diet.15”
From High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome (2016) · cites this paper as [15]
In the citing paper
“Practice patterns vary across transplantation centers, particularly with regard to antibiotics and nutrition — two critical determinants of microbiota injury.25–27”
From Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation (2020) · cites this paper as [25]
In the citing paper
“another uncertainty of FMT is the highly dynamic composition of live microbiota, which is sensitive to external factors such as diet and drugs.6”
From Fecal microbiota transplantation: Review and update (2019) · cites this paper as [6]
In the citing paper
“Dietary intervention represents an alternative strategy to control the microbial biotransformation of drugs (Fig. 5), as diet has been shown to rapidly and reproducibly alter the gut microbiota in humans and animal models8, 148.”
From The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism (2016) · cites this paper as [8]
In the citing paper
“For instance, plant proteins are associated with greater Bifidobacterium, Roseburia, Ruminococcus bromii, Lactobacillus, and Roseburia content [161], as opposed to Bacteroides, Alistipes, Bilophila, and Clostridium perfrigens, found primarily in animal proteins [64,162].”
From Impact of Protein Intake in Older Adults with Sarcopenia and Obesity: A Gut Microbiota Perspective (2020) · cites this paper as [64]
In the citing paper
“It is suggested that protein sources and amino-acid balance may influence gut microbial diversity. For instance, plant proteins are associated with greater Bifidobacterium, Roseburia, Ruminococcus bromii, Lactobacillus, and Roseburia content [161], as opposed to Bacteroides, Alistipes, Bilophila, and Clostridium perfrigens, found primarily in animal proteins [64,162].”
From Impact of Protein Intake in Older Adults with Sarcopenia and Obesity: A Gut Microbiota Perspective (2020) · cites this paper as [64]
In the citing paper
“Diet is intimately linked to the gut microbiome’s composition and can rapidly shift its taxonomic structure in healthy individuals (David et al., 2014).”
From Microbiota-centered interventions to boost immune checkpoint blockade therapies (2025) · cites this paper as David et al., 2014
In the citing paper
“dietary intake can also promote differential composition of the microbiome, with evidence that profound and intensive changes in dietary regimens can significantly alter the gut microbiota in a relatively short amount of time (David et al., 2014).”
From The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy (2018) · cites this paper as David et al., 2014
In the citing paper
“Diet profoundly influences gut microbiota composition and functions [57], an effect that can promote disease.”
From Antibiotic-Induced Changes in the Intestinal Microbiota and Disease (2016) · cites this paper as [57]
In the citing paper
“In fact, the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles; for instance, the low consumption of dietary fiber and resistant starch may lead to a decrease in bowel movements resulting in decreased intestinal function, which would decrease the diversity of intestinal bacteria [91].”
From The 4R’s Framework of Nutritional Strategies for Post-Exercise Recovery: A Review with Emphasis on New Generation of Carbohydrates (2020) · cites this paper as [91]
In the citing paper
“for instance, the low consumption of dietary fiber and resistant starch may lead to a decrease in bowel movements resulting in decreased intestinal function, which would decrease the diversity of intestinal bacteria [91].”
From The 4R’s Framework of Nutritional Strategies for Post-Exercise Recovery: A Review with Emphasis on New Generation of Carbohydrates (2020) · cites this paper as [91]
In the citing paper
“Protein intake appears to be a strong modulator of the microbiota [20, 32, 34]”
From International Society of Sports Nutrition Position Stand: Probiotics (2019) · cites this paper as [32]
In the citing paper
“Diet is an established modulator of gut microbiota composition, with significant change reported within 24 h of a dietary modification [32].”
From International Society of Sports Nutrition Position Stand: Probiotics (2019) · cites this paper as [32]
In the citing paper
“Diet is an established modulator of gut microbiota composition, with significant alterations reported within 24 h of a dietary change [134].”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“David et al. [134] showed a rapid shift in gut microbial community composition and increased populations of Alistipes, Bilophila, and Bacteroides after consuming a high-fat/protein diet for 5 days and these changes were thought to be a result of increased bile secretion.”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“In humans, ingestion of an animal-based diet for 5 days, high in fat (69% of total energy) and protein (30% of total energy) and almost entirely void of carbohydrates (including dietary fiber), induced rapid and significant changes in microbial community structure”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“Specific alterations included gut bacterial taxonomic shifts and transcriptional responses characteristic of carnivorous mammals”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“and overwhelmed inter-individual differences in microbial gene expression.”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“with higher concentrations of bile-tolerant bacteria”
From The athletic gut microbiota (2020) · cites this paper as [134]
In the citing paper
“Short term consumption of a mostly animal or mostly plant diet can dramatically alter the microbiota composition and function [26], as fast as 24 hours [27].”
From Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes (2016) · cites this paper as [26]
In the citing paper
“The insufficient consumption of fiber and resistant starch may promote a ‘loss’ of microbiota diversity and function in the GI [26].”
From Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes (2016) · cites this paper as [26]
In the citing paper
“Short term consumption of a mostly animal or mostly plant diet can dramatically alter the microbiota community [26].”
From Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes (2016) · cites this paper as [26]
In the citing paper
“Food is a major factor that shapes the proportional representation of organisms present in the gut microbial community (microbiota), and its gene content (microbiome).”
From Persistent gut microbiota immaturity in malnourished Bangladeshi children (2014) · cites this paper as [13]
In the citing paper
“For example, changes in diet even for a short duration (24 h) can drastically alter the composition of the gut microbiota [385].”
From Anxiety, depression, and the microbiome: A role for gut peptides (2018) · cites this paper as [385]
In the citing paper
“Diet is known to have a substantial short and long term impact on the microbiome profile (David et al., 2014).”
From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as David et al., 2014
In the citing paper
“David et al. [94] showed that an animal-based diet shifted the gut microbial structure in humans such that the abundance of bile-tolerant microbes increased at the expense of those that metabolized dietary plant polysaccharides, an effect associated with concomitant changes in the proportion of SCFAs that originated from different macronutrients.”
In the citing paper
“The catabolic starvation state of critical illness results in decreased immigration of food-associated bacteria and decreased nutritional supply for commensal microbes.”
From The microbiome and critical illness (2016) · cites this paper as [6]
In the citing paper
“Both short- (37) and long-term (3) dietary habits have been recognized as one of the drivers of microbial composition and diversity”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [37]
In the citing paper
“In mice, animal-based protein increases potential detrimental gut microbes, e.g., Peptostreptococcaceae, Ruminococcaceae, Enterococcus, Streptococcus, Turicibacter, or Escherichia (92), and plant-based protein boosts the abundance of Bifidobacterium, Roseburia, and Lactobacillus and lowers the abundance of pathogens such as Bacteroides fragilis and Clostridium perfringens (37,42,80).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [37]
In the citing paper
“In human intervention studies, animal-based protein elicits a more pronounced effect on microbiota composition than plant-based protein (37).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [37]
In the citing paper
“Both acute [12], [14], [15], [16] and long-term [16], [17] changes in diet have been demonstrated to alter the abundance of bacterial species in the gut, as well as their functional capacity to process various nutrients, with such changes being detectable within days of dietary interventions in humans [15], [16].”
From Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals (2016) · cites this paper as [15]
In the citing paper
“Indeed, Faecalibacterium taxa possess anti-inflammatory properties as well as actively contribute to the intestinal health and the maintenance of gut homeostasis [55], as does Roseburia genus [56].”
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Metadata
- Authors
- David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J.
- Affiliations
- Harvard University (US)
- Boston Children's Hospital (US)
- QB3 (US)
- Corresponding author
- Turnbaugh, Peter J.
- ORCID
- Venue
- Nature
- Published
- 2013-12-11
- Volume
- 505
- Issue
- 7484
- Pages
- 559-563
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3957428
- OpenAlex
- W2166562121
- Cited by
- 10,100
- References
- 57
- Citations by year
- 2026: 688 · 2025: 802 · 2024: 924 · 2023: 933 · 2022: 1054 · 2021: 1212 · 2020: 1056 · 2019: 871 · 2018: 737 · 2017: 634 · 2016: 505 · 2015: 420 · 2014: 245 · 2013: 5
- FWCI
- 175.57
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (P50GM068763)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK0046200, P30DK046200)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, dietary intervention, plant-based diet, animal-based diet, macronutrient composition, Bilophila wadsworthia, inflammatory bowel disease, microbial gene expression, dietary fat, bile acids, Firmicutes, Roseburia, Eubacterium rectale, Ruminococcus bromii
- MeSH terms
- Adult, Bacteria, Bacteroides, Bile Acids and Salts, Diet, Dietary Fats, Feces, Female, Fermentation, Food Microbiology, Humans, Male, Time Factors, Diet, Vegetarian, Inflammatory Bowel Diseases, Gene Expression Regulation, Bacterial, Gastrointestinal Tract, Bilophila, Metagenome, Young Adult, Herbivory, Carnivory, Microbiota
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