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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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Citations
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“16S rRNA gene sequencing and quantitative PCR of cecal and fecal samples demonstrated that GP dramatically increased the growth of Akkermansia muciniphila and decreased the proportion of Firmicutes to Bacteroidetes, consistent with prior reports that similar changes in microbial community structure can protect from di…”
BackgroundInfluentialSelf-citationGut microbiome-host interactions in health and disease
Kinross, J. K., Darzi, A. W., & Nicholson, J. K. (2011) · Genome Medicine · doi:10.1186/gm228 · Cited by 714
High-fat diet alters gut microbiota physiology in mice
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BackgroundResultDiet-Induced Dysbiosis of the Intestinal Microbiota and the Effects on Immunity and Disease
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“However, there is growing evidence that the microbial ecology can be influenced by several epigenetic factors including mode of infant delivery [15], antibiotic exposure [16], neonatal nutrition [17], adult nutrition [18],”
BackgroundPlant root-microbe communication in shaping root microbiomes
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“…1997; Hooper et al. 2002; Flint et al. 2012), and it is known that these microbial communities can be deliberately manipulated or inadvertently influenced through factors such as host diet (Turnbaugh et al. 2009), antibiotic use (Willing et al. 2011) and fecal transplants (Song et al. 2013).”
BackgroundObesity, Diabetes, and Gut Microbiota
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“The relationship between diet, gut microbiota, and energy homeostasis was further investigated in models of dietinduced obesity (4,5), e.”
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Insights into the role of the microbiome in obesity and type 2 diabetes
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Role and Mechanism of Gut Microbiota in Human Disease
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“Firmicutes/Bacteroidetes ratio is an important parameter to reflect GM disorder (Turnbaugh et al., 2006; Turnbaugh et al., 2009; Thaiss et al., 2016).”
BackgroundDevelopment of the gut microbiota in infancy and its impact on health in later life
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Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity
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“Similarly, Turnbaugh et al. (Turnbaugh et al 2009) demonstrated that a feeding an HF carbohydrate diet in humanised gnotobiotic mice correlated with an enhanced proportion of PTS and ABC transporters.”
Review article: dietary fibre-microbiota interactions
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“On the basis of 16S rRNA analysis of intestinal microbiota samples taken from different individuals, it has been shown that, despite the great diversity of bacterial species, the majority (98 % of all species) belong to only four bacterial phyla: Firmicutes (64 %), Bacteroidetes (23 %), Proteobacteria (8”
InfluentialCharbonneau, M. R., O’Donnell, D., Blanton, L. V., Totten, S. M., Davis, J. C. C., Barratt, M. J., Cheng, J., Guruge, J., Talcott, M., Bain, J. R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.01.024 · Cited by 606
“Microbial RNA-Seq - Protocols for microbial RNA-Seq are described in our previous publications (Faith et al., 2011; McNulty et al., 2013; Turnbaugh et al., 2009).”
MethodSelf-citationDiet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues
Krautkramer, K. A., Kreznar, J. H., Romano, K. A., Vivas, E. I., Barrett-Wilt, G. A., Rabaglia, M. E., Keller, M. P., Attie, A. D., Rey, F. E., & Denu, J. M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.025 · Cited by 607
“Germ-free 15-week-old C57BL/6J male mice were inoculated via a single oral gavage with 0.2 mL of cecal inocula (Turnbaugh et al., 2009b) and kept in sealed filter-top gnotobiotic cages for 4 weeks.”
InfluentialSelf-citationWalter, J., Armet, A. M., Finlay, B. B., & Shanahan, F. (2020) · Cell · doi:10.1016/j.cell.2019.12.025 · Cited by 596
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“However, studies across mice and humans suggest that common aspects of the modern Western lifestyle, including antibiotics [26, 33–35] and high-fat diets [27], can alter commensal microbial communities.”
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“Bacteroidetes in the gut microbiome is directly related to lean body mass: levels are reduced with obesity [8,13,36] and elevated when obese individuals lose weight [8].”
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Mouse models for human intestinal microbiota research: a critical evaluation
Hugenholtz, F., & de Vos, W. M. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2693-8 · Cited by 610
“Humanizing these mice with human microbiota seemed quite successful: 88% of the genus-level taxa were found in the mice and in the donor samples [85].”
BackgroundMicrobial Ecology along the Gastrointestinal Tract
Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017) · Microbes and Environments · doi:10.1264/jsme2.me17017 · Cited by 614
“This is achieved by inoculating human gut microbiota into germ-free (GF) mice (192) or mice treated with antibiotics to eliminate their gut microbiome (83).”
BackgroundImpact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity
Vrieze, A., Out, C., Fuentes, S., Jonker, L., Reuling, I. J., Kootte, R. S., van Nood, E., Holleman, F., Knaapen, M., Romijn, J. A., et al. (2013) · Journal of Hepatology · doi:10.1016/j.jhep.2013.11.034 · Cited by 594
“In line, obesity has been found to be associated with significant alterations in the composition of the intestinal microbiota [7–10].”
BackgroundMicrobial regulation of organismal energy homeostasis
Cani, P. D., Van Hul, M., Lefort, C., Depommier, C., Rastelli, M., & Everard, A. (2019) · Nature Metabolism · doi:10.1038/s42255-018-0017-4 · Cited by 569
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“Obese subjects have an altered gut microbiota compared to lean individuals, which may be an important contributing factor to the obesity epidemic (Turnbaugh et al., 2009a).”
InfluentialSelf-citation(2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.08.014 · Cited by 536
“…Morgan et al., 2012); (2) the MLI (Mucosal Luminal Interface) cohort recruiting from Cedars-Sinai Medical Center (McHardy et al., 2013; Tong et al., 2013); and (3) a pediatric IBD cohort recruiting from Emory University and Cincinnati Children’s Hospital (Gevers et al., 2014; Walters et al., 2014).”
MethodMicrobial Dysbiosis Is Associated with Human Breast Cancer
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“First, microbial community composition and relative abundance of bacterial species can be contributory factors to health and disease [3,4,35].”
BackgroundGut microbiota, obesity and diabetes
Patterson, E., Ryan, P. M., Cryan, J. F., Dinan, T. G., Ross, R. P., Fitzgerald, G. F., & Stanton, C. (2016) · Postgraduate Medical Journal · doi:10.1136/postgradmedj-2015-133285 · Cited by 552
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“Metatranscriptomics has been elegantly applied to assess gut microbial gene regulation upon dietary intervention in amousemodel, as well as a preliminary arraybased approach for infant fecal bacteria (84, 85), but no application to polyphenols has been reported.”
MethodA Comprehensive Review on the Role of the Gut Microbiome in Human Neurological Disorders
Sorboni, S. G., Moghaddam, H. S., Esfehani, R. J., & Soleimanpour, S. (2022) · Clinical Microbiology Reviews · doi:10.1128/cmr.00338-20 · Cited by 586
Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice
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Self-citationThe hologenome concept of evolution after 10 years
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“It was demonstrated that shifting to a high-sugar high-fat, “Western” diet from a plant polysaccharide-rich, low-fat or from a low-fiber/high-fat diet to a high-fiber/low-fat diet can change the mouse microbiota within a day (181) the monitoring of temporal dynamics of microbial communities within an individual throug…”
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A catalog of the mouse gut metagenome
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“onized with the microbiota from low fat diet-fed donors [95].”
BackgroundThe links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD)
Safari, Z., & Gérard, P. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03011-w · Cited by 522
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Microbes Drive Evolution of Animals and Plants: the Hologenome Concept
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“In mice, a 1-day change in diet from high fiber to high fat brought about a rapid change in the gut microbiota (70); because the diverse microbial population of holobionts contains a large amount of genetic information, gain or loss of microbiota can be a powerful mechanism for adapting to changing conditions.”
BackgroundFeeding the microbiota–gut–brain axis: Diet, microbiome, and neuropsychiatry
Sandhu, K. V., Sherwin, E., Schellekens, H., Stanton, C., Dinan, T. G., & Cryan, J. F. (2017) · Translational Research · doi:10.1016/j.trsl.2016.10.002 · Cited by 491
Chapter 12: Human Microbiome Analysis
Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496
“Similarly, gnotobiotic systems in which an organism’s natural microbiota are replaced with their human analog are a current growth area for closer study of the phenotypic consequences of controlled microbiotic perturbations [145].”
BackgroundExploring host–microbiota interactions in animal models and humansPreprint
Kostic, A. D., Howitt, M. R., & Garrett, W. S. (2013) · Genes & Development · doi:10.1101/gad.212522.112 · Cited by 516
“…to examine intersections of the microbiome, diet, genetics, and obesity and metabolic syndrome as well as intestinal inflammation (Ley et al. 2005; Turnbaugh et al. 2006, 2008a, 2009; Hildebrandt et al. 2009; Faith et al. 2011; Tilg and Kaser 2011; Devkota et al. 2012; Tremaroli and Ba¨ckhed…”
The role of Gut Microbiota in the development of obesity and Diabetes
Baothman, O. A. S., Zamzami, M. A., Taher, I., Abubaker, J. A., & Abu‐Farha, M. (2016) · Lipids in Health and Disease · doi:10.1186/s12944-016-0278-4 · Cited by 509
“In an earlier study, Turnbaugh et al used humanized mice that were generated by transplanting human feces into germ-free mice to study the effect of diet on microbiota [65].”
BackgroundMethodProbiotics improve gut microbiota dysbiosis in obese mice fed a high-fat or high-sucrose diet
Kong, C., Gao, R., Yan, X., Huang, L., & Qin, H. (2018) · Nutrition · doi:10.1016/j.nut.2018.10.002 · Cited by 497
The function of our microbiota: who is out there and what do they do?
Ottman, N., Smidt, H., de Vos, W. M., & Belzer, C. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00104 · Cited by 523
“…either fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice revealed a stable and heritable colonization which enabled a diet intervention, where the mice were switched from a low-fat, plant polysaccharide to a high-fat, high-sugar diet (Turnbaugh et al., 2009b).”
BackgroundSupervised classification of human microbiota
Knights, D., Costello, E. K., & Knight, R. D. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00251.x · Cited by 494
“For example, as the cost of DNA sequencing continues to decline, it may become possible to perform gut microbiota surveys of all individuals in a diseased population in order to recommend personalized therapy (Turnbaugh et al ., 2009b).”
Self-citationTurnbaugh, P. J., Quince, C., Faith, J. J., McHardy, A. C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002355107 · Cited by 478
“Using a method for rRNA depletion based on a combination of size selection (to remove 5S rRNA and tRNA), and streptavidin beadbased pull-down of biotinylated oligonucleotides hybridized to domains conserved among gut bacterial rRNA genes (5), we enriched for fecal mRNA and then generated 12–16 million sequencing reads…”
MethodSelf-citationComplex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice
Kashyap, P. C., Marcobal, A., Ursell, L. K., Larauche, M., Duboc, H., Earle, K. A., Sonnenburg, E. D., Ferreyra, J. A., Higginbottom, S. K., Million, M., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.01.047 · Cited by 451
Self-citationIntestinal microbiota, diet and health
Power, S. E., O'Toole, P. W., Stanton, C., Ross, R. P., & Fitzgerald, G. F. (2014) · British Journal Of Nutrition · doi:10.1017/s0007114513002560 · Cited by 476
“Those in long-term care had a less diverse microbiota with a higher proportion of bacteria of the phylum Bacteroidetes, while community-dwelling subjects had a more diverse microbiota with a higher proportion of bacteria of the phylum Firmicutes.”
InfluentialThe Intestinal Immune System in Obesity and Insulin Resistance
Winer, D. A., Luck, H., Tsai, S. J., & Winer, S. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.01.003 · Cited by 493
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Diversity is the question, not the answer
Shade, A. L. (2016) · The ISME Journal · doi:10.1038/ismej.2016.118 · Cited by 491
Quantitative imaging of gut microbiota spatial organization
Earle, K. A., Billings, G., Sigal, M., Lichtman, J. S., Hansson, G. C., Elias, J. E., Amieva, M. R., Huang, K. C., & Sonnenburg, J. L. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.002 · Cited by 433
“To address this question, we colonized germ-free mice with human fecal microbiota by oral gavage and allowed the community to equilibrate for 40 days (Marcobal et al., 2013; Turnbaugh et al., 2009).”
MethodHildebrand, F., Nguyen, T. L. A., Brinkman, B. M. N., Yunta, R. G., Cauwe, B., Vandenabeele, P., Liston, A., & Raes, J. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r4 · Cited by 478
“causality in disease and therefore the relevance of these model systems [34-37].”
The gut microbiota and its relationship to diet and obesity
Clarke, S. F., Murphy, E. F., Nilaweera, K. N., Ross, R. P., Shanahan, F., O’Toole, P. W., & Cotter, P. D. (2012) · Gut Microbes · doi:10.4161/gmic.20168 · Cited by 474
“…genera and species present in mice are not detected in humans and vice versa.2 With a view to addressing this, and to thus improve the murine model, Turnbaugh et al. 2009,11 created an animal model of the human gut ecosystem by transplanting human fecal microbial communities into germ-free mice.”
BackgroundNutritional psychiatry: Towards improving mental health by what you eat
Adan, R. A. H., van der Beek, E. M., Buitelaar, J. K., Cryan, J. F., Hebebrand, J., Higgs, S., Schellekens, H., & Dickson, S. L. (2019) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2019.10.011 · Cited by 454
“While gut microbiota composition is determined by the ost’s genetics, and external factors, such lifestyle, the ey determinants of gut microbiota composition and funcion remain, namely diet and nutrition ( David et al., 2014 ; ortune et al., 2016 ; Turnbaugh et al., 2009 ; Xu and night, 2015 ).”
BackgroundDietary effects on human gut microbiome diversity
Xu, Z., & Knight, R. (2015) · British Journal Of Nutrition · doi:10.1017/s0007114514004127 · Cited by 456
“gene expression, and, ultimately, host physiological status in response to controlled changes in diet((15,51)).”
BackgroundSelf-citationDiet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health
Berding, K., Vlckova, K., Marx, W., Schellekens, H., Stanton, C., Clarke, G., Jacka, F., Dinan, T. G., & Cryan, J. F. (2021) · Advances in Nutrition · doi:10.1093/advances/nmaa181 · Cited by 451
Altered Gut Microbiota in a Mouse Model of Alzheimer’s Disease
Zhang, L., Wang, Y., Xiayu, X., Shi, C., Chen, W., Song, N., Fu, X., Zhou, R., Xu, Y.-F., Huang, L., et al. (2017) · Journal of Alzheimer s Disease · doi:10.3233/jad-170020 · Cited by 449
Etxeberria, U., Arias, N., Boqué, N., Macarulla, M. T., Portillo, M. P., Martínez, J. A., & Milagro, F. I. (2015) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2015.01.002 · Cited by 446
“obese mice [64].”
Bacterial Community Mapping of the Mouse Gastrointestinal Tract
Gu, S., Chen, D., Zhang, J., Lv, X., Wang, K., Duan, L.-P., Nie, Y., & Wu, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074957 · Cited by 455
“These include intestinal motility, pH, redox potential, nutrient supplies and host secretions [26,27,28].”
BackgroundGoing viral: next-generation sequencing applied to phage populations in the human gut
Reyes, A., Semenkovich, N. P., Whiteson, K., Rohwer, F. L., & Gordon, J. I. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2853 · Cited by 449
Self-citationDo, M. H., Lee, E., Oh, M.-J., Kim, Y., & Park, H.-Y. (2018) · Nutrients · doi:10.3390/nu10060761 · Cited by 441
“It is well-known that high-sugar diets promote obesity [53], however the present study showed high-monosaccharide diet groups did not change the body weight compared with ND group.”
ResultKetone body metabolism and cardiovascular disease
Cotter, D. G., Schugar, R. C., & Crawford, P. A. (2013) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00646.2012 · Cited by 459
Layer‐by‐Layer Encapsulation of Probiotics for Delivery to the Microbiome
Anselmo, A. C., McHugh, K. J., Webster, J., Langer, R., & Jaklenec, A. (2016) · Advanced Materials · doi:10.1002/adma.201603270 · Cited by 440
Mechanisms controlling pathogen colonization of the gut
Stecher, B., & Hardt, W. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.10.003 · Cited by 431
Marcos-Zambrano, L. J., Karađuzović-Hadžiabdić, K., Lončar-Turukalo, T., Przymus, P., Trajkovik, V., Aasmets, O., Berland, M., Gruca, A., Telalović, J. H., Hron, K., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.634511 · Cited by 447
The progress of gut microbiome research related to brain disorders
Zhu, S., Jiang, Y., Xu, K., Cui, M., Ye, W., Zhao, G., Jin, L., & Chen, X. (2020) · Journal of Neuroinflammation · doi:10.1186/s12974-020-1705-z · Cited by 419
“Changing to a high-fat or high-sugar dietary pattern from a low-fat or plant fiber-rich dietary pattern can shift of the microbiome even within one day [83].”
BackgroundResponses of gut microbiota to diet composition and weight loss in lean and obese mice
Ravussin, Y., Koren, O., Spor, A., LeDuc, C., Gutman, R., Stombaugh, J., Knight, R., Ley, R. E., & Leibel, R. L. (2012) · Obesity · doi:10.1038/oby.2011.111 · Cited by 406
“Significant differences have been demonstrated in the diversity of the microbiotas of rodents and humans ingesting high fat and low fat diets (13,15,23), but these studies do not adequately control for differences in body mass or body composition.”
BackgroundSelf-citationThe influence of neuroinflammation in Autism Spectrum Disorder
Matta, S. M., Hill‐Yardin, E. L., & Crack, P. J. (2019) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2019.04.037 · Cited by 431
Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes
Johnson, E. L., Heaver, S. L., Walters, W. A., & Ley, R. E. (2017) · Journal of Molecular Medicine · doi:10.1007/s00109-016-1492-2 · Cited by 389
“Bacteroidetes abundance upon a dietary shift to a high-fat, high-sugar BWestern^ diet [24].”
BackgroundInteraction Between Obesity and the Gut Microbiota: Relevance in Nutrition
Delzenne, N. M., & Cani, P. D. (2011) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-072610-145146 · Cited by 418
“In addition, transcriptomic analysis of the cecal microbial genome (microbiome) revealed a shift in the gut microbiota in favor of carbohydrate fermentation in obese mice fed a Western diet (117).”
BackgroundDiet, Microbiota and Gut-Lung Connection
Anand, S., & Mande, S. S. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02147 · Cited by 423
“The gut microbiota of younger adults highly depends on their diet and lifestyle (Turnbaugh et al., 2009).”
BackgroundCommunity characteristics of the gut microbiomes of competitive cyclists
Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., Sodergren, E., & Weinstock, G. M. (2017) · Microbiome · doi:10.1186/s40168-017-0320-4 · Cited by 377
The gut microbiome and its role in obesity
Davis, C. D. (2016) · Nutrition Today · doi:10.1097/nt.0000000000000167 · Cited by 407
“Moreover, switching from a low-fat, plant polysaccharideYrich diet to a high-fat/high-sugar ‘‘Western’’ diet may shift the composition of the microbiota within a single day in gnotobiotic mice colonized with bacteria from human feces.(20) Similar results have been obtained in humans.”
ResultRienzi, S. C. D., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., Goodrich, J. K., Bell, J. T., Spector, T. D., Banfield, J. F., et al. (2013) · eLife · doi:10.7554/elife.01102 · Cited by 410
“As Cyanobacteria are photosynthetic organisms, it has been assumed that these sequences represent genomic material derived from ingestion of chloroplasts or Cyanobacterial cells (Turnbaugh et al., 2009; Koenig et al., 2011; Consortium HMP, 2012).”
BackgroundPrecision Nutrition and the Microbiome, Part I: Current State of the Science
Mills, S., Stanton, C., Lane, J. A., Smith, G., & Ross, R. P. (2019) · Nutrients · doi:10.3390/nu11040923 · Cited by 426
Exploring Braak’s hypothesis of Parkinson’s disease
Rietdijk, C. D., Perez-Pardo, P., Garssen, J., van Wezel, R. J. A., & Kraneveld, A. D. (2017) · Frontiers in Neurology · doi:10.3389/fneur.2017.00037 · Cited by 395
“Dietary components and dietary patterns have a considerable effect on the composition of the gut microbiome (66).”
BackgroundMucin-type O-glycans and their roles in intestinal homeostasis
Bergstrom, K. S. B., & Xia, L. (2013) · Glycobiology · doi:10.1093/glycob/cwt045 · Cited by 360
Wang, D. D., Nguyen, L. H., Li, Y., Yan, Y., Ma, W., Rinott, E., Ivey, K. L., Shai, I., Willett, W. C., Hu, F. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01223-3 · Cited by 386
Gut microbiota and cardiovascular disease: opportunities and challenges
Kazemian, N., Mahmoudi, M., Halperin, F. A., Wu, J. C., & Pakpour, S. (2020) · Microbiome · doi:10.1186/s40168-020-00821-0 · Cited by 404
Ferreyra, J. A., Wu, K. J., Hryckowian, A. J., Bouley, D. M., Weimer, B. C., & Sonnenburg, J. L. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.003 · Cited by 383
“Shifts in diet have been shown to affect the composition and diversity of the microbiota (Turnbaugh et al., 2009; Wu et al., 2011; McNulty et al., 2013), and the extent to which diet-induced transitions in microbiota membership share ecosystem disturbance-characteristics with antibiotic use is unknown.”
BackgroundMetatranscriptomic Approach to Analyze the Functional Human Gut Microbiota
Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez‐Hernández, N., Pérez‐Cobas, A. E., Latorre, A., & Moyá, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017447 · Cited by 395
“and comparison of microbial community composition between different environments [9,14,17,19,20,21,22,23,24,25,26,27,28].”
BackgroundLlewellyn, S. R., Britton, G. J., Contijoch, E. J., Vennaro, O. H., Mortha, A., Colombel, J.-F., Grinspan, A., Clemente, J. C., Merad, M., & Faith, J. J. (2018) · Gastroenterology · doi:10.1053/j.gastro.2017.11.030 · Cited by 364
Self-citationMethods for normalizing microbiome data: An ecological perspective
McKnight, D. T., Huerlimann, R., Bower, D. S., Schwarzkopf, L., Alford, R. A., & Zenger, K. R. (2018) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13115 · Cited by 373
Microbial nutrient niches in the gut
Pereira, F. C., & Berry, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13659 · Cited by 390
“Though various factors such as host genotype, immune status, and health state can affect the composition of the gut microbiota, the primary driver appears to be the composition and intake levels of host diet (Turnbaugh et al., 2009; Wu et al., 2011; David et al., 2014b; Zarrinpar et al., 2014; Carmody et al., 2015).”
BackgroundEvolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
Amato, K. R., Sanders, J. G., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L., Morton, J. T., Amir, A., McKenzie, V. J., Humphrey, G., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0175-0 · Cited by 381
Self-citationGubert, C., Kong, G., Renoir, T., & Hannan, A. J. (2019) · Neurobiology of Disease · doi:10.1016/j.nbd.2019.104621 · Cited by 387
“A short-term dietary change can alter gut microbial populations within 24 hours, although the main enterotypes remain largely similar (Turnbaugh et al., 2009).”
BackgroundThe Role of the Gut Microbiota in the Relationship Between Diet and Human Health
Perler, B. K., Friedman, E. S., & Wu, G. D. (2022) · Annual Review of Physiology · doi:10.1146/annurev-physiol-031522-092054 · Cited by 402
Tremellen, K., & Pearce, K. (2012) · Medical Hypotheses · doi:10.1016/j.mehy.2012.04.016 · Cited by 359
“growth of beneficial ‘‘good’’ bacteria such as Bifidobacteria and Lactobaccilus [24–28].”
BackgroundInteractions between Intestinal Microbiota and Host Immune Response in Inflammatory Bowel Disease
Zhang, M., Sun, K., Wu, Y., Yang, Y., Tso, P., & Wu, Z. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00942 · Cited by 347
“Similar results were observed when switching from a plant-based diet to a typical Western diet for 1 day (115), thus highlighting the possibility of restoring the gut microbiota in IBD by nutritional interventions.”
BackgroundResultMetabolic Effects of Dietary Nitrate in Health and Disease
Lundberg, J. O., Carlström, M., & Weitzberg, E. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.06.007 · Cited by 374
The Relationship Between Gut Microbiota and Weight Gain in Humans
Angelakis, E., Armougom, F., Million, M., & Raoult, D. (2011) · Future Microbiology · doi:10.2217/fmb.11.142 · Cited by 371
Altered Microbiota Contributes to Reduced Diet-Induced Obesity upon Cold Exposure
Ziętak, M., Kovatcheva‐Datchary, P., Markiewicz, L. H., Ståhlman, M., Kozak, L. P., & Bäckhed, F. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.05.001 · Cited by 358
“previous reports, we found that diet is a key factor in shaping phylogenetic diversity (Hildebrandt et al., 2009; Turnbaugh et al., 2009) and observed that the caecal microbiota of mice on CHD had higher phylogenetic diversity compared with mice on HFD.”
BackgroundMarcobal, A. M., Kashyap, P., Nelson, T. A., Aronov, P. A., Donia, M. S., Spormann, A. M., Fischbach, M. A., & Sonnenburg, J. L. (2013) · The ISME Journal · doi:10.1038/ismej.2013.89 · Cited by 356
“These findings support the idea that many functional attributes are shared between microbiotas that differ compositionally (Turnbaugh et al., 2009a).”
BackgroundInfluentialThe therapeutic potential of manipulating gut microbiota in obesity and type 2 diabetes mellitus
Kootte, R. S., Vrieze, A., Holleman, F., Dallinga‐Thie, G. M., Zoetendal, E. G., de Vos, W. M., Groen, A. K., Hoekstra, J. B. L., Stroes, E. S. G., & Nieuwdorp, M. (2011) · Diabetes Obesity and Metabolism · doi:10.1111/j.1463-1326.2011.01483.x · Cited by 357
“At the same time, the cholesterol metabolism and adiposity of the donor were preserved [24,118,119].”
BackgroundEcological Physiology of Diet and Digestive Systems
Karasov, W. H., del Rio, C. M., & Caviedes‐Vidal, E. (2011) · Annual Review of Physiology · doi:10.1146/annurev-physiol-012110-142152 · Cited by 359
“(136) switched mice with relatively homogeneous microbiomes from a plant-based, low-fat diet to a sugar- and fatrich diet that resembles Western human diets in nutrient content.”
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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