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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Open accessAbstract
A translational medicine pipeline is described where human gut microbial communities and diets are re-created in gnotobiotic mice and the impact on microbe and host is defined using metagenomics.
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“The majority of studies in humans and mice rely on faecal samples, which provide some representation of what is occurring throughout the digestive tract”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [120]
In the citing paper
“aspects of microbial communities and host responses that are specific to the small intestine might be obscured by faecal sampling119,120.”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [120]
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“Our study corroborates previous studies showing an association between altered diets and an increase in Erysipelotrichi and Allobaculum, but various effects are shown for fat-enriched diets 29, 30, 31, 32.”
From The composition of the gut microbiota shapes the colon mucus barrier (2015) · cites this paper as [32]
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 [206]
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“was associated with a change in the ecology of the intestinal microbiota [6,7] with an increase in gram-negative bacteria.”
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Overtraining Syndrome as a Complex Systems Phenomenon
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Regulating inflammation with microbial metabolites
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Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire
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“A major part of the gradual change in gut microbiota is likely caused by a shift in diet (Doré & Blottiere, 2015; Turnbaugh et al., 2009).”
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“Massive changes to gut microbial community structure are detectablewithin 1 day of consuming the Western diet, well before a clear host phenotype emerges (Turnbaugh et al., 2009).”
BackgroundSelf-citationMicrobiome engineering: enhancing climate resilience in corals
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Gut microbiota in wild and captive Guizhou snub‐nosed monkeys, Rhinopithecus brelichi
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“Diet also affects microbial composition (David et al., 2014; Muegge et al., 2011; Turnbaugh et al., 2009).”
Self-citationJejunum: The understudied meeting place of dietary lipids and the microbiota
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A dietary change to a high-fat diet initiates a rapid adaptation of the intestine
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Innate inflammation in type 1 diabetes
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“More recently, successful transplantation of human fresh or frozen fecal microbial communities into germ-free mice resulted in microbial diversity in the humanized gnotobiotic mice that closely resembled that of the host (60).”
Zhang, L., Bahl, M. I., Roager, H. M., Fonvig, C. E., Hellgren, L. I., Frandsen, H. L., Pedersen, O. B., Holm, J., Hansen, T. F., & Licht, T. R. (2016) · The ISME Journal · doi:10.1038/ismej.2016.151 · Cited by 83
“The fraction of bacterial taxa from human faecal microbiota that establishes in transplanted mice is 50–90% at the genus level (Turnbaugh et al., 2009; Ridaura et al., 2013).”
BackgroundImpact of dietary gut microbial metabolites on the epigenome
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Human Gut Microbiome Response Induced by Fermented Dairy Product Intake in Healthy Volunteers
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“While data on clinical associations for this bacterial family are ambiguous, there are a number of studies linking their increased abundance to inflammatory bowel diseases, as well as obesity, while other studies suggest opposite associations [42,43].”
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From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome
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“man donor sample and the opposite (low Clostridia and high Erysipelotrichi abundance) in the recipient mice (11).”
BackgroundGut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality?
Morán‐Ramos, S., López-Contreras, B. E., & Canizales‐Quinteros, S. (2017) · Archives of Medical Research · doi:10.1016/j.arcmed.2017.11.003 · Cited by 91
Dietary sugar silences a colonization factor in a mammalian gut symbiont
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BackgroundThe Role of the Gut Microbiome in Energy Balance With a Focus on the Gut-Adipose Tissue Axis
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“Each of these methods has distinct advantages and disadvantages, as described previously [3,7,8] and summarized in Table 1.”
MethodAlignment and clustering of phylogenetic markers - implications for microbial diversity studies
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“As 16S rRNA surveys are increasingly applied in a clinical setting [5,32-35] (e.g. to determine how microbiota correlate with human disease states), it is critical to accurately measure taxonomic diversity and identify individual species.”
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Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice
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“(45) where a Western diet induced an enrichment of genes for transporters and ABC transporters in the cecal microbiota of humanized gnotobiotic mice compared to mice receiving a low-fat diet.”
BackgroundThe Challenge of Maintaining a Healthy Microbiome during Long-Duration Space Missions
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“It is likely that these negative effects might be potentially controlled or even prevented by diet-based therapies proven to promote a healthier GI microbial composition, such as those with a higher content of fiber (Turnbaugh et al., 2009; Zeng et al., 2014).”
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“Higher adiposity has also been observed in conventional mice on autoclaved normal diets, as well as high fat diets, compared to germ-free mice [80,85].”
BackgroundInfluentialGut Microbiota: The Missing Link Between Helicobacter pylori Infection and Metabolic Disorders?
Martín‐Núñez, G. M., Cornejo-Pareja, I. M., Clemente‐Postigo, M., & Tinahones, F. J. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.639856 · Cited by 86
“Yanagi et al., reported that changes in the Bacteroidetes:Firmicutes ratio were inversely related to changes in plasma ghrelin levels after the administration of triple therapy forH. pylori eradication (24).”
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“Future research over a longer experimental period, the use of humanized gnotobiotic mice [57], and well-designed human studies is warranted to further investigate the impact of dietary intervention on gut microbiota and physiological functions.”
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Background
Metadata
- Authors
- Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- University of Colorado Boulder (US)
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Science Translational Medicine
- Published
- 2009-11-11
- Volume
- 1
- Issue
- 6
- Pages
- 6ra14-6ra14
- ISSN
- 1946-6234 (ISSN-L)
- 1946-6242
- PMC
- PMC2894525
- OpenAlex
- W2136552678
- Cited by
- 3,058
- References
- 27
- Citations by year
- 2026: 71 · 2025: 112 · 2024: 140 · 2023: 158 · 2022: 201 · 2021: 251 · 2020: 269 · 2019: 288 · 2018: 248 · 2017: 246 · 2016: 237 · 2015: 198 · 2014: 183 · 2013: 173 · 2012: 131
- FWCI
- 37.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science Translational Medicine (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Crohn's and Colitis Foundation
- National Institute of Diabetes and Digestive and Kidney Diseases (DK 70977, R01DK070977)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- gut microbiota, diet, fecal microbiota transplantation, Western diet, high-fat high-sugar diet, bacterial colonization, intergenerational transmission, adiposity, metabolic pathways, germ-free mice, 16S rRNA gene sequences
- MeSH terms
- Animals, Bacteria, Diet, Energy Metabolism, Germ-Free Life, Humans, Intestines, Male, Mice, Inbred C57BL, Molecular Sequence Data, RNA, Ribosomal, 16S, Genomics, Adiposity, Mice
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