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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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Items 501–600 of 1,018
Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions
Alexander, M., & Turnbaugh, P. J. (2020) · Immunity · doi:10.1016/j.immuni.2020.07.015 · Cited by 151
“One issue is whether or not the altered microbial community structure initiated by diet is maintained in the recipient animals in the absence of the original selection pressure (Turnbaugh et al., 2009).”
BackgroundSelf-citationDoroszkiewicz, J., Groblewska, M., & Mroczko, B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221810028 · Cited by 166
“The Western diet, characterized by an increased dietary intake of saturated fat, sugar, and red meat, results in a shift to Firmicutes, with a decreased abundance of Bacteroides and a disturbed Firmicutes/Bacteroidetes ratio [23].”
BackgroundNutritional regulation of microbiota-derived metabolites: Implications for immunity and inflammation
Arifuzzaman, M., Collins, N., Guo, C., & Artis, D. (2024) · Immunity · doi:10.1016/j.immuni.2023.12.009 · Cited by 159
Captivity results in disparate loss of gut microbial diversity in closely related hosts
Kohl, K. D., Skopec, M. M., & Dearing, M. D. (2014) · Conservation Physiology · doi:10.1093/conphys/cou009 · Cited by 152
“Furthermore, diet greatly influences microbial community diversity (Ley et al., 2008; Turnbaugh et al., 2009b; Kohl and Dearing, 2012), and thus returning animals to their natural diet in captivity may rescue microbial diversity.”
BackgroundInfluentialGut microbiota and nonalcoholic fatty liver disease
Machado, M. V., & Cortez‐Pinto, H. (2012) · Annals of Hepatology · doi:10.1016/s1665-2681(19)31457-7 · Cited by 151
The role of diet in multiple sclerosis: A review
Esposito, S., Bonavita, S., Sparaco, M., Gallo, A., & Tedeschi, G. (2017) · Nutritional Neuroscience · doi:10.1080/1028415x.2017.1303016 · Cited by 158
Guo, W., Pan, Y., Lü, L., Li, T., Liu, B., & Lv, X. (2018) · Food & Function · doi:10.1039/c8fo00836a · Cited by 151
Impact of Gut Microbiota and Diet on the Development of Atherosclerosis in Apoe −/− Mice
Jonsson, A. L., Caesar, R., Akrami, R., Reinhardt, C., Hållenius, F. F., Borén, J., & Bäckhed, F. (2018) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.118.311233 · Cited by 157
“rich to a high-fat, high-sugar Western diet rapidly changes the microbiome, even within a day.(43,44) In this study, the macronutrient composition of the diet was the most important factor influencing the overall composition of the gut microbiota, and we observed distinct clustering of chow- and Western diet-fed mice.”
BackgroundTowards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors
Simpson, R. C., Shanahan, E. R., Scolyer, R. A., & Long, G. V. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00803-9 · Cited by 153
The Gordian Knot of dysbiosis, obesity and NAFLD
Mehal, W. Z. (2013) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2013.146 · Cited by 156
Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
Engel, P., Stepanauskas, R., & Moran, N. A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004596 · Cited by 153
“hosts or between hosts with different environments or diets [6–9].”
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The gut microbiome and cardiovascular disease: current knowledge and clinical potential
Ahmad, A. F., Dwivedi, G., O’Gara, F., Caparros-Martin, J. A., & Ward, N. C. (2019) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00376.2019 · Cited by 165
Cooking shapes the structure and function of the gut microbiome
Carmody, R. N., Bisanz, J. E., Bowen, B. P., Maurice, C. F., Lyalina, S., Louie, K., Treen, D. G. C., Chadaideh, K. S., Rekdal, V. M., Bess, E. N., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0569-4 · Cited by 158
Self-citationLinking microbiota to human diseases: a systems biology perspective
Wu, H., Tremaroli, V., & Bäckhed, F. (2015) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2015.09.011 · Cited by 150
“Humanized mice have proved to be of great value for studying host metabolic and immune phenotypes [109,110].”
BackgroundGetting Started with Microbiome Analysis: Sample Acquisition to Bioinformatics
Kumar, R., Eipers, P. G., Little, R. B., Crowley, M., Crossman, D. K., Lefkowitz, E. J., & Morrow, C. D. (2014) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1808s82 · Cited by 150
“The power of linking microbiome transplantation with animal models has been highlighted in recent publications using transplanted human microbiota into gnotobiotic animals to study the impact of diet on obesity (Turnbaugh et al., 2009b; Faith et al., 2013).”
BackgroundA Possible Link between Food and Mood: Dietary Impact on Gut Microbiota and Behavior in BALB/c Mice
Jørgensen, B. P., Hansen, J. T., Krych, Ł., Larsen, C. S., Klein, A. B., Nielsen, D. S., Josefsen, K. E., Hansen, A. K., & Sørensen, D. B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103398 · Cited by 157
“Consuming a high-fat diet significantly changed the GM in both feces and cecum, which is in accordance with previous studies comparing the GM of mice fed a high-fat or a starch-rich diet [5].”
Functional gastrointestinal disorders and gut-brain axis: What does the future hold?
Mukhtar, K., Nawaz, H., & Abid, S. (2019) · World Journal of Gastroenterology · doi:10.3748/wjg.v25.i5.552 · Cited by 157
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“also demonstrated that colonization of human or murine microbiota in GF mice is greatly influenced by diet: they demonstrated that a switch of diet – a low-fat, plant polysaccharide-rich or a high-fat, high sugar “western” diet – was able to shift the structure of the microbiota within a single day and altered microbi…”
BackgroundMethodJašarević, E., Rodgers, A. B., & Bale, T. L. (2014) · Neurobiology of Stress · doi:10.1016/j.ynstr.2014.10.005 · Cited by 152
“…sensitive to a variety of factors such as body composition, diet, infection, antibiotic treatment and stress (Bennet et al., 2002; Cho et al., 2012; Turnbaugh et al., 2009; Ravel et al., 2011; Koenig et al., 2011), and is poised to communicate information about the state of the pending external…”
BackgroundStabilization of the murine gut microbiome following weaning
Schloss, P. D., Schubert, A. M., Zackular, J. P., Iverson, K. D., Young, V. B., & Petrosino, J. F. (2012) · Gut Microbes · doi:10.4161/gmic.21008 · Cited by 154
“For example, several studies have used humanized and gnotobiotic mouse models to demonstrate a clear effect of diet changes on the structure of the murine microbiome.(14,19,20) In this study, we investigated the dynamics of the gut microbiota obtained from 12 conventionally raised and colonized inbred mice living in a…”
BackgroundSequencing the human microbiome in health and disease
Cox, M. J., Cookson, W. O. C. M., & Moffatt, M. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt398 · Cited by 159
“Functional annotation allows the comparison of the physiological capabilities between communities and environmental conditions (63).”
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“In human gastrointestinal tract, the vast majority of microbial residents play a critical role for themaintenance of host health (Gill et al. 2006), and the disturbance of gut microbiota is associated with metabolic syndromes (Turnbaugh et al. 2009).”
BackgroundTang, W., Yao, X., Xia, F., Yang, M., Chen, Z., Zhou, B., & Liu, Q. (2018) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2018/7261619 · Cited by 151
“The expression of genes encoding ABC transporters is reportedly increased in the fecal microbiome of mice fed with a HFD compared to mice fed with standard chow or a low-fat diet [52, 53].”
BackgroundHuang, Z., Chen, J., Li, B., Zeng, B., Chou, C., Zheng, X. M., Xie, J., Li, H., Yu, H., Chen, G., et al. (2020) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2019-216471 · Cited by 148
Strain-level epidemiology of microbial communities and the human microbiome
Yan, Y., Nguyen, L. H., Franzosa, E. A., & Huttenhower, C. (2020) · Genome Medicine · doi:10.1186/s13073-020-00765-y · Cited by 152
Impact of the Gut Microbiota on the Development of Obesity: Current Concepts
DiBaise, J. K., Frank, D. N., & Mathur, R. (2012) · The American Journal of Gastroenterology Supplements · doi:10.1038/ajgsup.2012.5 · Cited by 153
Diet therapy for inflammatory bowel diseases: The established and the new
Durchschein, F., Petritsch, W., & Hammer, H. F. (2016) · World Journal of Gastroenterology · doi:10.3748/wjg.v22.i7.2179 · Cited by 147
Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster
Rudman, S. M., Greenblum, S. I., Hughes, R. C., Rajpurohit, S., Kiratli, O. L. Z., Lowder, D. B., Lemmon, S. G., Petrov, D. A., Chaston, J. M., & SCHMIDT, P. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907787116 · Cited by 145
“Future work manipulating microbiomes on a variety of diets, which are known to influence the microbiome (36, 52, 53), could help disentangle the role of diet and microbiome in driving local adaptation.”
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Tools for the Microbiome: Nano and Beyond
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Self-citationA potential role for the gut microbiome in substance use disorders
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“While the gut microbiome can remain relatively stable throughout one’s lifetime, it can be altered through changes in diet, medications, and stress (Turnbaugh et al. 2009; Aziz et al. 2013; Faith et al. 2013; Kelly et al. 2015; Sandhu et al. 2017; Wu et al. 2017; Singh et al. 2017; Xu et al. 2017).”
Gallardo-Becerra, L., Cornejo‐Granados, F., García-López, R., Valdez-Lara, A. G., Bikel, S., Canizales‐Quinteros, S., López-Contreras, B. E., Mendoza-Vargas, A., Nielsen, H., & Ochoa‐Leyva, A. (2020) · Microbial Cell Factories · doi:10.1186/s12934-020-01319-y · Cited by 145
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“73 Turnbaugh PJ, et al. (2009) The effect of diet on the human gut”
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Metagenomic profile of gut microbiota in children during cholera and recovery
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“As diet and metabolism have a profound relation with indigenous bacterial populations [26-28], it is possible that these children might possess individual microbiota inventory related to the nature of diets.”
BackgroundLeulier, F., MacNeil, L. T., Lee, W., Rawls, J. F., Cani, P. D., Schwarzer, M., Zhao, L., & Simpson, S. J. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.02.001 · Cited by 152
“Shifts from a fiber-rich diet to a high-fat diet change the relative abundance of different taxa as well as the microbiome transcriptional responses (Turnbaugh et al., 2009).”
BackgroundTashiro, H., & Shore, S. A. (2018) · Allergology International · doi:10.1016/j.alit.2018.10.004 · Cited by 149
Factors influencing the gut microbiome in children: from infancy to childhood
Kumbhare, S. V., Patangia, D. V., Patil, R. H., Shouche, Y. S., & Patil, N. P. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9860-z · Cited by 143
“Apart from the studies performed in children, many studies have been performed in adults (Zoetendal et al. 2001; Turnbaugh et al. 2009a; Goodrich et al. 2014) involving gene targeted approaches which provide clear evidence that the host genetic make-up influences the gut microbial composition.”
BackgroundCrohn’s disease and the mycobacterioses: A quarter century later. Causation or simple association?
Chiodini, R. J., Chamberlin, W., Sarosiek, J., & McCallum, R. W. (2012) · Critical Reviews in Microbiology · doi:10.3109/1040841x.2011.638273 · Cited by 147
“In addition, there appears also to be at least two distinct microbiota in healthy individuals: a luminal microbiome (which is dynamic (Turnbaugh et al., 2009, Gillevet et al., 2010)) and a mucosal bacterial microbiome or mucosal biofilm which forms a synergistic and stable interaction with the host…”
BackgroundLymphotoxin regulates commensal responses to enable diet-induced obesity
Upadhyay, V., Poroyko, V. A., Kim, T.-J., Devkota, S., Fu, S., Liu, D., Tumanov, A. V., Koroleva, E. P., Deng, L., Nagler‐Anderson, C., et al. (2012) · Nature Immunology · doi:10.1038/ni.2403 · Cited by 145
Variable responses of human and non-human primate gut microbiomes to a Western diet
Amato, K. R., Yeoman, C. J., Cerda, G., Schmitt, C. A., Cramer, J. D., Miller, M. E. B., Gomez, A. M., Turner, T. R., Wilson, B. A., Stumpf, R. M., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0120-7 · Cited by 145
“A common theme in human gut microbiome research currently is the effect of diet on gut microbiota composition, and ultimately, host physiology [1].”
BackgroundSelf-citationTransplantation of human microbiota into conventional mice durably reshapes the gut microbiota
Wrzosek, L., Ciocan, D. M., Borentain, P., Spatz, M., Puchois, V., Hugot, C., Ferrere, G., Mayeur, C., Perlemuter, G., & Cassard, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-25300-3 · Cited by 150
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Polyphenols and type 2 diabetes: A prospective review
Anhê, F. F., Desjardins, Y., Pilon, G., Dudonné, S., Genovese, M. I., Lajolo, F. M., & Marette, A. (2013) · PharmaNutrition · doi:10.1016/j.phanu.2013.07.004 · Cited by 150
“metabolic endotoxemia) [146,147].”
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases
Leone, V., Chang, E. B., & Devkota, S. (2013) · Journal of Gastroenterology · doi:10.1007/s00535-013-0777-2 · Cited by 147
“perspective, that have been shown to play a role in complex disorders such as IBD in both human and animal studies [10–16].”
BackgroundMicrobiota, NASH, HCC and the potential role of probiotics
Brandi, G., Lorenzo, S. D., Candela, M., Pantaleo, M. A., Bellentani, S., Tovoli, F., Saccoccio, G., & Biasco, G. (2017) · Carcinogenesis · doi:10.1093/carcin/bgx007 · Cited by 141
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The Immunopathogenesis of Alzheimer’s Disease Is Related to the Composition of Gut Microbiota
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Gut Microbiota in Obesity and Undernutrition
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“Interestingly, when the obese-transplanted mice were cohoused with the lean-transplanted mice, the obese-transplanted mice were protected from developing the increased adiposity and body mass (116).”
BackgroundImmuno-microbiota cross and talk: The new paradigm of metabolic diseases
Burcelin, R., Garidou, L., & Pomié, C. (2012) · Seminars in Immunology · doi:10.1016/j.smim.2011.11.011 · Cited by 148
“Hence, more energy is harvested from food and taken up by the body [26].”
BackgroundMucosal Immunology of Food Allergy
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“baugh and Gordon have raised important insights into the role of gut bacteria for the metabolic syndrome.(14,17,18,32,33) Lean mice transplanted with the microbiome of obese mice showed a significant”
BackgroundRoy, U., Gálvez, E. J. C., Iljazović, A., Lesker, T. R., Błażejewski, A. J., Pils, M. C., Heise, U., Huber, S., Flavell, R. A., & Strowig, T. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.09.097 · Cited by 140
Chronic Stress-Induced Depression and Anxiety Priming Modulated by Gut-Brain-Axis Immunity
Westfall, S., Caracci, F., Estill, M. S., Frolinger, T., Shen, L., & Pasinetti, G. M. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.670500 · Cited by 148
“This novel genera was identified a part of the family Erysipelotrichaceae known to be important for host metabolism and inflammatory conditions associated with diet (54).”
BackgroundUse of dietary indices to control for diet in human gut microbiota studies
Bowyer, R. C. E., Jackson, M. A., Pallister, T., Skinner, J., Spector, T. D., Welch, A. A., & Steves, C. J. (2018) · Microbiome · doi:10.1186/s40168-018-0455-y · Cited by 140
“ing blooming of related bacteria (Erysipelotrichi) in the context of an unhealthy diet [5]; similarly, genus Oscillospira”
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“Comparisons of 16 S rRNA gene profiles between mice harboring a humanized microbiota and fed a high-fat/high-sugar diet (‘‘Western diet’’) versus those maintained on a low-fat/high polysaccharide diet revealed shifts in Bacteroidetes and an expansion of Bacilli and Erysipelotrichi [25].”
BackgroundInfluentialAdaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners
Rienzi, S. C. D., & Britton, R. A. (2019) · Advances in Nutrition · doi:10.1093/advances/nmz118 · Cited by 141
“Furthermore, in metagenomic studies of mice fed a high-sugar/high-fat diet (by energy: 16–30% sucrose, 10–25% starch and maltodextrin, 40–45% fat, 15–19% protein), genes involved in sugar transport and metabolism were enriched (15, 22).”
BackgroundSoy and Gut Microbiota: Interaction and Implication for Human Health
Huang, H., Krishnan, H. B., Pham, Q., Yu, L. L., & Wang, T. T. Y. (2016) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.6b03725 · Cited by 138
Lymphotoxin signalling in immune homeostasis and the control of microorganisms
Upadhyay, V., & Fu, Y. (2013) · Nature reviews. Immunology · doi:10.1038/nri3406 · Cited by 136
Probiotics, Enteric and Diarrheal Diseases, and Global Health
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“[77-79] Metabolism could be regulated by individual microbes; for example, S.”
BackgroundImportance of gut microbiota in obesity
Cornejo-Pareja, I. M., Muñoz‐Garach, A., Clemente‐Postigo, M., & Tinahones, F. J. (2018) · European Journal of Clinical Nutrition · doi:10.1038/s41430-018-0306-8 · Cited by 147
Effects of Antidiabetic Drugs on Gut Microbiota Composition
Montandon, S., & Jornayvaz, F. (2017) · Genes · doi:10.3390/genes8100250 · Cited by 135
“Moreover, energy-rich diets can alter gut microbiota composition in a single day [39].”
BackgroundMechanistic links between gut microbial community dynamics, microbial functions and metabolic health
Ha, C. W. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i44.16498 · Cited by 137
Microbiota‐dependent and ‐independent effects of dietary fibre on human health
Cai, Y., Folkerts, J., Folkerts, G., Maurer, M., & Braber, S. (2019) · British Journal of Pharmacology · doi:10.1111/bph.14871 · Cited by 142
“3.1 | Dietary fibre increases Bifidobacterium and/or Lactobacillus spp. growth Dietary fibre intervention, especially with ITF, FOS and GOS, has been widely used to stimulate the growth of Bifidobacterium and/or Lactobacillus species and the production of SCFAs (Turnbaugh et al., 2009).”
BackgroundInfluentialHost Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype
Chaston, J. M., Dobson, A. J., Newell, P. D., & Douglas, A. E. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.03301-15 · Cited by 145
Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease
Basson, A. R., Trotter, A., Rodriguez‐Palacios, A., & Cominelli, F. (2016) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00290 · Cited by 140
Cheng, M., Zhang, X., Miao, Y., Cao, J., Wu, Z., & Weng, P. (2016) · Food Research International · doi:10.1016/j.foodres.2016.12.008 · Cited by 137
metagenomeSeq: Statistical analysis for sparse high-throughput sequencing
Paulson, J. N. (2017) · Cited by 138
Ijaz, M. U., Ahmed, M. I., Zou, X., Hussain, M., Zhang, M., Zhao, F., Xu, X., Zhou, G., & Li, C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02200 · Cited by 138
“Dietary intervention is a promising way by manipulating the composition of gut microbiota and its potential effects on host metabolism (Turnbaugh et al., 2009).”
BackgroundControl of immunity via nutritional interventions
Collins, N., & Belkaid, Y. (2022) · Immunity · doi:10.1016/j.immuni.2022.01.004 · Cited by 131
Hintze, K. J., Cox, J. E., Rompato, G., Benninghoff, A. D., Ward, R. E., Broadbent, J., & Lefevre, M. (2014) · Gut Microbes · doi:10.4161/gmic.28403 · Cited by 135
“The other principle method for humanizing the mouse microbiome requires the use of germ-free mice, yet this approach does not result in a complete transfer of donor bacteria to the recipient mice.(10,13) Similarly, the antibiotic method described here also yielded an imperfect transfer of either human donor microbiome.”
MethodDynamic responses of B acteroides thetaiotaomicron during growth on glycan mixtures
Rogers, T. E., Pudlo, N. A., Koropatkin, N. M., Bell, J. S. K., Balasch, M. M., Jasker, K., & Martens, E. C. (2013) · Molecular Microbiology · doi:10.1111/mmi.12228 · Cited by 140
“Diet is a well-established parameter that influences the taxonomic composition of the microbiota, often on the timescale of just hours (Turnbaugh et al., 2009; Martinez et al., 2010; Faith et al., 2011).”
BackgroundMetatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling
Zhang, Y., Thompson, K. N., Branck, T. A., Yan, Y., Nguyen, L. H., Franzosa, E. A., & Huttenhower, C. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-031121-103035 · Cited by 150
The Link between Gut Dysbiosis and Neuroinflammation in Parkinson’s Disease
Baizabal-Carvallo, J. F., & Alonso-Juarez, M. (2020) · Neuroscience · doi:10.1016/j.neuroscience.2020.02.030 · Cited by 130
The NLRP6 inflammasome in health and disease
Ghimire, L., Paudel, S., Jin, L., & Jeyaseelan, S. (2020) · Mucosal Immunology · doi:10.1038/s41385-020-0256-z · Cited by 136
Lozupone, C., Faust, K., Raes, J., Faith, J. J., Frank, D. N., Zaneveld, J., Gordon, J. I., & Knight, R. D. (2012) · Genome Research · doi:10.1101/gr.138198.112 · Cited by 138
“(2007) (B) Results from humanized gnotobiotic mice (Turnbaugh et al. 2009b).”
InfluentialSelf-citationThe microbiome and its potential as a cancer preventive intervention
Bultman, S. J. (2016) · Seminars in Oncology · doi:10.1053/j.seminoncol.2015.09.001 · Cited by 134
“Recent studies have demonstrated that fiber consumption alters the composition of our gut microbiome to a greater extent than other dietary factors and increases the number of butyrateproducing bacteria [10–12].”
BackgroundHuang, E. Y., Leone, V. A., Devkota, S., Wang, Y., Brady, M. J., & Chang, E. B. (2013) · Journal of Parenteral and Enteral Nutrition · doi:10.1177/0148607113486931 · Cited by 133
Manipulating the Gut Microbiota: Methods and Challenges: Figure 1
Ericsson, A. C., & Franklin, C. L. (2015) · ILAR Journal · doi:10.1093/ilar/ilv021 · Cited by 140
“While mice and humans share common bacterial phyla in their intestinal microbiota, there aremarked differences at the genus and species level (Kibe et al. 2005; Ley et al. 2005; Turnbaugh et al. 2009).”
BackgroundMethodInfluentialLang, J., Eisen, J. A., & Zivkovic, A. M. (2014) · PeerJ · doi:10.7717/peerj.659 · Cited by 138
“In fact, major shifts occur within 1 day of a significant dietary change (Wu et al., 2011; Turnbaugh et al., 2009).”
Tripathi, A., Melnik, A. V., Xue, J., Poulsen, O., Meehan, M. J., Humphrey, G., Jiang, L., Ackermann, G. L., McDonald, D. T., Zhou, D., et al. (2018) · mSystems · doi:10.1128/msystems.00020-18 · Cited by 135
Self-citationThe microbial ecology of Escherichia coli in the vertebrate gut
Foster-Nyarko, E., & Pallen, M. J. (2022) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuac008 · Cited by 161
“For example, the gut microbiota cells help maintain the balance between host metabolism and the immune system and in the large intestine, metabolize the indigestible components of the diet (Bäckhed et al. 2005, Turnbaugh et al. 2009).”
Kong, L. C., Holmes, B. A., Cotillard, A., Habi-Rachedi, F., Brazeilles, R., Gougis, S., Gausserès, N., Cani, P. D., Fellahi, S., Bastard, J.-P., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109434 · Cited by 132
“Interestingly, a rapid adaptation of gut microbiota could be observed after 24 h of switching from a low-fat, plant polysaccharide-rich diet to a high fat high sugar ‘‘western’’ diet [15], whereas the diversity of species within the gut microbiota organized into identifiable clusters or enterotypes are correlated with…”
BackgroundThe Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders?
Ochoa‐Repáraz, J., & Kasper, L. H. (2016) · Current Obesity Reports · doi:10.1007/s13679-016-0191-1 · Cited by 141
Fujii, Y., Nguyen, T. T. T., Fujimura, Y., Kameya, N., Nakamura, S., Arakawa, K., & Morita, H. (2019) · Bioscience Biotechnology and Biochemistry · doi:10.1080/09168451.2019.1644149 · Cited by 135
“This result indicates that mice were successfully humanized, with engraftment rate higher than that previously achieved [12,34].”
ResultMuralitharan, R. R., Jama, H. A., Xie, L., Peh, A., Snelson, M., & Marques, F. Z. (2020) · Hypertension · doi:10.1161/hypertensionaha.120.14473 · Cited by 131
Clinical Consequences of Diet-Induced Dysbiosis
Chan, Y. K., Estaki, M., & Gibson, D. L. (2013) · Annals of Nutrition and Metabolism · doi:10.1159/000354902 · Cited by 140
Giving back to the community: microbial mechanisms of plant–soil interactions
Paredes, S. H., & Lebeis, S. L. (2016) · Functional Ecology · doi:10.1111/1365-2435.12684 · Cited by 136
Role of the intestinal microbiome and its therapeutic intervention in cardiovascular disorder
Luqman, A., Hassan, A., Ullah, M., Naseem, S., Ullah, M., Zhang, L., Din, A. U., Ullah, K., Ahmad, W., & Wang, G. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1321395 · Cited by 145
Latest approaches for the treatment of obesity
Jackson, V. M., Breen, D. M., Fortin, J.-P., Liou, A., Kuzmiski, J. B., Loomis, A. K., Rives, M.-L., Shah, B., & Carpino, P. A. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1044966 · Cited by 132
“Preclinically, transfer experiments of human intestinal microbial communities into germ-free mice demonstrated that an “obese” microbiome directly confers greater adiposity to its recipient than a “lean” microbiome [149,156] .”
Role of nutrition and microbiota in susceptibility to inflammatory bowel diseases
Gentschew, L., & Ferguson, L. R. (2012) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201100630 · Cited by 133
Antibiotic perturbation of the preterm infant gut microbiome and resistome
Gasparrini, A. J., Crofts, T. S., Gibson, M. K., Tarr, P. I., Warner, B. B., & Dantas, G. A. (2016) · Gut Microbes · doi:10.1080/19490976.2016.1218584 · Cited by 132
Bhute, S. S., Suryavanshi, M. V., Joshi, S. M., Yajnik, C. S., Shouche, Y. S., & Ghaskadbi, S. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00214 · Cited by 129
Lv, X., Guo, W., Li, L., Yu, X., & Liu, B. (2019) · Journal of Functional Foods · doi:10.1016/j.jff.2019.03.043 · Cited by 137
Boland, M. L., Oró, D., Tølbøl, K. S., Thrane, S. T., Nielsen, J. C., Cohen, T. S., Tabor, D. E., Fernandes, F., Tovchigrechko, A., Veidal, S. S., et al. (2019) · World Journal of Gastroenterology · doi:10.3748/wjg.v25.i33.4904 · Cited by 129
Fecal microbiota variation across the lifespan of the healthy laboratory rat
Flemer, B., Gaci, N., Borrel, G., Sanderson, I. R., Chaudhary, P. P., Tottey, W., O'Toole, P. W., & Brugère, J.-F. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1334033 · Cited by 128
“This so-called “ humanization ” of the rodent GIT with human gut microbiota 11,12 has improved the applicability of mice as a model for human gut-related studies.”
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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