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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]
In the citing paper
“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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Rates of gut microbiome divergence in mammals
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“…availability of food and modifications to the diet of individuals have been shown to influence microbiome composition in several mammalian species (Amato et al., 2014; Davenport et al., 2014; Degnan et al., 2012; Gomez et al., 2016; Kohl & Dearing, 2014; Sun et al., 2016; Turnbaugh et al., 2009).”
BackgroundPan, F., Zhang, L., Li, M., Hu, Y., Zeng, B., Yuan, H., Zhao, L., & Zhang, C. (2018) · Microbiome · doi:10.1186/s40168-018-0440-5 · Cited by 241
MECHANISMS IN ENDOCRINOLOGY: Gut microbiota in patients with type 2 diabetes mellitus
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“Transfer of human microbiota into germ-free mice by fecal microbiota transplantation (FMT) results in successful transfer of ~85% of genera after 7 days [14], and this HMA mouse model is increasingly being used to study the pathophysiology of human diseases such as obesity [15].”
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“Interestingly, this modified gut microbiota could be transferred to germ free mice concomitantly with the obese phenotype [6].”
BackgroundA Clinician's Primer on the Role of the Microbiome in Human Health and Disease
Khanna, S., & Tosh, P. K. (2014) · Mayo Clinic Proceedings · doi:10.1016/j.mayocp.2013.10.011 · Cited by 237
Muramyl Dipeptide-Based Postbiotics Mitigate Obesity-Induced Insulin Resistance via IRF4
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Relationships between diet-related changes in the gut microbiome and cognitive flexibility
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“A similar increase in this order has been seen with humanized mice on a diet enriched in fat (Turnbaugh et al., 2009).”
The role of the gut microbiota in dietary interventions for depression and anxiety
Bear, T. L. K., Dalziel, J. E., Coad, J., Roy, N. C., Butts, C. A., & Gopal, P. K. (2020) · Advances in Nutrition · doi:10.1093/advances/nmaa016 · Cited by 229
Microbiological Survey of the Human Gastric Ecosystem Using Culturing and Pyrosequencing Methods
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“These sequences were compared with those available in the server of the same variable region of the 16S rDNA from other positions in the gastrointestinal tract, including oral cavity [16], throat and nose [17] and faeces [18].”
BackgroundMethodThe interplay between the gut microbiota and the immune system
Geuking, M. B., Köller, Y., Rupp, S., & McCoy, K. D. (2014) · Gut Microbes · doi:10.4161/gmic.29330 · Cited by 239
“In mice, changes can occur very rapidly after changing to a high-fat diet leading to altered microbiome gene expression and metabolic pathways.(8) Changes in the microbiota can then influence immune homeostasis through a variety of different pathways.”
BackgroundThe gut microbiota of Colombians differs from that of Americans, Europeans and Asians
Escobar, J. S., Klotz, B., Valdés-Duque, B. E., & Agudelo, G. M. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0311-6 · Cited by 232
“Studies in laboratories with animal models usually lack genetic variation and control macroenvironmental variables, which might explain why results in obese and lean animals are more consistent than in humans [15-19,95-97].”
BackgroundResultTorres, J., Hu, J., Seki, A., Eisele, C., Nair, N., Huang, R., Tarassishin, L., Jharap, B., Cote-Daigneault, J., Mao, Q., et al. (2020) · Gut · doi:10.1136/gutjnl-2018-317855 · Cited by 218
Self-citationDamman, C. J., Miller, S. I., Surawicz, C. M., & Zisman, T. L. (2012) · The American Journal of Gastroenterology · doi:10.1038/ajg.2012.93 · Cited by 229
“Stool frozen at –80°C has been shown to be equally transplantable to fresh stool (18).”
BackgroundMethodSignificance of the microbiome in obstructive lung disease
Han, M. K., Huang, Y. J., LiPuma, J. J., Boushey, H. A., Boucher, R. C., Cookson, W., Curtis, J. L., Erb‐Downward, J. R., Lynch, S. V., Sethi, S., et al. (2012) · Thorax · doi:10.1136/thoraxjnl-2011-201183 · Cited by 235
Anthony, W., Wang, B., Sukhum, K. V., D’Souza, A. W., Hink, T., Cass, C., Seiler, S. M., Reske, K. A., Coon, C., Dubberke, E. R., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110649 · Cited by 240
“Murine models have shown that antibiotic perturbation alongside diet can modulate compositional differences in the microbiome (Turnbaugh et al., 2009; Cabral et al., 2020) and host susceptibility to infection by Salmonella enterica (Sekirov et al., 2008) and C. difficile (Theriot et al., 2014;…”
Composition of the early intestinal microbiota
Fouhy, F., Ross, R. P., Fitzgerald, G. F., Stanton, C., & Cotter, P. D. (2012) · Gut Microbes · doi:10.4161/gmic.20169 · Cited by 245
Clostridium ramosum Promotes High-Fat Diet-Induced Obesity in Gnotobiotic Mouse Models
Woting, A., Pfeiffer, N., Loh, G., Klaus, S., & Blaut, M. (2014) · mBio · doi:10.1128/mbio.01530-14 · Cited by 224
“An increased abundance of intestinal Erysipelotrichi was also observed in mice fed a Western diet (6, 7) and in an obese human individual (8).”
BackgroundThe Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention
McFadden, R.-M. T., Larmonier, C. B., Shehab, K. W., Midura‐Kiela, M. T., Ramalingam, R., Harrison, C. A., Besselsen, D. G., Chase, J., Caporaso, J. G., Jobin, C., et al. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000522 · Cited by 233
Wang, J., Ghosh, S. S., & Ghosh, S. (2017) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00235.2016 · Cited by 225
“Although the effects of WD in modulating the diversity of gut bacteria are well characterized (4, 26), the mechanism(s) by which it increases intestinal permeability is not known.”
Beneficial modulation of the gut microbiota
Walsh, C. J., Guinane, C. M., O'Toole, P. W., & Cotter, P. D. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.03.035 · Cited by 274
“A further study by the same group showed that this response of the microbiome to dietary intervention is rapid and can occur within 24 h [41], a phenomenon also observed by Wu et al.”
BackgroundGut microbiota of healthy and malnourished children in bangladesh
Monira, S., Nakamura, S., Gotoh, K., Izutsu, K., Watanabe, H., Alam, N. H., Endtz, H. P., Cravioto, A., Ali, S. I., Nakaya, T., et al. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00228 · Cited by 223
“As gut microbiota play an important role in nutrient extraction from food in the lower part of GI tract, the nutritional value of food is influenced partially by a person’s gut microbial community (microbiota) and its component genes (microbiome; Turnbaugh et al., 2009).”
BackgroundInfluentialMacia, L., Thorburn, A. N., Binge, L. C., Mariño, E., Rogers, K. E., Maslowski, K. M., Vieira, A. T., Kranich, J., & Mackay, C. R. (2011) · Immunological Reviews · doi:10.1111/j.1600-065x.2011.01080.x · Cited by 227
“Colonization of germ-free mice with defined bacterial strains or human gut enterotypes (118, 119) should be a powerful way to address several questions about the relationships between diet, the gut microbiota, and effects on epithelial biology and immune and inflammatory responses.”
BackgroundFecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations
Sinha, R. R., Ahn, J., Sampson, J. N., Shi, J., Yu, G., Xiong, X., Hayes, R. B., & Goedert, J. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152126 · Cited by 226
“[1, 12–14] Targeted insights have come from studies of microbial consortia, dietary interventions, gnotobiotic mouse models, and transfer of fecal microbiota from diseased or healthy people.[3, 13, 15] Despite such progress, a comprehensive comparison of all detectable metabolites with all microbes in the distal human…”
BackgroundMechanisms underlying the weight loss effects of RYGB and SG: similar, yet different
Pucci, A. B. F., & Batterham, R. L. (2018) · Journal of Endocrinological Investigation · doi:10.1007/s40618-018-0892-2 · Cited by 230
“Transplantation of gut bacteria from obese mice to normal weight germ-free mice results in weight gain in the recipients [49].”
BackgroundMaking Sense of … the Microbiome in Psychiatry
Bastiaanssen, T. F. S., Cowan, C. S. M., Claesson, M. J., Dinan, T. G., & Cryan, J. F. (2018) · The International Journal of Neuropsychopharmacology · doi:10.1093/ijnp/pyy067 · Cited by 234
The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community
Brand, M. W., Wannemuehler, M. J., Phillips, G. J., Proctor, A., Overstreet, A.-M. C., Jergens, A. E., Orcutt, R. P., & Fox, J. G. (2015) · ILAR Journal · doi:10.1093/ilar/ilv012 · Cited by 223
“In this regard, it is unclear how bacteria from a human source would adapt during long-term colonization and vertical transmission in murine hosts in order to maintain genetic and numerical stability, or organizational structure (Faith et al. 2013; Turnbaugh et al. 2009).”
BackgroundGerber, G. K. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.02.037 · Cited by 219
A brief history of animal modeling.
Ericsson, A. C., Crim, M. J., & Franklin, C. L. (2013) · Europe PMC (PubMed Central) · Cited by 217
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“…characteristics of an obese microbiota include an increased Firmicutesto-Bacteroidetes (F:B) ratio (the predominant bacterial phyla in the human and mouse gut), reductions in microbial diversity, and changes in specific bacterial families, or species (Ley et al., 2006; Turnbaugh et al., 2009).”
BackgroundInfluence of Early Life, Diet, and the Environment on the Microbiome
Dong, T. S., & Gupta, A. (2018) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.08.067 · Cited by 232
“The gut microbiota can change within days of a new diet, but to what extent these changes are permanent once the new diet has terminated remains uncertain.(48) In this section, we review the current literature, focusing on popular diets and how the microbiome is connected (summarized in Table 2).”
InfluentialYang, K., Zhang, L., Liao, P., Xiao, Z., Zhang, F., Daniel, S., Xin, Z., Tan, C., Deng, J., Yin, Y., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.580208 · Cited by 232
Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota
Bauer, P. V., Hamr, S. C., & Duca, F. A. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-2083-z · Cited by 231
“For example, high fat feeding can induce drastic and rapid changes in the gut microbiome [146, 147] and obese rodents and humans exhibit significantly altered gut microbiota, with both changes in composition and/or reductions in diversity [148, 149].”
BackgroundThe promise of the gut microbiome as part of individualized treatment strategies
Schupack, D. A., Mars, R. A. T., Voelker, D. H., Abeykoon, J. P., & Kashyap, P. C. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00499-1 · Cited by 217
Current perspectives on gut microbiome dysbiosis and depression
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Dietary Practices and Beliefs in Patients with Inflammatory Bowel Disease
Limdi, J. K., Aggarwal, D., & McLaughlin, J. T. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000585 · Cited by 216
A bacteriophages journey through the human body
Barr, J. J. (2017) · Immunological Reviews · doi:10.1111/imr.12565 · Cited by 219
Impact of Diet on Human Intestinal Microbiota and Health
Salonen, A., & de Vos, W. M. (2014) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030212-182554 · Cited by 220
Ly, N. P., Litonjua, A. A., Gold, D. R., & Celedon, J. C. (2011) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2011.02.015 · Cited by 213
Obesity, diabetes, and the gut microbiome: an updated review
Singer-Englar, T., Barlow, G. M., & Mathur, R. (2018) · Expert Review of Gastroenterology & Hepatology · doi:10.1080/17474124.2019.1543023 · Cited by 224
“fat/high-sugar versus low-fat/plant polysaccharide-rich or vice versa – revealed bacterial clustering in accordance with the diet consumed [48].”
BackgroundPathways and functions of gut microbiota metabolism impacting host physiology
Krishnan, S., Alden, N., & Lee, K. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.08.015 · Cited by 216
Host adaptive immunity alters gut microbiota
Zhang, H., Sparks, J. B., Karyala, S. V., Settlage, R. E., & Luo, X. (2014) · The ISME Journal · doi:10.1038/ismej.2014.165 · Cited by 223
“In addition, gnotobiotic mice transplanted with human gut microbiota can be modulated with the diet (Turnbaugh et al., 2009).”
BackgroundPark, J. C., & Im, S. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0473-2 · Cited by 232
“Indeed, Turnbaugh et al.(36) clearly demonstrated how following FMT of human feces into mice, the feeding of a high-fat, high-sugar “Western Diet” severely disrupts the gut flora, especially when compared with mice on a low-fat, plantpolysaccharide-based diet.”
BackgroundIntestinal Barrier and Permeability in Health, Obesity and NAFLD
Portincasa, P., Bonfrate, L., Khalil, M., Angelis, M. D., Calabrese, F. M., D’Amato, M., Wang, D. Q. ‐., & Ciaula, A. D. (2021) · Biomedicines · doi:10.3390/biomedicines10010083 · Cited by 219
“Animal studies have addressed additional issues [377].”
Moya-Pérez, A., Neef, A., & Sanz, Y. (2015) · PLOS ONE · doi:10.1371/journal.pone.0126976 · Cited by 211
“In our study we confirm that HFD-induced gut microbiota alterations involve increases in Firmicutes and decreases in Bacteroidetes, as reported in other animal studies [19,31,40,41,42].”
ResultDey, P. (2019) · Pharmacological Research · doi:10.1016/j.phrs.2019.104367 · Cited by 216
Patterson, E., O' Doherty, R. M., Murphy, E. F., Wall, R., O' Sullivan, O., Nilaweera, K., Fitzgerald, G. F., Cotter, P. D., Ross, R. P., & Stanton, C. (2014) · British Journal Of Nutrition · doi:10.1017/s0007114514000117 · Cited by 211
“For this purpose, mice were fed high-fat (HF, 45 % energy from fat) diets containing either (1) palm oil (mainly SFA), (2) olive oil (MUFA), (3) safflower oil (n-6 PUFA) or (4) flaxseed/fish oil (n-3 PUFA).”
MethodThe intestinal microbiota and obesity
Kallus, S. J., & Brandt, L. J. (2012) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0b013e31823711fd · Cited by 210
Modulation of the human gut microbiota by phenolics and phenolic fiber‐rich foods
Loo, Y. T., Howell, K. S., Chan, M., Zhang, P., & Ng, K. (2020) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12563 · Cited by 223
Symbiosis and development: The hologenome concept
ROSENBERG, E. B., & Zilber‐Rosenberg, I. (2011) · Birth Defects Research Part C Embryo Today Reviews · doi:10.1002/bdrc.20196 · Cited by 216
Caloric restriction disrupts the microbiota and colonization resistance
von Schwartzenberg, R. J., Bisanz, J. E., Lyalina, S., Spanogiannopoulos, P., Ang, Q. Y., Cai, J., Dickmann, S., Friedrich, M., Liu, S.-Y., Collins, S. L., et al. (2021) · Nature · doi:10.1038/s41586-021-03663-4 · Cited by 216
Self-citationIs bile acid a determinant of the gut microbiota on a high-fat diet?
Yokota, A., Fukiya, S., Islam, K. B. M. S., Ooka, T., Ogura, Y., Hayashi, T., Hagio, M., & Ishizuka, S. (2012) · Gut Microbes · doi:10.4161/gmic.21216 · Cited by 213
Alterations of the gut microbiota in high-fat diet mice is strongly linked to oxidative stress
Qiao, Y., Sun, J., Ding, Y., Le, G., & Shi, Y. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4323-6 · Cited by 207
“After switching mice to a high-fat Western diet, drastic changes occur in the composition of their gut microbiota with a higher proportion of intestinal Firmicutes (Fleissner et al. 2010; Hildebrandt et al. 2009; Turnbaugh et al. 2009).”
BackgroundGut Microbiota, Immunity, and Disease: A Complex Relationship
Kosiewicz, M. M., Zirnheld, A. L., & Alard, P. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00180 · Cited by 207
“…GF mice colonized with human fecal microbial communities a high-fat, high sugar “Western” diet instead of a low-fat, plant polysaccharide-rich diet significantly altered the microbiota composition, resulting in an increase in Firmicutes and decrease in Bacteroidetes (Turnbaugh et al., 2009).”
BackgroundA pig model of the human gastrointestinal tract
Zhang, Q., Widmer, G., & Tzipori, S. R. (2013) · Gut Microbes · doi:10.4161/gmic.23867 · Cited by 212
“Lower-triangle matrices of pairwise UniFrac distances were imported into GenAlex(52) and distances between samples visualized using the Principal Coordinate experiments in rodents.(11,44,45) If confirmed with additional experiments in pigs, the putative impact of diet on the composition of the microbiome would support…”
BackgroundMethodReprograming of gut microbiome energy metabolism by the FUT2 Crohn’s disease risk polymorphism
Tong, M., McHardy, I. H., Ruegger, P. M., Goudarzi, M., Kashyap, P., Haritunians, T., Li, X., Graeber, T. G., Schwager, E., Huttenhower, C., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.64 · Cited by 213
“…microbiota, has been associated with the development and progression of many conditions, including inflammatory bowel diseases (IBDs) (Frank et al., 2007; Willing et al., 2010; Lepage et al., 2011; Morgan et al., 2012), type 2 diabetes (Qin et al., 2012) and obesity (Turnbaugh et al., 2009a).”
BackgroundMethodInfluentialThe gastrointestinal microbiota and colorectal cancer
Keku, T. O., Dulal, S., Deveaux, A. E., Jovov, B., & Han, X. (2014) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00360.2012 · Cited by 207
“The composition of intestinal microbiota is determined by various factors, including host genetics (159), environment (16, 21), diet (26, 43, 103, 160, 176), and hygiene (7).”
BackgroundGhoshal, U. C., Shukla, R., & Ghoshal, U. (2017) · Gut and Liver · doi:10.5009/gnl16126 · Cited by 218
“Subsequently, feeding Western diet resulted in change in composition of gut microbiota leading to increased number of Firmicutes, Clostridium species, Eubacterium, Enterococcus and decreased number of Bacteroides.(137) Moreover, diet rich in complex carbohydrates favors growth of less pathogenic bacteria (Mycobacteriu…”
BackgroundThe role of the gut microbiota in multiple sclerosis
Correale, J., Hohlfeld, R., & Baranzini, S. E. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00697-8 · Cited by 207
Gut Microbiome and Obesity: A Plausible Explanation for Obesity
Sanmiguel, C. P., Gupta, A., & Mayer, E. A. (2015) · Current Obesity Reports · doi:10.1007/s13679-015-0152-0 · Cited by 210
Kawano, Y., Nakae, J., Watanabe, N., Kikuchi, T., Tateya, S., Tamori, Y., Kaneko, M., Abe, T., Onodera, M., & Itoh, H. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.07.009 · Cited by 207
Changes in the Gut Microbiota of Children with Autism Spectrum Disorder
Zou, R., Xu, F., Wang, Y., Duan, M., Guo, M., Zhang, Q., Zhao, H., & Zheng, H. (2020) · Autism Research · doi:10.1002/aur.2358 · Cited by 216
“This could be explained by regional eating habits, as the fecal microbiota of the population consuming a Western-diet contains proportionally less Bacteroidetes [Turnbaugh et al., 2009].”
BackgroundGut microbiota influences pathological angiogenesis in obesity‐driven choroidal neovascularization
Andriessen, E. M., Wilson, A. M., Mawambo, G., Dejda, A., Miloudi, K., Sennlaub, F., & Sapieha, P. (2016) · EMBO Molecular Medicine · doi:10.15252/emmm.201606531 · Cited by 201
Gut metabotypes govern health effects of dietary polyphenols
Bolca, S., de Wiele, T. V., & Possemiers, S. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.09.009 · Cited by 201
“Yet, so far, gut metagenomic and metatranscriptomic techniques and pipelines have primarily been developed for and applied to human fecal samples and cecal samples of humanized mice [11 ,35–37].”
BackgroundThe antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse
Morgan, A. P., Crowley, J. J., Nonneman, R. J., Quackenbush, C. R., Miller, C. N., Ryan, A. K., Bogue, M. A., Paredes, S. H., Yourstone, S., Carroll, I. M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115225 · Cited by 197
“The specific alterations in gut community composition that we attribute to olanzapine are similar to those attributed to high-fat diet [19, 21, 22, 30, 31].”
BackgroundThe role of the gut microbiota in metabolic health
Janssen, A. W. F., & Kersten, S. (2015) · The FASEB Journal · doi:10.1096/fj.14-269514 · Cited by 209
Human gut microbiota and healthy aging: Recent developments and future prospective
Kumar, M., Babaei, P., Ji, B., & Nielsen, J. (2016) · Nutrition and Healthy Aging · doi:10.3233/nha-150002 · Cited by 211
“[42] Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R,”
BackgroundEmerging Technologies for Gut Microbiome Research
Arnold, J. W., Roach, J. M., & Azcárate-Peril, M. A. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.06.008 · Cited by 206
“By colonizing germ-free mice with healthy human gut microbiota via fecal microbiota transplantation, researchers showed that humanized mouse gut microbiota successfully transferred from generation to generation without loss of microbial diversity [58] resulting in a method to grow and study human-associated microbes w…”
Haiser, H. J., Seim, K. L., Balskus, E. P., & Turnbaugh, P. J. (2014) · Gut Microbes · doi:10.4161/gmic.27915 · Cited by 197
“These results suggest that host diet might provide one avenue with which to tune the rate of microbial drug metabolism, and provide further evidence for the intimate links between nutritional status and our associated microbial communities.(32-34) Of course, the two diets tested in this study reflect dramatic changes…”
BackgroundSelf-citationIntestinal microbiota in metabolic diseases
Clavel, T., Desmarchelier, C., Haller, D., Gérard, P., Rohn, S., Lepage, P., & Daniel, H. (2014) · Gut Microbes · doi:10.4161/gmic.29331 · Cited by 198
Mathematical modeling of primary succession of murine intestinal microbiota
Marino, S., Baxter, N. T., Huffnagle, G. B., Petrosino, J. F., & Schloss, P. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311322111 · Cited by 200
“The availability of dense time-series datasets is limited as there are few studies that have more than 10 samples per individual animal with a fixed time increment (14, 33).”
BackgroundNutritional Immunology: A Multi-Dimensional Approach
Ponton, F., Wilson, K. L., Cotter, S. C., Raubenheimer, D., & Simpson, S. J. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002223 · Cited by 200
“Furthermore, diet has a strong effect on the gut microbiota [29–32], both by serving as a vector for microorganisms and by affecting the physical, chemical, and structural properties of the gut [33–37].”
BackgroundJoyce, S. A., Kamil, A., Fleige, L. E., & Gahan, C. G. M. (2019) · Frontiers in Nutrition · doi:10.3389/fnut.2019.00171 · Cited by 210
On phagocytes and macular degeneration
Guillonneau, X., Eandi, C. M., Paques, M., Sahel, J.-A., Sapieha, P., & Sennlaub, F. (2017) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2017.06.002 · Cited by 185
“Diet has a profound impact on modifying gut microbial composition by shifting the ratio of the two dominant phyla in the distal gut the Bacteroidetes and Firmicutes (David et al., 2014; Scott et al., 2013; Turnbaugh et al., 2009).”
BackgroundInvolvement of the gut microbiota and barrier function in glucocorticoid-induced osteoporosis
Schepper, J. D., Collins, F., Rios-Arce, N. D., Kang, H. J., Schaefer, L., Gardinier, J. D., Raghuvanshi, R., Quinn, R. A., Britton, R., Parameswaran, N., et al. (2020) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.3947 · Cited by 199
“Fecal material was pooled from each mouse group (1 g) and homogenized in 10 mL pre-reduced sterile PBS; this slurry was used to gavage the recipient mice.((89,94)) To deplete their microbiota, recipient mice were treated with antibiotics (broad-spectrum: ampicillin 1.”
MethodAdipose tissue derived bacteria are associated with inflammation in obesity and type 2 diabetes
Massier, L., Chakaroun, R., Tabei, S., Crane, A., Didt, K. D., Fallmann, J., von Bergen, M., Haange, S.-B., Heyne, H., Stumvoll, M., et al. (2020) · Gut · doi:10.1136/gutjnl-2019-320118 · Cited by 194
Inflammaging and Cancer: A Challenge for the Mediterranean Diet
Ostan, R., Lanzarini, C., Pini, E., Scurti, M., Vianello, D., Bertarelli, C., Fabbri, C., Izzi, M., Palmas, M. G., Biondi, F., et al. (2015) · Nutrients · doi:10.3390/nu7042589 · Cited by 198
“The balance of carbohydrates, proteins and fats has a profound influence on the maintenance of GM homeostasis [189–191].”
BackgroundAnimal models of NAFLD from a hepatologist's point of view
Jahn, D., Kircher, S., Hermanns, H. M., & Geier, A. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2018.06.023 · Cited by 201
Possibilities of early life programming in broiler chickens via intestinal microbiota modulation
Rubio, L. A. (2018) · Poultry Science · doi:10.3382/ps/pey416 · Cited by 198
Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans
David, L. A., Weil, A. A., Ryan, E. T., Calderwood, S. B., Harris, J. B., Chowdhury, F., Begum, Y. A., Qadri, F., LaRocque, R. C., & Turnbaugh, P. J. (2015) · mBio · doi:10.1128/mbio.00381-15 · Cited by 187
Self-citationDiet, microbiota and autoimmune diseases
Vieira, S., Pagovich, O., & Kriegel, M. A. (2014) · Lupus · doi:10.1177/0961203313501401 · Cited by 197
Zhang, Z., Deng, Y., Feng, K., Cai, W., Li, S., Yin, H., Xu, M., Ning, D., & Qu, Y. (2019) · Environmental Science & Technology · doi:10.1021/acs.est.8b06044 · Cited by 192
Chae, Y., & An, Y. (2020) · Environmental Science Nano · doi:10.1039/c9en01335k · Cited by 194
Causality of small and large intestinal microbiota in weight regulation and insulin resistance
Scheithauer, T. P. M., Dallinga-Thie, G. M., de Vos, W. M., Nieuwdorp, M., & van Raalte, D. H. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.06.002 · Cited by 188
Gut microbiota and immune crosstalk in metabolic disease
Burcelin, R. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.05.016 · Cited by 195
“To design treatments for chronic, metabolic impairments, one should consider the molecular underpinnings of both the impaired microbiome and the impaired immune system The causal role of gut microbiota on metabolic diseases has been shown in rodents through microbiota transfer experiments [1] and in humans [2] demonst…”
BackgroundCommensal microbiota induces colonic barrier structure and functions that contribute to homeostasis
Hayes, C. L., Dong, J., Galipeau, H. J., Jury, J., McCarville, J. L., Huang, X., Wang, X.-Y., Naidoo, A., Anbazhagan, A. N., Libertucci, J., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-32366-6 · Cited by 190
Microbiota and Lifestyle: A Special Focus on Diet
Redondo-Useros, N., Nova, E., González-Zancada, N., Díaz, L. E., Gómez-Martínez, S., & Marcos, A. (2020) · Nutrients · doi:10.3390/nu12061776 · Cited by 189
Chu, D. M., Meyer, K. M., Prince, A., & Aagaard, K. M. (2016) · Gut Microbes · doi:10.1080/19490976.2016.1241357 · Cited by 188
Bletz, M. C., Goedbloed, D. J., Sanchez, E., Reinhardt, T., Tebbe, C. C., Bhuju, S., Geffers, R., Jarek, M., Vences, M., & Steinfartz, S. (2016) · Nature Communications · doi:10.1038/ncomms13699 · Cited by 188
Harnessing Gut Microbes for Mental Health: Getting From Here to There
Bruce‐Keller, A. J., Salbaum, J. M., & Berthoud, H. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.08.014 · Cited by 192
Yeshi, K., Ruscher, R., Hunter, L., Daly, N. L., Loukas, A. C., & Wangchuk, P. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9051273 · Cited by 190
“There is a growing concern that the western diet, rich in fats and sugars, is responsible for the change in the diversity and metabolic activity of human gut microbiota, thereby contributing to the increasing incidence of IBD [87,88].”
BackgroundSympatric chimpanzees and gorillas harbor convergent gut microbial communitiesPreprint
Moeller, A. H., Peeters, M., Ndjango, J.-B., Li, Y., Hahn, B. H., & Ochman, H. (2013) · Genome Research · doi:10.1101/gr.154773.113 · Cited by 188
“…transmission of gut microbes (Vaishampayan et al. 2010), and environmental factors, suchas host diet and geography (Ley et al. 2008a,b; Turnbaugh et al. 2008, 2009; De Filippo et al. 2010; La Serre et al. 2010; Muegge et al. 2011; Claesson et al. 2012; Yatsunenko et al. 2012).”
Pathogenesis of Necrotizing Enterocolitis
Tanner, S. M., Berryhill, T. F., Ellenburg, J., Jilling, T., Cleveland, D., Lorenz, R. G., & Martin, C. A. (2014) · American Journal Of Pathology · doi:10.1016/j.ajpath.2014.08.028 · Cited by 196
“In addition, the recently developed ability to colonize germfree mice with human fecal microbiota is a new opportunity for developing models of the disease that are based on the fecal communities of NEC and control patients, and these models may result in a dramatic new understanding of the disease while avoiding the…”
BackgroundDeveloping a metagenomic view of xenobiotic metabolism
Haiser, H. J., & Turnbaugh, P. J. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.07.009 · Cited by 186
“In addition, a unique advantage of studying the human microbiome is the potential to use germ-free and intentionally colonized animal models (including “humanized” mice, formerly germ-free animals colonized with human microbial communities) [7,13,14], allowing extensive control over host genotype, environmental parame…”
BackgroundSelf-citation
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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