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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
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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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BackgroundNutrition in Inflammatory Bowel Disease
Schreiner, P., Martinho-Grueber, M., Studerus, D., Vavricka, S. R., Tilg, H., Biedermann, L., & on behalf of Swiss IBDnet, A. O. W. G. O. T. S. S. O. G. (2020) · Digestion · doi:10.1159/000505368 · Cited by 110
Characterization of the Gastrointestinal Microbiota in Health and Inflammatory Bowel Disease
Cruz, P. P. D., Prideaux, L., Wagner, J., Ng, S. C., McSweeney, C. S., Kirkwood, C. D., Morrison, M., & Kamm, M. A. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21751 · Cited by 97
“Germ-free mice receiving adult human fecal transplants subsequently transmitted their microbial community to their offspring.(87) A study employing culture of enteric bacteria showed that the fecal-associated microbiota (FAM) of monozygotic”
BackgroundPu, S., Khazanehei, H., Jones, P. J. H., & Khafipour, E. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01612 · Cited by 95
den Abbeele, P. V., Taminiau, B., Pinheiro, I., Duysburgh, C., Jacobs, H., Pijls, L. T. J., & Marzorati, M. (2018) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.7b04611 · Cited by 97
Zacarías, M. F., Collado, M. C., Gómez-Gallego, C., Flinck, H., Aittoniemi, J., Isolauri, E., & Salminen, S. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200305 · Cited by 102
Preguiça, I., Alves, A., Nunes, S., Fernandes, R., Gomes, P., Viana, S., & Reis, F. (2020) · Obesity Reviews · doi:10.1111/obr.13081 · Cited by 123
“At the same time, the microbial composition is highly shaped by dietary substrates, and HFD supply has been associated with changes in gut microbial composition and diversity, often referred to as obese microbiota.(271) Conversely, other studies reported body fat accumulation, hepatic steatosis and fasting hyperglycae…”
BackgroundDiet leaves a genetic signature in a keystone member of the gut microbiota
Dapa, T., Ramiro, R. S., Pedro, M. F., Gordo, I., & Xavier, K. B. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.01.002 · Cited by 91
Houghton, D., Hardy, T., Stewart, C. J., Errington, L., Day, C. P., Trenell, M. I., & Avery, L. (2018) · Diabetologia · doi:10.1007/s00125-018-4632-0 · Cited by 97
Alteration of gut microbiota induced by DPP-4i treatment improves glucose homeostasis
Liao, X., Song, L., Zeng, B., Liu, B., Qiu, Y., Qu, H., Zheng, Y., Long, M., Zhou, H., Wang, Y., et al. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.03.057 · Cited by 98
“Previous studies have revealed that HFD results in a shift of the gutmicrobiota that is correlated with increasing plasma glucose and glucose intolerance [17,56,57].”
BackgroundGut microbiome interventions in human health and diseases
Nie, P., Li, Z., Wang, Y., Zhang, Y., Zhao, M., Luo, J., Du, S., Deng, Z., Chen, J., Wang, Y., et al. (2019) · Medicinal Research Reviews · doi:10.1002/med.21584 · Cited by 94
“detailed taxonomic units, transplanting microbes from human feces into the intestines of sterile mice to transform them into so‐called humanized mice sheds light on the function of the human gut microbiota, but researchers have still failed to establish a subset of human‐derived gut microbes.(151,253,254) Furthermore,…”
BackgroundMucin-derived O -glycans supplemented to diet mitigate diverse microbiota perturbations
Pruss, K. M., Marcobal, A. M., Southwick, A. M., Dahan, D., Smits, S. A., Ferreyra, J. A., Higginbottom, S. K., Sonnenburg, E. D., Kashyap, P., Choudhury, B., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-00798-6 · Cited by 101
Hu, Y., Łukasik, P., Moreau, C. S., & Russell, J. A. (2013) · Molecular Ecology · doi:10.1111/mec.12607 · Cited by 95
Beilharz, J. E., Kaakoush, N. O., Maniam, J., & Morris, M. J. (2016) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2016.07.151 · Cited by 93
Commensal flora and the regulation of inflammatory and autoimmune responses
Kranich, J., Maslowski, K. M., & Mackay, C. R. (2011) · Seminars in Immunology · doi:10.1016/j.smim.2011.01.011 · Cited by 93
Huang, K., Dong, W., Liu, W., Yan, Y., Wan, P., Peng, Y., Xu, Y., Zeng, X., & Cao, Y. (2019) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.9b04411 · Cited by 93
Song, E., Han, K., Lim, T.-J., Lim, S., Chung, M.-J., Nam, M. H., Kim, H., & Nam, Y. (2020) · The EPMA Journal · doi:10.1007/s13167-020-00198-y · Cited by 101
The human microbiome in the 21st century
Rackaityte, E., & Lynch, S. V. (2020) · Nature Communications · doi:10.1038/s41467-020-18983-8 · Cited by 101
Raufaste-Cazavieille, V., Santiago, R., & Droit, A. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.962743 · Cited by 101
The human microbiome in hematopoiesis and hematologic disorders
Manzo, V. E., & Bhatt, A. S. (2015) · Blood · doi:10.1182/blood-2015-04-574392 · Cited by 95
“In a nowclassic study, adult germ-freemicewere colonized by the microbiota of obese mice or lean mice; the mice colonized with an obese microbiota had a significantly greater percentage increase in total body fat 2 weeks later.(9) As has been clearly demonstrated, the microbiota is critical for the proper maturation o…”
BackgroundLiu, T., Hougen, H. Y., Vollmer, A. C., & Hiebert, S. M. (2012) · Anaerobe · doi:10.1016/j.anaerobe.2012.02.004 · Cited by 100
“proportion stabilizing in as few as seven days [8,9].”
BackgroundResultInfluentialLearning from microbial strategies for polysaccharide degradation
Hemsworth, G. R., Déjean, G., Davies, G. J., & Brumer, H. (2016) · Biochemical Society Transactions · doi:10.1042/bst20150180 · Cited by 96
de Moraes, A. C. F., de Almeida-Pititto, B., Fernandes, G. D. R., Gomes, E. P., Pereira, A. C., & Ferreira, S. R. G. (2017) · Diabetology & Metabolic Syndrome · doi:10.1186/s13098-017-0261-x · Cited by 97
“However, our result is concordant with a report of an association of high abundance of Bacilli with the western diet [53] and diabetes [54], both conditions associated with low-grade inflammation and insulin resistance.”
ResultEvolving Concepts: How Diet and the Intestinal Microbiome Act as Modulators of Breast Malignancy
Shapira, I., Sultan, K. S., Lee, A., & Taioli, E. (2013) · ISRN Oncology · doi:10.1155/2013/693920 · Cited by 96
Antiobesity molecular mechanisms of action: Resveratrol and pterostilbene
Pan, M., Wu, J.-C., Ho, C., & Lai, C. (2018) · BioFactors · doi:10.1002/biof.1409 · Cited by 96
“The experimental data suggested that gut microbiota manipulation through dietary intervention may be beneficial for the treatment of obesity [72,73].”
BackgroundFlavonoids and Colorectal Cancer Prevention
Li, Y., Zhang, T., & Chen, G. (2018) · Antioxidants · doi:10.3390/antiox7120187 · Cited by 95
“There is increasing evidence that the gut microbiome can also contribute to colorectal cancer risk, and changes in the gut microbiome are strongly linked to the diet, which in turn, has been associated with colorectal cancer risk [13,14].”
BackgroundInteractions Between Food and Gut Microbiota: Impact on Human Health
Wu, Y., Wan, J., Choe, U., Pham, Q., Schoene, N. W., He, Q., Li, B., Yu, L. L., & Wang, T. T. Y. (2019) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-032818-121303 · Cited by 96
Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal
Kearney, S. M., Gibbons, S. M., Erdman, S. E., & Alm, E. J. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.07.032 · Cited by 90
Improved 18S and 28S rDNA primer sets for NGS-based parasite detection
Kounosu, A., Murase, K., Yoshida, A., Maruyama, H., & Kikuchi, T. (2019) · Scientific Reports · doi:10.1038/s41598-019-52422-z · Cited by 92
Yang, Y., Ye, H., Zhao, C., Ren, L., Wang, C., Georgiev, M. I., Xiao, J., & Zhang, T. (2021) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2021.117668 · Cited by 94
Díez-Sainz, E., Lorente‐Cebrián, S., Aranaz, P., Riezu‐Boj, J. I., Martínez, J. A., & Milagro, F. I. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.586564 · Cited by 94
Silva, D., Viana, S., Carvalho, E., Reis, F., & Matafome, P. N. (2023) · Internal and Emergency Medicine · doi:10.1007/s11739-023-03262-3 · Cited by 103
“In fact, in C57BL/6 J mice, HFD consumption for 4 weeks, was sufficient to induce marked alterations in gut flora composition [21–24], and fecal transplantation to germ-free mice induced a massive increase in adiposity [19].”
BackgroundInfluentialAlteration of the rat cecal microbiome during colonization with the helminthHymenolepis diminuta
McKenney, E. A., Williamson, L. L., Yoder, A. D., Rawls, J. F., Bilbo, S. D., & Parker, W. (2015) · Gut Microbes · doi:10.1080/19490976.2015.1047128 · Cited by 94
Valatas, V., Bamias, G., & Kolios, G. C. (2015) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2015.03.017 · Cited by 92
“Furthermore, transplantation of adult human fecal microbiota into germ-free mice has been found to establish a relatively stable gut community in the recipient mice similar to that of the donor that can be partly transferred from generation to generation (Turnbaugh et al., 2009).”
BackgroundMacronutrients mediate the functional relationship between Drosophila and Wolbachia
Ponton, F., Wilson, K. L., Holmes, A. J., Raubenheimer, D., Robinson, K. L., & Simpson, S. J. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2014.2029 · Cited by 92
“While the specific nutritional components influencing infection dynamics have not always been clearly identified, recent research on gut microbiota has shown that dietary macronutrients, notably protein (P) and carbohydrate (C), have a major impact on bacterial species composition and abundance [31–35].”
BackgroundMeisel, M., Mayassi, T., Fehlner-Peach, H., Koval, J., O'Brien, S. L., Hinterleitner, R., Lesko, K., Kim, S. M., Bouziat, R., Chen, L., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.114 · Cited by 95
“Furthermore, an important immune regulatory role played by the microbiota is linked to its ability to produce short chain fatty acids (SCFAs), in particular butyrate (Turnbaugh et al., 2009; Maslowski and Mackay, 2011).”
BackgroundMicrobiota intestinal en la salud y la enfermedad
Icaza-Chávez, M. E. (2013) · Revista de Gastroenterología de México · doi:10.1016/j.rgmx.2013.04.004 · Cited by 114
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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