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High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity
Open accessAbstract
Background & aims The composition of the gut microbiome is affected by host phenotype, genotype, immune function, and diet. Here, we used the phenotype of RELMbeta knockout (KO) mice to assess the influence of these factors.Methods Both wild-type and RELMbeta KO mice were lean on a standard chow diet, but, upon switching to a high-fat diet, wild-type mice became obese, whereas RELMbeta KO mice remained comparatively lean. To investigate the influence of diet, genotype, and obesity on microbiome composition, we used deep sequencing to characterize 25,790 16S rDNA sequences from uncultured bacterial communities from both genotypes on both diets.Results We found large alterations associated with switching to the high-fat diet, including a decrease in Bacteroidetes and an increase in both Firmicutes and Proteobacteria. This was seen for both genotypes (ie, in the presence and absence of obesity), indicating that the high-fat diet itself, and not the obese state, mainly accounted for the observed changes in the gut microbiota. The RELMbeta genotype also modestly influenced microbiome composition independently of diet. Metagenomic analysis of 537,604 sequence reads documented extensive changes in gene content because of a high-fat diet, including an increase in transporters and 2-component sensor responders as well as a general decrease in metabolic genes. Unexpectedly, we found a substantial amount of murine DNA in our samples that increased in proportion on a high-fat diet.Conclusions These results demonstrate the importance of diet as a determinant of gut microbiome composition and suggest the need to control for dietary variation when evaluating the composition of the human gut microbiome.
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“administration of an HFD to healthy subjects caused a decrease in Bacteroidetes levels with an increase in both Firmicutes and Proteobacteria levels of gut microbiota (Hildebrandt et al., 2009;Zhang et al., 2012a).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Hildebrandt et al., 2009
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“animal models fed an HFD demonstrated an alteration in their gut microbiota profile with a reduction in Bacteroidetes levels and an increase in both Proteobacteria and Firmicute levels (Hildebrandt et al., 2009).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Hildebrandt et al., 2009
In the citing paper
“Those with cystic fibrosis are recommended to consume a diet high in protein and fat (and therefore a comparative reduction in carbohydrates) which has been previously associated with an increase in Firmicutes to Bacteriodetes ratio in mice [96], though dietary data was not collected within the cystic fibrosis study [95].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [96]
In the citing paper
“These changes were observed in mice resistant to weight gain, implying a direct effect of dietary lipids on the microbiota (26, 27).”
From The gut microbiota at the intersection of diet and human health (2018) · cites this paper as [26]
In the citing paper
“Experimental mice fed a high-fat diet (40 to 80% total caloric intake) exhibit decreases at the phyla-level in Bacteroidetes and increases in Firmicutes and Proteobacteria.”
From The gut microbiota at the intersection of diet and human health (2018) · cites this paper as [26]
In the citing paper
“a high-fat diet, independent of obesity, altered the composition of the intestinal microbiome (Hildebrandt, 2009).”
From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Hildebrandt, 2009
In the citing paper
“Similar to the Western diet, high-fat diets in animal studies reproducibly change gut microbial community structure, decreasing the overall microbiota diversity and beneficial bacteria (e.g., A. muciniphila, Bifidobacterium, Lactobacillus, and Lactococcus) and increasing the Firmicutes:Bacteroidetes ratio and the abundance of Enterobacteriales, Clostridium cluster XVIa, Mollicutes, and B. wadswort”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [90]
In the citing paper
“To further isolate the solitary impact of sleep on the microbiota – separate from the previously documented impact of e.g. high-fat diet [32] – participants were provided with a non-sugar sweetened, low-fat diet throughout the three meals, the exception being the oral glucose tolerance (OGTT) test on day 2”
From Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals (2016) · cites this paper as [32]
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Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Lees, H., Swann, J. R., Poucher, S. M., Nicholson, J. K., Holmes, E. C., Wilson, I. D., & Marchesi, J. R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100916 · Cited by 46
“5%) [7].”
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Song, H., Han, W., Yan, F., Xu, D., Chu, Q., & Zheng, X. (2015) · Journal of Functional Foods · doi:10.1016/j.jff.2015.10.022 · Cited by 44
The Role of the Gut Microbiota in Childhood Obesity
Pihl, A. F., Fonvig, C. E., Stjernholm, T., Hansen, T. F., Pedersen, O. B., & Holm, J. (2016) · Childhood Obesity · doi:10.1089/chi.2015.0220 · Cited by 49
Roles of Hepatic Innate and Innate-Like Lymphocytes in Nonalcoholic Steatohepatitis
Chen, Y., & Tian, Z. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01500 · Cited by 47
Self-citationGut microbiota as a key player in triggering obesity, systemic inflammation and insulin resistance.
Escobedo, G., López‐Ortiz, E., & Torres-Castro, I. (2014) · PubMed · Cited by 42
Lei, Z., Wu, H., Yang, Y., Hu, Q. C., Lei, Y., Liu, W., Nie, Y., Yang, L., Zhang, X., Yang, C., et al. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.708838 · Cited by 42
Role of Stress, Depression, and Aging in Cognitive Decline and Alzheimer’s Disease
Daulatzai, M. A. (2014) · Current topics in behavioral neurosciences · doi:10.1007/7854_2014_350 · Cited by 42
“Age affects the gut microbiota with a decrease in beneficial organisms such as anaerobes and bifidobacteria and an increase in enterobacteria (Woodmansey 2007; Guigoz et al. 2008; Hildebrandt et al. 2009; Jumpertz et al. 2011).”
BackgroundMorphoquantitative analysis of the Ileum of C57BL/6 mice (Mus musculus) fed with a high-fat diet.
Navarrete, J. G., Vásquez, B., & Sol, M. D. (2015) · PubMed Central · Cited by 41
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“In this study, a combination of probiotic strains will be used, as there are suggestions that multispecies products are more effective than single strain products [45,46].”
BackgroundThe microbiota in inflammatory bowel disease: friend, bystander, and sometime-villain
Shanahan, F. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00502.x · Cited by 43
Onishi, J. C., Campbell, S. C., Moreau, M., Patel, F. B., Brooks, A. I., Zhou, Y. X., Häggblom, M. M., & Storch, J. (2017) · Microbiology · doi:10.1099/mic.0.000496 · Cited by 41
“Others have also reported an increase in the Firmicutes to Bacteroidetes ratio in faecal samples collected from mice fed an HF diet [10, 11].”
BackgroundMethodInfluentialGao, Z., Wu, H., Zhang, K., Hossen, I., Wang, J., Wang, C., Xu, D., Xiao, J., & Cao, Y. (2019) · Journal of Functional Foods · doi:10.1016/j.jff.2019.103663 · Cited by 42
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“It has been reported that a high-fat diet (HFD) is a potent inducer of gut microbiota imbalance (dysbiosis) and responsible for the development of metabolic diseases (obesity or diabetes) [7].”
BackgroundMethodDing, Q., Guo, R., Pei, L., Lai, S., Li, J., Yin, Y., Xu, T., Yang, W., Song, Q., Han, Q., et al. (2022) · Food & Function · doi:10.1039/d1fo03952k · Cited by 41
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Critical Correlation Between Obesity and Cardiovascular Diseases and Recent Advancements in Obesity
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“Another study comparing obese and lean twins discovered that while there was no discernible difference in the proportion of Firmicutes, obese individuals had lower bacterial diversity and a higher abundance of Actinobacteria [25].”
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“In murine models, high fat diets have been associated with lower bacteroidetes to firmicutes ratio (Hildebrandt et al., 2009; Ding et al., 2010), while in humans both high fat diets and high protein diets have been shown to reduce the relative abundance of bacteroidetes (Russell et al.”
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“(Hildebrandt et al., 2009) in the families of Bacteroidaceae, Prevotellaceae and Rikenellaceae.”
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Tang, W., Zhu, G., Shi, Q., Yang, S., Ma, T., Mishra, S. K., Wen, A., Xu, H., Wang, Q., Jiang, Y., et al. (2019) · MicrobiologyOpen · doi:10.1002/mbo3.789 · Cited by 40
“This speculation is in agreement with a previous study of the composition ratio of Bacteroidetes in obese and lean hosts in which more Bacteroidetes were found in lean hosts (Filippo et al., 2010; Hildebrandt et al., 2009).”
ResultHigh-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner
Hases, L., Archer, A., Indukuri, R., Birgersson, M., Savva, C., Korach-André, M., & Williams, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-73166-1 · Cited by 42
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“Another study compared the effects of glucose and fructose after a feeding period of 12 weeks [29], while in another study, mice were fed HF diets for 21 weeks before feces collection [30].”
BackgroundGut microbiota and sirtuins in obesity-related inflammation and bowel dysfunction
Lakhan, S. E., & Kirchgessner, A. L. (2011) · Journal of Translational Medicine · doi:10.1186/1479-5876-9-202 · Cited by 41
“Members of the Bacteroidetes and Firmicutes phyla have been shown to be influenced by HF feeding and obesity [32-34].”
BackgroundKwon, J., Kim, B., Lee, C., Joung, H., Kim, B.-K., Choi, I. S., & Hyun, C. (2020) · PLoS ONE · doi:10.1371/journal.pone.0228932 · Cited by 39
“At the phylum level, while the HFD-induced microbiota dysbiosis was characterized by increased Actinobacteria and decreased Bacteroidetes compared to ND-fed controls, the abundance of Actinobacteria was significantly lower in both low- and high-dose L. plantarum treated groups (in the case of Bacteroidetes, higher abu…”
BackgroundInfluentialThe role of gut microbiome in chemical-induced metabolic and toxicological murine disease models
Dey, P. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.118172 · Cited by 44
Ethnic variability associating gut and oral microbiome with obesity in children
Balakrishnan, B., Selvaraju, V., Chen, J., Ayine, P., Yang, L., Babu, J. R., Geetha, T., & Taneja, V. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1882926 · Cited by 41
Steegenga, W. T., Mischke, M., Lute, C., Boekschoten, M. V., Lendvai, Á., Pruis, M. G. M., Verkade, H. J., van de Heijning, B. J. M., Boekhorst, J., Timmerman, H. M., et al. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600141 · Cited by 39
“However, the abundance of bacterial families not affected by the WS diet (Bacteroidaceae, Porphyromonadaceae, and Lachnospiraceae) correlated with the expression of genes playing a key role in intestinal development and functioning (e.g. Pitx2 and Ace2).”
BackgroundThe effects of time-restricted feeding on lipid metabolism and adiposity
Chaix, A., & Zarrinpar, A. (2015) · Adipocyte · doi:10.1080/21623945.2015.1025184 · Cited by 40
Oami, T., Shimazui, T., Yumoto, T., Otani, S., Hayashi, Y., & Coopersmith, C. M. (2025) · Journal of Intensive Care · doi:10.1186/s40560-025-00786-y · Cited by 42
“Furthermore, studies indicate that excessive fat intake is associated with increased proportions of Firmicutes and Proteobacteria , which have been linked to obesity in animal models, while weight loss through dietary restriction can help restore the microbiome to its original state [119].”
Troy, A. E., Simmonds, S., Stocker, S. D., & Browning, K. N. (2015) · The Journal of Physiology · doi:10.1113/jp271558 · Cited by 38
“…neurons is not yet clear, it is known that chronic ingestion of HFD alters the gut microbiota and induces intestinal inflammation (Cani et al. 2008; Hildebrandt et al. 2009; de La Serre et al. 2010; Ding et al. 2010), insulin resistance in neurons (reviewed in Kim & Feldman, 2012) and alters…”
BackgroundTakakura, K., Oikawa, T., Nakano, M., Saeki, C., Torisu, Y., Kajihara, M., & Saruta, M. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.00762 · Cited by 40
Metadata
- Authors
- Hildebrandt, M. A., Hoffmann, C., Sherrill–Mix, S. A., Keilbaugh, S. A., Hamady, M., Chen, Y., Knight, R., Ahima, R. S., Bushman, F., & Wu, G. D.
- Affiliations
- University of Pennsylvania (US)
- University of Colorado Boulder (US)
- Corresponding author
- Bushman, Frederic
- Wu, Gary D.
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2009-11
- Volume
- 137
- Issue
- 5
- Pages
- 1716-1724.e2
- ISSN
- 0016-5085 (ISSN-L)
- PMC
- PMC2770164
- OpenAlex
- W2158630697
- Cited by
- 1,576
- References
- 43
- Citations by year
- 2026: 40 · 2025: 61 · 2024: 96 · 2023: 76 · 2022: 130 · 2021: 117 · 2020: 158 · 2019: 148 · 2018: 115 · 2017: 94 · 2016: 104 · 2015: 96 · 2014: 87 · 2013: 82 · 2012: 71
- FWCI
- 22.84
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Gastroenterology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- University of Pennsylvania
- National Institutes of Health
- National Human Genome Research Institute (R01HG004872, HG004872)
- National Institute of General Medical Sciences (T32GM065103)
- National Institute of Allergy and Infectious Diseases (R01AI039368, AI39368)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-50306, DK078669, P01DK078669, DK-019525, DK062348, R01DK062348, R56DK062348, P30DK019525, P30DK050306)
- National Center for Research Resources (S10RR024525)
- 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 › Endocrinology, Diabetes and Metabolism › Adipokines, Inflammation, and Metabolic Diseases
- Keywords
- gut microbiota, high-fat diet, obesity, diet-induced obesity, Bacteroidetes, Firmicutes, Proteobacteria, gut microbiota composition, metagenomics, microbial gene content, 16S rRNA gene sequencing
- MeSH terms
- Animals, Diet, Dietary Fats, Female, Hormones, Ectopic, Intestines, Mice, Inbred C57BL, Obesity, RNA, Ribosomal, 16S, Mice, Knockout, Intercellular Signaling Peptides and Proteins, Mice, Metagenome
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