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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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An obesity-associated gut microbiome with increased capacity for energy harvest
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Items 201–300 of 1,018
Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet
Bisanz, J. E., Upadhyay, V., Turnbaugh, J. A., Ly, K., & Turnbaugh, P. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.06.013 · Cited by 333
“…ENA ERP008902 Park 2013 SRA ERP000935 Perry 2016 SRA ERP015064 Roopchand 2015 MGRAST mgp13326 Ruan 2016 SRA SRP074626 Turnbaugh 2008 SRA SRP154925 Turnbaugh 2009 SRA SRP154925 Ussar 2015 SRA ERP010838 Volynets 2017 SRA SRP072537 Wu 2011 SRA SRP002424 Xiao 2015 SRA ERP008710 Xiao 2017 SRA…”
Self-citationden Abbeele, P. V., Grootaert, C., Marzorati, M., Possemiers, S., Verstraete, W., Gérard, P., Rabot, S., Bruneau, A., Aidy, S. E., Derrien, M., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00759-10 · Cited by 359
“Such new strategies are often evaluated during human trials or in vivo studies of animals associated with conventional or human microbiota (50).”
BackgroundProbiotics in prevention and treatment of obesity: a critical view
Kobyliak, N. M., Conte, C., Cammarota, G., Haley, A. P., Štyriak, I., Gašpar, Ľ., Fusek, J., Rodrigo, L., & Kružliak, P. (2016) · Nutrition & Metabolism · doi:10.1186/s12986-016-0067-0 · Cited by 373
“a low-fat, plant polysaccharide-rich diet to a high-fat/ high-sugar “Western” diet may shift the structure of the microflora within a single day, changing the representation of metabolic pathways and altering microbiome gene expression [26].”
BackgroundA Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Finucane, M. M., Sharpton, T. J., Laurent, T. J., & Pollard, K. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084689 · Cited by 321
“The substantial between-study variability could be due to an unmeasured factor such as diet [22] or due to technical factors such as DNA extraction technique, region of the 16 S locus targeted, or sequencing platform [23].”
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“Moreover, relatively small differences in individual diets, or minor differences in the interaction between the host immune system and the gut microbiota, that affect keystone species may be sufficient to organize gut microbial consortia into distinct types of communities, or ‘‘enterotypes’’ [24,25].”
BackgroundSodium chloride inhibits the suppressive function of FOXP3+ regulatory T cells
Hernandez, A., Kitz, A., Wu, C., Lowther, D. E., Rodriguez, D. M., Vudattu, N. K., Deng, S., Herold, K. C., Kuchroo, V. K., Kleinewietfeld, M., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci81151 · Cited by 345
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“If an individual’s gut microbiota can shift over the course of days, weeks, or months in response to changes in diet [28–30], associated shifts in host digestive efficiency may make meeting nutritional demands less challenging for animals during periods of resource limitation [31–33].”
BackgroundComputational meta'omics for microbial community studies
Segata, N., Boernigen, D., Tickle, T. L., Morgan, X. C., Garrett, W. S., & Huttenhower, C. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.22 · Cited by 347
Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice
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“This notion is supported by previous reports showing that the gut microbiota of both human and mice can change very rapidly with an alteration in diet (25, 26).”
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“Obese (ob/ob) mice and diet-induced obese mice are characterized by an altered composition of the gut microbiota (Ley et al., 2005; Cani et al., 2007a,b; Turnbaugh et al., 2008, 2009).”
BackgroundBenedict, C., Vogel, H., Jonas, W., Woting, A., Blaut, M., Schürmann, A., & Cedernaes, J. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.10.003 · Cited by 324
Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice
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“Bacteroides spp. concentrations were increased at day 2 but were low at 8 weeks.”
InfluentialThe gut microbiota in obesity and weight management: microbes as friends or foe?
Hul, M. V., & Cani, P. D. (2023) · Nature Reviews Endocrinology · doi:10.1038/s41574-022-00794-0 · Cited by 353
Immune homeostasis, dysbiosis and therapeutic modulation of the gut microbiota
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Altered Gut Microbiome Composition and Tryptic Activity of the 5xFAD Alzheimer’s Mouse Model
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Gut microbiota and the polycystic ovary syndrome: influence of sex, sex hormones, and obesity
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A taxonomic signature of obesity in a large study of American adults
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“were RYGB-specific and different from changes due to weight loss interventions [26].”
BackgroundSeasonal Variation in Human Gut Microbiome Composition
Davenport, E. R., Mizrahi-Man, O., Michelini, K., Barreiro, L. B., Ober, C., & Gilad, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090731 · Cited by 314
Sewage Reflects the Microbiomes of Human Populations
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“Given the relatively minor difference in population obesity percentage (as low as 9%) between city populations considered lean and obese, the observed correlations between obesity and the microbial community in sewage might reflect other, more pronounced lifestyle differences in these cities, including the influence o…”
BackgroundImpact of the gut microbiota on the development of obesity and type 2 diabetes mellitus
Moreno‐Indias, I., Cardona, F., Tinahones, F. J., & Queipo‐Ortuño, M. I. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00190 · Cited by 325
“The prevalence of obesity and its associated disorders, such as type 2 diabetes mellitus (TDM2), has increased substantially worldwide over the last decades.”
BackgroundThe Human Microbiome and Its Potential Importance to Pediatrics
Johnson, C. L., & Versalovic, J. A. (2012) · PEDIATRICS · doi:10.1542/peds.2011-2736 · Cited by 317
Gut Microbiota, Intestinal Permeability, Obesity‐Induced Inflammation, and Liver Injury
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“The use of this “humanized” mouse model may be very useful in future investigations on the role of diet and other interventions on the gut microbiota and its function.(33) Several other investigators have now confirmed changes in the microbiota composition and the development of an inflammatory response in mice ingest…”
MethodChallenges and Opportunities of Metabolomics
Johnson, C. H., & Gonzalez, F. J. (2012) · Journal of Cellular Physiology · doi:10.1002/jcp.24002 · Cited by 287
“These mice are germ-free at birth and are colonized with human adult fecal microbiota (Turnbaugh et al., 2009) or human newborn fecal microbiota (Martin et al., 2007).”
BackgroundCurtis, M. M., Hu, Z., Klimko, C., Narayanan, S. K., DeBerardinis, R. J., & Sperandio, V. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.005 · Cited by 316
“…composition exist between healthy and diseased patients; however, it is not well understood if these shifts occur prior to disease or are a product of the disease (Gevers et al., 2014; Larsen et al., 2010; Peterson et al., 2008; Turnbaugh et al., 2009a; Turnbaugh et al., 2009b; Wang et al., 2009).”
Mining the microbiota for microbial and metabolite-based immunotherapies
Skelly, A. N., Sato, Y., Kearney, S., & Honda, K. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-019-0144-5 · Cited by 306
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“The intestinal microbiota plays a demonstrable role in weight gain/loss (24–30) and energy extraction from the diet (29,30,36) in human and animal models.”
BackgroundInfluences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases
Paul, B., Barnes, S., Demark-Wahnefried, W., Morrow, C., Salvador, C., Skibola, C., & Tollefsbol, T. O. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0144-7 · Cited by 306
“It has been shown that maternal and neonatal nutrition have a major impact on the epigenome of the offspring in that the food consumed modulates the composition of the gut microbiota and also the metabolites that they produce [89].”
BackgroundGut microbiota dictates the metabolic response ofDrosophilato diet
Wong, A. C.-N., Dobson, A. J., & Douglas, A. E. (2014) · Journal of Experimental Biology · doi:10.1242/jeb.101725 · Cited by 311
“DISCUSSION It is widely recognized that the relationship between animals and their gut microbiota involves multiple interactions that vary with composition of the microbiota, host genotype and environmental factors, especially diet (Faith et al., 2011; Human Microbiome Project Consortium, 2012; Kau et al., 2011; Turnb…”
BackgroundEffects of the gut microbiota on obesity and glucose homeostasis
Greiner, T. U., & Bäckhed, F. (2011) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2011.01.002 · Cited by 312
The impact of rearing environment on the development of gut microbiota in tilapia larvae
Giatsis, C., Sipkema, D., Smidt, H., Heilig, H. G. H. J., Benvenuti, G., Verreth, J. A. J., & Verdegem, M. C. J. (2015) · Scientific Reports · doi:10.1038/srep18206 · Cited by 311
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McNulty, N. P., Wu, M., Erickson, A. R., Pan, C., Erickson, B. K., Martens, E. C., Pudlo, N. A., Muegge, B. D., Henrissat, B., Hettich, R. L., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001637 · Cited by 298
“composition and function of the microbiota [6–10].”
Self-citationKashyap, P. C., Marcobal, A., Ursell, L. K., Smits, S. A., Sonnenburg, E. D., Costello, E. K., Higginbottom, S. K., Domino, S. E., Holmes, S. P., Relman, D. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306070110 · Cited by 285
“We show how mice harboring a transplanted human gut microbiota can be used to study the interplay of host fucosylated glycans and dietary glycan availability on the composition and function of the microbiota under well defined and controlled environmental conditions (25).”
BackgroundSelf-citationMiranda, P. M., Palma, G. D., Serkis, V., Lu, J., Louis-Auguste, M., McCarville, J. L., Verdu, E. F., Collins, S. M., & Berčík, P. (2018) · Microbiome · doi:10.1186/s40168-018-0433-4 · Cited by 302
Food, immunity, and the microbiome
Tilg, H., & Moschen, A. R. (2015) · Gastroenterology · doi:10.1053/j.gastro.2014.12.036 · Cited by 292
Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection
Zackular, J. P., Moore, J. L., Jordan, A. T., Juttukonda, L. J., Noto, M. J., Nicholson, M. R., Crews, J. D., Semler, M. W., Zhang, Y., Ware, L. B., et al. (2016) · Nature Medicine · doi:10.1038/nm.4174 · Cited by 275
The Intestinal Microbiota in Metabolic Disease
Woting, A., & Blaut, M. (2016) · Nutrients · doi:10.3390/nu8040202 · Cited by 284
“Dietary modifications change the intestinal microbiota of mice and humans within one day [32,34,35].”
BackgroundResultInfluentialGut bacterial microbiota and obesity
Million, M., Lagier, J., Yahav, D., & Paul, M. (2013) · Clinical Microbiology and Infection · doi:10.1111/1469-0691.12172 · Cited by 297
“[28] successfully colonized mice with human faeces, and fed them with the western diet vs.”
BackgroundDiversity in gut bacterial community of school-age children in Asia
Nakayama, J., Watanabe, K., Jiang, J., Matsuda, K., Chao, S.-H., Haryono, P., La-ongkham, O., Sarwoko, M.-A., Sujaya, I. N., Zhao, L., et al. (2015) · Scientific Reports · doi:10.1038/srep08397 · Cited by 297
Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health
Parkar, S. G., Kalsbeek, A., & Cheeseman, J. F. (2019) · Microorganisms · doi:10.3390/microorganisms7020041 · Cited by 285
“The human intestine harbors a 10 trillion-cell microbial community that increases in abundance and diversity along the cephalocaudal axis with niche-specific variations in the spatial architecture of bacteria in the gut lumen and mucosal wall [10].”
BackgroundInfluentialComplementary symbiont contributions to plant decomposition in a fungus-farming termite
Poulsen, M., Hu, H., Li, C., Chen, Z., Xu, L., Otani, S., Nygaard, S., Nobre, T., Klaubauf, S., Schindler, P. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319718111 · Cited by 281
“Digestive symbiotic communities in animal guts provide excellent examples of such ambiguities; recent studies of human microbiotas show that gut communities vary by subject age, geography (5), and diet (6) and that deviating microbiotas can be associated with compromised health (7).”
Complexity and health functionality of plant cell wall fibers from fruits and vegetables
Padayachee, A., Day, L., Howell, K. S., & Gidley, M. J. (2015) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2013.850652 · Cited by 297
“, 2012), the majority of evidence shows that dietary intake does affect gut microbiota composition (Turnbaugh et al., 2009; Wu et al., 2011).”
BackgroundГригорьева, И. Н. (2020) · Journal of Personalized Medicine · doi:10.3390/jpm11010013 · Cited by 293
“Increased efficiency of energy harvest, due to alterations in the gut microbiota has been implicated in obesity in mice [31,32,62] and humans [38].”
BackgroundGut–liver axis, nutrition, and non-alcoholic fatty liver disease
Kirpich, I. A., Marsano, L. S., & McClain, C. J. (2015) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2015.06.023 · Cited by 327
“in mice [68], and from a high-fat/low-fiber diet to a low-fat/high-fiber diet in humans [70] caused”
BackgroundHOCKING, S. L., Samocha‐Bonet, D., Milner, K., Greenfield, J. R., & Chisholm, D. J. (2013) · Endocrine Reviews · doi:10.1210/er.2012-1041 · Cited by 295
Jiao, N., Baker, S. S., Nugent, C. A., Tsompana, M., Cai, L., Wang, Y., Buck, M. J., Genco, R. J., Baker, R. D., Zhu, R., et al. (2018) · Physiological Genomics · doi:10.1152/physiolgenomics.00114.2017 · Cited by 290
The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get
Yang, J., & Yu, J. Q. (2018) · Protein & Cell · doi:10.1007/s13238-018-0543-6 · Cited by 287
“…Western diet that is low in plant polysaccharides/fiber and high in fat, processed meat and sugar leads to a rapid shift in the composition and abundance of microbiome along with an increased Ki-67 index in colon tissues (Turnbaugh et al., 2008; 2009; David et al., 2014b; O’Keefe et al., 2015).”
BackgroundThe Role of Gut Microbiota on Insulin Resistance
Caricilli, A. M., & Saad, M. A. (2013) · Nutrients · doi:10.3390/nu5030829 · Cited by 285
“the microbiota within 24 h [33].”
Hyde, E. R., Haarmann, D. P., Lynne, A. M., BUCHELI, S. R., & Petrosino, J. F. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077733 · Cited by 287
“This clustering pattern is not surprising as other studies have shown that oral communities differ from GI tract communities [33,34,37,38].”
ResultMurphy, E. F., Cotter, P. D., Hogan, A., O’Sullivan, Ó., Joyce, A., Fouhy, F., Clarke, S. F., Marques, T. M., O’Toole, P. W., Stanton, C., et al. (2012) · Gut · doi:10.1136/gutjnl-2011-300705 · Cited by 283
Western diets, gut dysbiosis, and metabolic diseases: Are they linked?
Martinez, K., Leone, V., & Chang, E. B. (2017) · Gut Microbes · doi:10.1080/19490976.2016.1270811 · Cited by 291
“Transplant of microbes induced by Western diets or obesity result in an increase in fat mass in germ-free mouse recipients.(7,9) In contrast, transplant of gut microbiota from lean human individuals to those with metabolic syndrome has been shown to improve insulin sensitivity,(6)”
Backgroundvan den Munckhof, I., Kurilshikov, A., ter Horst, R., Riksen, N. P., Joosten, L. A. B., Zhernakova, A., Fu, J., Keating, S. T., Netea, M. G., Graaf, J. D., et al. (2018) · Obesity Reviews · doi:10.1111/obr.12750 · Cited by 281
“Similarly, faecal transfer from humans into germ-free mice mirrored the adiposity of its donor (106).”
BackgroundAdjusting microbiome profiles for differences in microbial load by spike-in bacteria
Stämmler, F., Gläsner, J., Hiergeist, A., Holler, E., Weber, D., Oefner, P. J., Gessner, A., & Spang, R. (2016) · Microbiome · doi:10.1186/s40168-016-0175-0 · Cited by 273
“In contrast to A. acidiphilus and R. radiobacter the ratios derived from relative abundances (standard data) of these OTUs is zero by experimental design.”
BackgroundInfluentialPostprandial remodeling of the gut microbiota in Burmese pythons
Costello, E. K., Gordon, J. I., Secor, S. M., & Knight, R. D. (2010) · The ISME Journal · doi:10.1038/ismej.2010.71 · Cited by 275
“E-mail: rob.knight@colorado.edu The ISME Journal (2010) 4, 1375–1385 & 2010 International Society for Microbial Ecology All rights reserved 1751-7362/10 www.nature.com/ismej intermittently available (Backhed et al., 2004; Ley et al., 2005; Turnbaugh et al., 2006, 2009a; Samuel et al., 2008).”
InfluentialSelf-citationGuo, C., Wang, Y., Zhang, S., Zhang, X., Du, Z., Li, M., & Ding, K. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.03.137 · Cited by 273
Xenobiotic Metabolomics: Major Impact on the Metabolome
Johnson, C. H., Patterson, A. D., Idle, J. R., & Gonzalez, F. J. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134748 · Cited by 285
“Studies have used germ-free mice transplanted with human adult fecal microbiota (90) and microflora isolated from human baby feces (91).”
MethodTargeting the gut microbiome to treat the osteoarthritis of obesity
Schott, E. M., Farnsworth, C. W., Grier, A., Lillis, J. A., Soniwala, S., Dadourian, G. H., Bell, R. D., Doolittle, M. L., Villani, D. A., Awad, H. A., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.95997 · Cited by 277
“…from it have already been established (63), and antagonizing proinflammatory species has been proposed as a disease-modifying strategy in pathologic conditions including obesity (19, 20, 23, 64) and several skeletal disorders including steroid-related bone loss (27) and rheumatoid arthritis (65).”
BackgroundGut microbiota phenotypes of obesity
Stanislawski, M. A., Dabelea, D., Lange, L. A., Wagner, B. D., & Lozupone, C. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-019-0091-8 · Cited by 273
Voluntary and forced exercise differentially alters the gut microbiome in C57BL/6J mice
Allen, J. M., Berg Miller, M. E., Pence, B. D., Whitlock, K., Nehra, V., Gaskins, H. R., White, B. A., Fryer, J. D., & Woods, J. A. (2015) · Journal of Applied Physiology · doi:10.1152/japplphysiol.01077.2014 · Cited by 266
“A large body of work has been aimed at understanding the environmental impacts, especially diet, on the GI microbiome (7, 17, 45).”
Long‐term monitoring of the human intestinal microbiota composition
Rajilić-Stojanović, M. D., Heilig, H. G. H. J., Tims, S., Zoetendal, E. G., & de Vos, W. M. (2012) · Environmental Microbiology · doi:10.1111/1462-2920.12023 · Cited by 286
Legrand, T. P. R. A., Wynne, J. W., Weyrich, L. S., & Oxley, A. P. A. (2019) · Reviews in Aquaculture · doi:10.1111/raq.12375 · Cited by 277
Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer
Bultman, S. J. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500902 · Cited by 275
Metabolic activities and probiotic potential of bifidobacteria
Russell, D. A., Ross, R. P., Fitzgerald, G. F., & Stanton, C. (2011) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2011.06.003 · Cited by 274
Bauer, P. V., Duca, F. A., Waise, T. M. Z., Rasmussen, B. A., Abraham, M. A., Dranse, H. J., Puri, A., O’Brien, C. A., & Lam, T. K. T. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2017.09.019 · Cited by 265
Guts and Gall: Bile Acids in Regulation of Intestinal Epithelial Function in Health and Disease
Hegyi, P., Maléth, J., Walters, J. R., Hofmann, A. F., & Keely, S. J. (2018) · Physiological Reviews · doi:10.1152/physrev.00054.2017 · Cited by 269
Biodiversity and functional genomics in the human microbiome
Morgan, X. C., Segata, N., & Huttenhower, C. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.09.005 · Cited by 271
“Furthermore, mice colonized with human gut microbiota showed large and rapid shifts in gut microbiome composition in response to diet; these were accompanied by stable changes in microbial taxa abundance and gene expression [43].”
BackgroundAraújo, J. R., Tomas, J., Brenner, C., & Sansonetti, P. J. (2017) · Biochimie · doi:10.1016/j.biochi.2017.05.019 · Cited by 271
The importance of the gut microbiota after bariatric surgery
Aron‐Wisnewsky, J., Dore, J. M., & Clément, K. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.161 · Cited by 271
Composition of the gut microbiota modulates the severity of malaria
Villarino, N. F., LeCleir, G. R., Denny, J. E., Dearth, S. P., Harding, C. L., Sloan, S. S., Gribble, J. L., Campagna, S. R., Wilhelm, S. W., & Schmidt, N. W. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1504887113 · Cited by 261
“Finally, dietary changes are capable of inducing significant changes in the gut microbiome (25) that reach steady state within 3–4 d in mice (26).”
BackgroundAshrafian, F., Shahryari, A., Behrouzi, A., Moradi, H. R., Raftar, S. K. A., Lari, A., Hadifar, S., Yaghoubfar, R., Badi, S. A., Khatami, S., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02155 · Cited by 268
Lundgren, S., Madan, J. C., Emond, J. A., Morrison, H. G., Christensen, B. C., Karagas, M. R., & Hoen, A. G. (2018) · Microbiome · doi:10.1186/s40168-018-0490-8 · Cited by 271
Gut microbiota and diabetes: from pathogenesis to therapeutic perspective
Burcelin, R., Sérino, M., Chabo, C., Blasco‐Baqué, V., & Amar, J. (2011) · Acta Diabetologica · doi:10.1007/s00592-011-0333-6 · Cited by 270
“[63, 64].”
Programming of Host Metabolism by the Gut Microbiota
Bäckhed, F. (2011) · Annals of Nutrition and Metabolism · doi:10.1159/000328042 · Cited by 267
Green areas around homes reduce atopic sensitization in children
Ruokolainen, L., Hertzen, L., Fyhrquist, N., Laatikainen, T., Lehtomäki, J., Auvinen, P., Karvonen, A. M., Hyvärinen, A., Tillmann, V., Niemelä, O., et al. (2015) · Allergy · doi:10.1111/all.12545 · Cited by 273
“To our knowledge, no previous study has investigated the relationship between the commensal microbiota and environmental land use, although it has been shown that, for example, microbiota in the gut is affected by diet (28, 29).”
BackgroundSweeney, T. E., & Morton, J. M. (2013) · JAMA Surgery · doi:10.1001/jamasurg.2013.5 · Cited by 252
“showed that fecal transplant from Westernized mice into germ-free mice was sufficient to induce obesity.(20) Only 2 studies have shown evidence contrary to the change in the Firmicutes to Bacteroidetes ratio in obesity: Schwiertz et al(17) and Zhang et al(19) showed a decrease in the phylum Firmicutes in obesity.”
BackgroundResultKrych, Ł., Hansen, C. H. F., Hansen, A. K., van den Berg, F. W. J., & Nielsen, D. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062578 · Cited by 256
“showed that a switch from a low fat to a high fat, high sugar diet in mice, which was associated with obesity, lowered the Bacteroidetes/Firmicutes ratio in the gut within one day [10].”
Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model
Hryckowian, A. J., Treuren, W. V., Smits, S. A., Davis, N. M., Gardner, J. O., Bouley, D. M., & Sonnenburg, J. L. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0150-6 · Cited by 239
McHardy, I. H., Li, X., Tong, M., Ruegger, P., Jacobs, J., Borneman, J., Anton, P., & Braun, J. (2013) · Microbiome · doi:10.1186/2049-2618-1-26 · Cited by 234
“Given the role of diet in driving microbial composition, one could imagine exploiting such differences in metabolic function by dietary optimization to enrich for preferred bacteria [65-67].”
BackgroundNagao‐Kitamoto, H., Shreiner, A. B., Gillilland, M. G., Kitamoto, S., Ishii, C., Hirayama, A., Kuffa, P., Zaatari, M. E., Grasberger, H., Seekatz, A. M., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.02.003 · Cited by 248
“For instance, hGB mice colonized with the microbiota isolated from obese patients, as compared with lean controls, tend to becomemore obesewhen they are fed a high-fat diet, indicating that functional features of the disease-associated microbiota can be recapitulated successfully in mice.(21) In the present study, we…”
ResultGut microbiota and non-alcoholic fatty liver disease: new insights
Aron‐Wisnewsky, J., Gaborit, B., Dutour, A., & Clément, K. (2013) · Clinical Microbiology and Infection · doi:10.1111/1469-0691.12140 · Cited by 257
“Likewise, when submitted to a high-fat [79,80] or western [61,81] diet, both mouse and humanized mouse models displayed the same changes.”
BackgroundConterno, L., Fava, F., Viola, R., & Tuohy, K. M. (2011) · Genes & Nutrition · doi:10.1007/s12263-011-0230-1 · Cited by 253
“Microbiota enriched in Firmicutes/Actinobacteria exhibited more less diverse functions Modulated functional microbiome with metagenomic differences in carbohydrate, lipid, and amino acid metabolism Turnbaugh et al. (2009a) Zucker fa/fa, fa/? and ?”
BackgroundThe microbiome in respiratory medicine: current challenges and future perspectives
Faner, R., Sibila, O., Agustí, A., Bernasconi, E., Chalmers, J. D., Huffnagle, G. B., Manichanh, C., Molyneaux, P. L., Paredes, R., Pérez Brocal, V., et al. (2017) · European Respiratory Journal · doi:10.1183/13993003.02086-2016 · Cited by 247
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M. C., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0494-6 · Cited by 250
Gut microbiota, host health, and polysaccharides
Xu, X., Xu, P., Ma, C., Tang, J., & Zhang, X. (2012) · Biotechnology Advances · doi:10.1016/j.biotechadv.2012.12.009 · Cited by 249
“Environmental factors were hypothesized to have amore significant impact than genetic factors on the microbial ecosystem (Turnbaugh et al., 2009a).”
InfluentialHeritable components of the human fecal microbiome are associated with visceral fat
Beaumont, M., Goodrich, J. K., Jackson, M. A., Yet, İ., Davenport, E., Vieira‐Silva, S., Debelius, J. W., Pallister, T., Mangino, M., Raes, J., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1052-7 · Cited by 246
Self-citationResveratrol, Metabolic Syndrome, and Gut Microbiota
Chaplin, A. M. L., Carpéné, C., & Mercader, J. (2018) · Nutrients · doi:10.3390/nu10111651 · Cited by 256
“Furthermore, even though gut microbiota is relatively stable throughout adulthood in humans [194], studies have shown that it can be rapidly modified by diet [195], with composition changes seen in as little as a few days of dietary intervention [174].”
BackgroundLiang, Y., Zhan, J., Liu, D., Luo, M., Han, J., Liu, X., Liu, C., Cheng, Z. Z., Zhou, Z., & Wang, P. (2019) · Microbiome · doi:10.1186/s40168-019-0635-4 · Cited by 248
Nutrition, immunity and viral infections in honey bees
DeGrandi‐Hoffman, G., & Chen, Y. (2015) · Current Opinion in Insect Science · doi:10.1016/j.cois.2015.05.007 · Cited by 242
Witchley, J. N., Penumetcha, P., Abon, N. V., Woolford, C. A., Mitchell, A. P., & Noble, S. M. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.02.008 · Cited by 245
Cantorna, M. T., Snyder, L. M., & Arora, J. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1611734 · Cited by 244
“Gut microbial ecology is regulated by the diet (Turnbaugh et al. 2009; Ooi et al. 2014; Carmody et al. 2015).”
BackgroundGallagher, E. J., & LeRoith, D. (2020) · Nature Reviews Cancer · doi:10.1038/s41568-020-0295-5 · Cited by 241
Obesity and gut–microbiota–brain axis: A narrative review
Asadi, A., Mehr, N. S., Mohamadi, M. H., Shokri, F., Heidary, M., Sadeghifard, N., & Khoshnood, S. (2022) · Journal of Clinical Laboratory Analysis · doi:10.1002/jcla.24420 · Cited by 266
Barelli, C., Albanese, D., Donati, C., Pindo, M., Dallago, C., Rovero, F., Cavalieri, D., Tuohy, K. M., Hauffe, H. C., & Filippo, C. D. (2015) · Scientific Reports · doi:10.1038/srep14862 · Cited by 251
The chemistry of gut microbial metabolism of polyphenols
Stevens, J. F., & Maier, C. S. (2016) · Phytochemistry Reviews · doi:10.1007/s11101-016-9459-z · Cited by 244
“In recent years, researchers have identified relationships between compositions of gut microbiota and health (Turnbaugh et al. 2009; Xu and Gordon 2003).”
Cândido, F. G., Valente, F. X., Grześkowiak, Ł., Moreira, A. P. B., Rocha, D. M. U. P., & Alfenas, R. D. C. G. (2017) · International Journal of Food Sciences and Nutrition · doi:10.1080/09637486.2017.1343286 · Cited by 248
Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment
Dollive, S., Chen, Y., Grunberg, S., Bittinger, K. L., Hoffmann, C., Vandivier, L. E., Cuff, C. F., Lewis, J. D., Wu, G. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071806 · Cited by 244
Community assembly of a euryhaline fish microbiome during salinity acclimation
Schmidt, V. T., Smith, K. F., Melvin, D. W., & Amaral‐Zettler, L. (2015) · Molecular Ecology · doi:10.1111/mec.13177 · Cited by 238
“2014), diet (Turnbaugh et al. 2009) and life stage (Wang et al.”
BackgroundResultHuman Microbiota-Associated Mice: A Model with Challenges
Arrieta, M., Walter, J., & Finlay, B. B. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.014 · Cited by 246
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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