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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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Cited by
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BackgroundDiet rapidly and reproducibly alters the human gut microbiome
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“Diet plays a central role in shaping the microbiota, as demonstrated by the fact that bacterial species associated with a highfat, high-sugar diet promote obesity in gnotobiotic mice (12).”
BackgroundCryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
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InfluentialSelf-citationThe human microbiome: at the interface of health and disease
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“For our fourth analysis, we applied MINE to a dataset that has not yet been exhaustively analyzed: a set of bacterial abundance levels in the human gut microbiota (29).”
Self-citationIntestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism
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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
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BackgroundSuccession of microbial consortia in the developing infant gut microbiome
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“The Bacteroidetes are specialized in the breakdown of complex plant polysaccharides (29); the introduction of plantderived carbohydrates into the diet could have boosted populations of Bacteroidetes, which is consistent with mouse microbiome studies (30).”
BackgroundSelf-citationHuman nutrition, the gut microbiome and the immune system
Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588
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BackgroundResultInfluentialSelf-citationMicrobiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits
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The NIH Human Microbiome ProjectPreprint
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“As shown in Figure 2B, the abundance of Bacteroidetes phylum was lower, while the abundance of Firmicutes and Proteobacteria phyla were both higher, in mice consuming the WSD as compared to the LFD, an expected effect of the WSD on the gut microbiota (35).”
ResultYou are what you eat: Diet, health and the gut microbiota
Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792
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“reminder that diet can have a profound impact on the available nutrients, and the structure, activity and function of the gut microbes (49-51).”
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BackgroundUnravelling the effects of the environment and host genotype on the gut microbiome
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Microbial co-occurrence relationships in the human microbiome
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“Further, all of these ecological relationships, detected here based on microbial abundance patterns across many subjects, are themselves distinct from the biogeographical ‘‘co-occurrence’’ patterns observed by previous studies of individual microbes within subjects [30,31].”
BackgroundAn insight into gut microbiota and its functionalities
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Signals from the gut microbiota to distant organs in physiology and disease
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“By using GF mice that were fecal-transplanted with human gut microbiota, one study demonstrated that switching from a lowfat, plant polysaccharide-rich diet to a high-fat, high-sugar diet can shift the configuration of the microbiome in one day.(104) This diet-altered microbiome was able to rapidly promote obesity in…”
BackgroundHow glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419
Gut microbial metabolites as multi-kingdom intermediates
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How informative is the mouse for human gut microbiota research?
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Environmental and Gut Bacteroidetes: The Food Connection
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“In a mouse model reproducing the human intestinal microbiome, the bacterial community composition and the representation of metabolic pathways was strongly dependant on the nature of the diet (Turnbaugh et al., 2009).”
BackgroundMartin, C. R., Osadchiy, V., Kalani, A., & Mayer, E. A. (2018) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2018.04.003 · Cited by 1,284
Psychobiotics: A novel class of psychotropic
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“(34) showed that switching from a low-fat, polysaccharide-rich diet to a high-fat, high-sugar diet shifted the structure of the microbiota within a single day and changed the representation of metabolic pathways in the microbiome.”
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“Dietary changes in mice can also lead to significant changes in bacterial metabolism, especially small chain fatty acids and amino acids, in as little as one week[49], and can lead to large changes after only one day[50].”
BackgroundSelf-citationJumpertz, R., Le, D. S., Turnbaugh, P. J., Trinidad, C., Bogardus, C., Gordon, J. I., & Krakoff, J. (2011) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.010132 · Cited by 1,232
“Several independent studieshavedocumentedhowswitchingmice with a mouse microbiota or gnotobiotic mice with a transplanted human gut microbiota from plant polysaccharide-rich feed pellets low in fat to a caloricallymore-dense high-fat, high-sugarWestern diet resulted in an increase in the proportional representation of…”
BackgroundSelf-citationGut immune maturation depends on colonization with a host-specific microbiota
Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241
“Different diets can drastically alter microbial community structure (Turnbaugh et al., 2009b); because mice and rats are fed a similar rodent diet, such effects are minimized in this model.”
BackgroundMethodInfluentialLi, B. J., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J. M., & Zhang, T. (2015) · The ISME Journal · doi:10.1038/ismej.2015.59 · Cited by 1,227
“It should be noted that the STP influents were collected from Hong Kong, whereas the human faeces samples were collected from residents living in the United States (Turnbaugh et al., 2009).”
BackgroundHabitat degradation impacts black howler monkey ( Alouatta pigra ) gastrointestinal microbiomes
Amato, K. R., Yeoman, C. J., Kent, A. D., Righini, N., Carbonero, F. G., Estrada, A., Gaskins, H. R., Stumpf, R. M., Yıldırım, S., Torralba, M., et al. (2013) · The ISME Journal · doi:10.1038/ismej.2013.16 · Cited by 1,224
“, 2008), while within species, dietary shifts alter GI microbiome composition (Ley et al., 2006; Turnbaugh et al., 2009).”
BackgroundThe first 1000 cultured species of the human gastrointestinal microbiota
Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182
“Animal model experiments have shown that members of this group are increased on high fat, and western type diets (Turnbaugh et al., 2009; Fleissner et al., 2010), while their increased abundance is associated with obesity (Turnbaugh et al., 2006).”
BackgroundDiet dominates host genotype in shaping the murine gut microbiota
Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103
“…various ages, from infants to adults, have failed to detect significantly more similar microbial communities in monozygotic versus dizygotic pairs, suggesting that environmental factors predominate over host genetics in shaping microbial ecology (Turnbaugh et al., 2009a; Yatsunenko et al., 2012).”
BackgroundSelf-citationMoving pictures of the human microbiome
Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r50 · Cited by 1,138
“…together, our observations paint a picture of a human microbiome that is highly variable over time (Figures 2 and 3; Additional files 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15), but from which stable patterns of similarities and differences among body habitats and individuals emerge (Figure…”
BackgroundSelf-citationThe Human Gut Microbiome – A Potential Controller of Wellness and Disease
Kho, Z. Y., & Lal, S. K. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01835 · Cited by 1,180
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“The increased throughput, the improved sensitivity of assays and the improvements in next generation sequencing technologies have enabled cataloging of microbial community membership and structure [12,19,27] as well as the metagenomic gene pool present in each community in large numbers of samples from large numbers o…”
BackgroundPitt, J. M., Vétizou, M., Daillère, R., Roberti, M. P., Yamazaki, T., Routy, B., Lepage, P., Boneca, I. G., Chamaillard, M., Kroemer, G., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.06.001 · Cited by 1,060
“…generally stable within each individual (Gophna, 2011), there exists a vast level of inter-individual heterogeneity (even between identical twins; Turnbaugh et al., 2009a) that is largely determined by the diet (Turnbaugh et al., 2009b; Wu et al., 2011) and environment (Lin et al., 2013;…”
Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer
Chen, W., Liu, F., Ling, Z., Tong, X., & Xiang, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039743 · Cited by 1,054
“Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae are enriched in obese human and obese mouse, as well as in ‘‘Western diet’’ or high-fat diet associated mouse, and they are closely related to energy production or adiposity [53,54,55,56,57,58].”
BackgroundIntestinal microbiota determines development of non-alcoholic fatty liver disease in mice
Le Roy, T., Llopis, M., Lepage, P., Bruneau, A., Rabot, S., Bevilacqua, C., Martin, P., Philippe, C., Walker, F., Bado, A., et al. (2013) · Gut · doi:10.1136/gutjnl-2012-303816 · Cited by 1,001
Forsyth, C. B., Shannon, K. M., Kordower, J. H., Voigt, R. M., Shaikh, M., Jaglin, J. A., Estes, J. D., Dodiya, H. B., & Keshavarzian, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028032 · Cited by 974
“The composition of this bacterial community is influenced by both genetic and environmental factors like diet [10].”
BackgroundConserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity
Liou, A. P., Paziuk, M., Luevano, J.-M., Machineni, S., Turnbaugh, P. J., & Kaplan, L. M. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3005687 · Cited by 1,007
“This was a surprising observation because inoculation of the entire complex microbial communities (14, 19, 20) or specific microorganisms (39) from either lean or obese mice has previously been shown to cause an increase in epididymal fat pad weight and overall adiposity in the face of decreased food intake (10, 20).”
BackgroundInfluentialSelf-citationMetformin retards aging in C. elegans by altering microbial folate and methionine metabolism
Cabreiro, F., Au, C., Leung, K.-Y., Vergara-Irigaray, N., Cochemé, H. M., Noori, T., Weinkove, D., Schuster, E., Greene, N. D. E., & Gems, D. (2013) · Cell · doi:10.1016/j.cell.2013.02.035 · Cited by 967
“Diet strongly influences the metabolism of the human microbiota (Turnbaugh et al., 2009).”
BackgroundEverard, A., Lazarevic, V., Derrien, M., Girard, M., Muccioli, G. G., Neyrinck, A. M., Possemiers, S., Van Holle, A., François, P., de Vos, W. M., et al. (2011) · Diabetes · doi:10.2337/db11-0227 · Cited by 1,076
“Importantly, several other studies have already characterized the gut microbiota composition of ob/ob and diet-induced obese mice by using similar metagenomic approaches (2,12,18,36,40,41).”
BackgroundMethodBile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats
Islam, K. B. M. S., Fukiya, S., Hagio, M., Fujii, N., Ishizuka, S., Ooka, T., Ogura, Y., Hayashi, T., & Yokota, A. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.046 · Cited by 918
Host lifestyle affects human microbiota on daily timescales
David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J. (2014) · Genome biology · doi:10.1186/gb-2014-15-7-r89 · Cited by 950
“However, studies across mice and humans suggest that common aspects of the modern Western lifestyle, including antibiotics [1,9-11] and high-fat diets [2], can persistently alter commensal microbial communities.”
BackgroundThe evolution of the host microbiome as an ecosystem on a leash
Foster, K. R., Schlüter, J., Coyte, K. Z., & Rakoff-Nahoum, S. (2017) · Nature · doi:10.1038/nature23292 · Cited by 958
Berer, K., Gerdes, L. A., Cekanaviciute, E., Jia, X., Xiao, L., Xia, Z., Liu, C., Klotz, L., Stauffer, U., Baranzini, S. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711233114 · Cited by 933
“Similar changes were noted in previous human-to-mouse transplant experiments (14, 15).”
ResultNext‐generation sequencing technologies for environmental DNA research
Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05538.x · Cited by 1,007
“Also, several studies have been conducted on the effect of diet on the gut microbiome of mice using 16S rDNA amplicons (Turnbaugh et al. 2008, 2009; Murphy et al. 2010; Ravussin et al. 2011; Serino et al. 2011).”
BackgroundDiet and feeding pattern affect the diurnal dynamics of the gut microbiome
Zarrinpar, A., Chaix, A., Yooseph, S., & Panda, S. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.11.008 · Cited by 926
“Metagenomic analysis of the obese microflora shows that it is enriched for genes associated with lipid and carbohydrate metabolism (Turnbaugh et al., 2009a).”
InfluentialMicrobiota: a key orchestrator of cancer therapy
Roy, S., & Trinchieri, G. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.13 · Cited by 883
Effects of gut microbes on nutrient absorption and energy regulation
Krajmalnik‐Brown, R., Ilhan, Z., Kang, D., & DiBaise, J. K. (2012) · Nutrition in Clinical Practice · doi:10.1177/0884533611436116 · Cited by 852
“For example, in a weight loss intervention study with obese individuals, the Bacteroidetes/Firmicutes ratio did not change following 4 weeks of low-carbohydrate followed by another 4 weeks of medium-carbohydrate weight loss diets.91 In contrast, Turnbaugh et al97 showed a reduced abundance of Bacteroidetes following a…”
BackgroundInfluentialMechanisms of inflammation-driven bacterial dysbiosis in the gut
Zeng, M. Y., Inohara, N., & Núñez, G. (2016) · Mucosal Immunology · doi:10.1038/mi.2016.75 · Cited by 896
Diet-microbiota interactions and personalized nutrition
Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879
US immigration westernizes the human gut microbiome
Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794
“, 2011) and can also respond quickly to dramatic dietary changes (David et al., 2014; Turnbaugh et al., 2009a).”
BackgroundCani, P. D., Osto, M., Geurts, L., & Everard, A. (2012) · Gut Microbes · doi:10.4161/gmic.19625 · Cited by 864
Sonnenburg, E. D., & Sonnenburg, J. L. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.003 · Cited by 901
“Highly controlled experiments in mice have shown that the quantity and type of carbohydrates that feed the microbiota alter simplified and complex microbial communities (Faith et al., 2011; Kashyap et al., 2013a; Sonnenburg et al., 2010; Turnbaugh et al., 2009b).”
Gut microbiome, obesity, and metabolic dysfunction
Tilg, H., & Kaser, A. (2011) · Journal of Clinical Investigation · doi:10.1172/jci58109 · Cited by 860
Guinane, C. M., & Cotter, P. D. (2013) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x13482996 · Cited by 884
Gut-liver axis: Pathophysiological concepts and clinical implications
Tilg, H., Adolph, T. E., & Trauner, M. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.09.017 · Cited by 843
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013) · Cell · doi:10.1016/j.cell.2012.10.052 · Cited by 811
“Metagenomics has enabled the analysis of the aggregate genomes of this microbial community (the gut microbiome) (Human Microbiome Project Consortium, 2012; Qin et al., 2010; Turnbaugh et al., 2009a; Yatsunenko et al., 2012).”
Greenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821
“Use of this transport system has been implicated in regulation of carbohydrate uptake (37) and was found to be up-regulated following a switch to a high-fat/high-sugar “Western” diet in mice (38).”
BackgroundSelf-citationGlobal Impacts of Western Diet and Its Effects on Metabolism and Health: A Narrative Review
Clemente‐Suárez, V. J., Beltrán-Velasco, A. I., Redondo-Flórez, L., Martín-Rodríguez, A., & Tornero-Aguilera, J. F. (2023) · Nutrients · doi:10.3390/nu15122749 · Cited by 933
“The Western diet evokes structural and behavioral changes in the resident microbiome, which alters the representation of metabolic pathways in the microbiome and alters microbiome gene expression [35], as well as inducing epigenetic changes in monocytes that affect their inflammatory response and cytokine production […”
BackgroundHost genetic variation impacts microbiome composition across human body sites
Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., Spector, T. D., Keinan, A., Ley, R. E., Gevers, D., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0759-1 · Cited by 745
“For example, changes in host diet affect gut microbiome communities at the taxonomic and functional level [5, 15].”
Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance
Saad, M. J. A., Santos, A., & Prada, P. O. (2016) · Physiology · doi:10.1152/physiol.00041.2015 · Cited by 836
High-Fat, Western-Style Diet, Systemic Inflammation, and Gut Microbiota: A Narrative Review
Malesza, I. J., Malesza, M., Walkowiak, J., Mussin, N. M., Walkowiak, D., Aringazina, R. A., Bartkowiak-Wieczorek, J., & Mądry, E. (2021) · Cells · doi:10.3390/cells10113164 · Cited by 847
Homeostasis and Inflammation in the Intestine
Garrett, W. S., Gordon, J. I., & Glimcher, L. H. (2010) · Cell · doi:10.1016/j.cell.2010.01.023 · Cited by 822
Self-citationTargeting gut microbiota in obesity: effects of prebiotics and probiotics
Delzenne, N. M., Neyrinck, A. M., Bäckhed, F., & Cani, P. D. (2011) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2011.126 · Cited by 805
Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 781
“We have reported that mice colonized with a complete human microbiota undergo marked changes in microbial community structure (even after a single day) when shifted from LF/PP chow to a high-fat, high-sugar Western diet (7).”
BackgroundSelf-citationColonocyte metabolism shapes the gut microbiota
Litvak, Y., Byndloss, M. X., & Bäumler, A. J. (2018) · Science · doi:10.1126/science.aat9076 · Cited by 789
“Yet it is a daunting task to define what a balanced microbial community in the colon represents, because the resident microbiota is highly diverse (2), differs between individuals (3), and shifts with changes in the diet (4).”
BackgroundKhan, I., Ullah, N., Zha, L., Bai, Y., Khan, A., Zhao, T., Che, T., & Zhang, C. (2019) · Pathogens · doi:10.3390/pathogens8030126 · Cited by 771
Human gut microbiota in health and disease: Unveiling the relationship
Afzaal, M., Saeed, F., Shah, Y. A., Hussain, M., Rabail, R., Socol, C. T., Hassoun, A., Pateiro, M., Lorenzo, J. M., Rusu, A. V., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.999001 · Cited by 762
“It has been found that, in response to a shift from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar diet, the microbiome composition changed rapidly (Turnbaugh et al., 2009).”
BackgroundThe gut microbiome: connecting spatial organization to function
Tropini, C., Earle, K. A., Huang, K. C., & Sonnenburg, J. L. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.03.010 · Cited by 685
“This results in greater species richness (Faith et al., 2013; Seedorf et al., 2014; Turnbaugh et al., 2009) and dominance of the saccharolytic Bacteroidales and Clostridiales orders.”
Negative Effects of a High-Fat Diet on Intestinal Permeability: A Review
Rohr, M., Narasimhulu, C. A., Rudeski-Rohr, T., & Parthasarathy, S. (2019) · Advances in Nutrition · doi:10.1093/advances/nmz061 · Cited by 794
“Obesity-mediated dysbiosis has been directly linked to dietary excess of fats and manifests in a reduced overall microbial load, a shift in species abundance, and an overall increase in intestinal permeability (136, 145).”
BackgroundLlewellyn, M. S., Boutin, S., Hoseinifar, S. H., & Derôme, N. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00207 · Cited by 771
Plottel, C. S., & Blaser, M. J. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.003 · Cited by 743
“Vegetarians have increased fecal excretion of conjugated estrogens (Goldin et al., 1982; Gorbach and Goldin, 1987) and dietary manipulations affect overall gut microbiome composition and function (Turnbaugh et al., 2009; Faith et al., 2011; Muegge et al., 2011).”
BackgroundSchroeder, B. O., Birchenough, G. M. H., Ståhlman, M., Arike, L., Johansson, M. E. V., Hansson, G. C., & Bäckhed, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.004 · Cited by 713
“However, microbial changes caused by a lack of fiber occur rapidly (Turnbaugh et al., 2009) and we accordingly observed significantly decreased diversity and reduced abundance of Bacteroidetes and Actinobacteria when we switched mice to low-fiber WSD.”
BackgroundResultThe human gut microbiota: Metabolism and perspective in obesity
Gomes, A. C., Hoffmann, C., & Mota, J. F. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1465157 · Cited by 773
“Several microbial genes involved in human metabolism are enriched or depleted in the guts of obese humans.(7) Obese people tend to have a higher proportion of genes which encode membrane transport functions(8) and are involved in butyrate production,(9) whereas the genes related to cofactor, vitamin, and nucleotide me…”
BackgroundSequencing and beyond: integrating molecular 'omics' for microbial community profiling
Franzosa, E. A., Hsu, T. Y., Sirota‐Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3451 · Cited by 761
Dewulf, E. M., Cani, P. D., Claus, S. P., Fuentes, S., Puylaert, P. G., Neyrinck, A. M., Bindels, L. B., de Vos, W. M., Gibson, G. R., Thissen, J.-P., et al. (2013) · Gut · doi:10.1136/gutjnl-2012-303304 · Cited by 825
The composition of the gut microbiota shapes the colon mucus barrier
Jakobsson, H. E., Rodríguez‐Piñeiro, A. M., Schütte, A., Ermund, A., Boysen, P., Bemark, M., Sommer, F., Bäckhed, F., Hansson, G. C., & Johansson, M. E. (2015) · The EMBO Reports · doi:10.15252/embr.201439263 · Cited by 700
The Gut Microbiome Modulates Colon Tumorigenesis
Zackular, J. P., Baxter, N. T., Iverson, K. D., Sadler, W. D., Petrosino, J. F., Chen, G. Y., & Schloss, P. D. (2013) · mBio · doi:10.1128/mbio.00692-13 · Cited by 629
“All bacterial phyla and 90% (62 of 69) of genuslevel taxa detected in donor samples were detected within the recipient germfree mice (see Table S3 in the supplemental material), which is higher than has been previously reported (28, 29).”
ResultExperimental and analytical tools for studying the human microbiome
Kuczynski, J., Lauber, C. L., Walters, W. A., Parfrey, L. W., Clemente, J. C., Gevers, D., & Knight, R. D. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3129 · Cited by 729
Self-citationMartinez-Guryn, K., Hubert, N., Frazier, K., Urlass, S., Musch, M. W., Ojeda, P., Pierre, J. F., Miyoshi, J., Sontag, T. J., Cham, C. M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.03.011 · Cited by 663
Nutrients, foods, and colorectal cancer prevention
Song, M., Garrett, W. S., & Chan, A. T. (2015) · Gastroenterology · doi:10.1053/j.gastro.2014.12.035 · Cited by 700
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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