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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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Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Self-citationThe RAST Server: Rapid Annotations using Subsystems Technology
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T. L., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-75 · Cited by 11,893
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Self-citationA core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Self-citationObesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
Self-citationThe Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn663 · Cited by 6,108
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091
Self-citationThe KEGG resource for deciphering the genome
Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,120
Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953
Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.015 · Cited by 2,915
Self-citation
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Sorted by citations
Items 601–700 of 1,018
den Ende, W. V., Peshev, D., & Gara, L. D. (2011) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2011.07.005 · Cited by 131
Rial, S. A., Karelis, A. D., Bergeron, K., & Mounier, C. (2016) · Nutrients · doi:10.3390/nu8050281 · Cited by 133
“The transplantation of fecal microbiota from obese mice and obese patients into germ-free lean mice transformed the lean mice into obese mice, while the germ-free mice receiving microbiota from lean mice did not show any metabolic symptoms related to obesity or insulin resistance [54,75–77].”
BackgroundInteraction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer
Yuan, C., Burns, M. B., Subramanian, S., & Blekhman, R. (2018) · mSystems · doi:10.1128/msystems.00205-17 · Cited by 132
“For example, the western diet (characterized by low fiber and high protein, fat, and sugar) affects gut microbiome composition in humanized mice, whereby mice fed with western diet have increased Firmicutes and decreased Bacteroidetes relative abundance [12, 13].”
Pellizzon, M., & Ricci, M. R. (2018) · Nutrition & Metabolism · doi:10.1186/s12986-018-0243-5 · Cited by 131
“Dramatic shifts in certain bacterial phyla can occur within a day after switching from a ‘lower fat, plant polysaccharide based diet’ (an undefined GB diet) to a high fat purified ingredient diet, and this stabilizes after only 7 days [24].”
BackgroundMicrobial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome
Cabral, D. J., Penumutchu, S., Reinhart, E. M., Zhang, C., Korry, B. J., Wurster, J. I., Nilson, R., Guang, A., Sano, W. H., Rowan-Nash, A. D., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.08.020 · Cited by 132
Prenatal and postnatal contributions of the maternal microbiome on offspring programming
Jašarević, E., & Bale, T. L. (2019) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2019.100797 · Cited by 131
Creating and characterizing communities of human gut microbes in gnotobiotic mice
Faith, J. J., Rey, F. E., O’Donnell, D., Karlsson, M., McNulty, N. P., Kallstrom, G., Goodman, A. L., & Gordon, J. I. (2010) · The ISME Journal · doi:10.1038/ismej.2010.110 · Cited by 124
Self-citationGall, A., Fero, J., McCoy, C. O., Claywell, B. C., Sanchez, C. A., Blount, P. L., Li, X., Vaughan, T. L., Matsen, F. A., IV, Reid, B. J., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129055 · Cited by 124
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis
Zackular, J. P., Baxter, N. T., Chen, G., & Schloss, P. D. (2015) · mSphere · doi:10.1128/msphere.00001-15 · Cited by 125
Collins, K. H., Paul, H. A., Hart, D. A., Reimer, R. A., Smith, I. C., Rios, J. L., Seerattan, R. A., & Herzog, W. (2016) · Scientific Reports · doi:10.1038/srep37278 · Cited by 125
Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats
Zhang, Q., Xiao, X., Li, M., Yu, M., Ping, F., Zheng, J., Wang, T., & Wang, X. (2017) · PLOS ONE · doi:10.1371/journal.pone.0184735 · Cited by 124
Incorporating the gut microbiota into models of human and non‐human primate ecology and evolution
Amato, K. R. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22908 · Cited by 127
“…diet, experience a dramatic increase in the abundance of several classes of bacteria belonging to the Firmicutes phylum within the span of one day (Turnbaugh et al., 2009), and humans adopting a meat-and-cheese-only diet exhibit increased relative abundances of Bilophila bacteria that are…”
Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases
Dolan, K. T., & Chang, E. B. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600129 · Cited by 136
“The contemporary diet of many Westerners contains high quantities of animal protein and fat, sugar, and processed foods, and low amounts of plant-based foods [12, 15, 16].”
BackgroundLinks between Soil Fungal Diversity and Plant and Soil Properties on the Loess Plateau
Yang, Y., Dou, Y., Huang, Y., & An, S. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02198 · Cited by 127
“The abundance-based coverage estimator (ACE) and Chao1 estimator were calculated, and then, the rarefaction curves were plotted using MOTHUR.3 Phylogenetic diversity (PD) was estimated using Chao1 (Chao, 1984) and Faith’s indices (Faith, 1992; Turnbaugh et al., 2009).”
MethodMetagenome and metabolism: the tissue microbiota hypothesis
Burcelin, R., Sérino, M., Chabo, C., Garidou, L., Pomié, C., Courtney, M., Amar, J., & Bouloumié, A. (2013) · Diabetes Obesity and Metabolism · doi:10.1111/dom.12157 · Cited by 130
“This dysbiosis is induced by a fatenriched diet [75,76].”
BackgroundDevelopment of the Digestive System—Experimental Challenges and Approaches of Infant Lipid Digestion
Abrahamse, E., Minekus, M., van Aken, G. A., van de Heijning, B., Knol, J., Bartke, N., Oozeer, R., van der Beek, E. M., & Ludwig, T. (2012) · Food Digestion · doi:10.1007/s13228-012-0025-x · Cited by 124
“Although the impact of a high-fat diet on human or rodent microbiota has been widely documented, the influence of undigested LCFA on microbiota function in infants remains to be elucidated [7, 80, 118, 140].”
BackgroundHigh fat diet drives obesity regardless the composition of gut microbiota in mice
Rabot, S., Membrez, M., Blancher, F., Berger, B. W., Moine, D., Krause, L., Bibiloni, R., Bruneau, A., Gérard, P., Siddharth, J., et al. (2016) · Scientific Reports · doi:10.1038/srep32484 · Cited by 131
“However, our results are in contrast to other studies that show microbiota composition is a determinative factor of body weight in mice fed diets rich in plant fibres 20–22 or saturated fat 23 .”
Causal effects of the microbiota on immune-mediated diseases
Round, J. L., & Palm, N. W. (2018) · Science Immunology · doi:10.1126/sciimmunol.aao1603 · Cited by 129
Intestinal microbiota profiling and predicted metabolic dysregulation in psoriasis patients
Chen, Y., Ho, H. J., Tseng, C., Lai, Z.-L., Shieh, J., & Wu, C. (2018) · Experimental Dermatology · doi:10.1111/exd.13786 · Cited by 123
Zhao, X., Jiang, Y., Xi, H., Chen, L., & Feng, X. (2020) · Geburtshilfe und Frauenheilkunde · doi:10.1055/a-1081-2036 · Cited by 124
“Dietary changes can rapidly change the relative abundance and species in GM [95], something that has been confirmed in patients with MS [96].”
BackgroundPhylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species
Amato, K. R., Martínez‐Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., Humphrey, G. C., Gogul, G., Gaffney, J., Lovelace, E., et al. (2015) · Oecologia · doi:10.1007/s00442-015-3507-z · Cited by 123
Self-citationDiet, Microbiota, Obesity, and NAFLD: A Dangerous Quartet
Machado, M. V., & Cortez‐Pinto, H. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17040481 · Cited by 129
“In fact, transplantation of microbiota harvested by either genetically-obese ob/ob mice [16] or high-fat diet induced obese mice [17] into germ free mice mimicked the obese insulin resistant phenotype.”
BackgroundThe gut microbiome in cardio-metabolic health
Hansen, T. H., Gøbel, R. J., Hansen, T. F., & Pedersen, O. B. (2015) · Genome Medicine · doi:10.1186/s13073-015-0157-z · Cited by 132
“In non-obese rats, Roux-en-Y gastric bypass (RYGB) confers a dramatic shift in microbiota composition, with a 52-fold increase Hansen et al. Genome Medicine (2015) 7:33 Page 12 of 16 in Proteobacteria and reduction of Firmicutes and Bacteroidetes.”
BackgroundInfluentialMcClements, D. J., DeLoid, G. M., Pyrgiotakis, G., Shatkin, J. A., Xiao, H., & Demokritou, P. (2016) · NanoImpact · doi:10.1016/j.impact.2016.10.002 · Cited by 129
“…the critical role of the gut microbiome and its role in overall health (Consortium, 2012; Pflughoeft and Versalovic, 2012; Theriot et al., 2014; Turnbaugh et al., 2009; Weir et al., 2013), potential effects of iENMs on the gut microbiome remain largely unstudied (Bergin and Witzmann, 2013;…”
BackgroundThe role of sodium in modulating immune cell function
Wilck, N., Balogh, A., Markó, L., Bartolomaeus, H., & Müller, D. N. (2019) · Nature Reviews Nephrology · doi:10.1038/s41581-019-0167-y · Cited by 129
The Potential of Lactobacillus spp. for Modulating Oxidative Stress in the Gastrointestinal Tract
Kong, Y., Olejar, K. J., On, S. L. W., & Chelikani, V. (2020) · Antioxidants · doi:10.3390/antiox9070610 · Cited by 127
“With regard to the GI tract, the alteration of dietary fat intake (from low to high) in mice was able to shift the structure and gene expression of their gut microbiota within one day [39].”
BackgroundHuman Gut Microbiota Associated with Obesity in Chinese Children and Adolescents
Hou, Y.-P., He, Q.-Q., Ouyang, H.-M., Peng, H.-S., Wang, Q., Li, J., Lv, X.-F., Zheng, Y.-N., Li, S.-C., Liu, H.-L., et al. (2017) · BioMed Research International · doi:10.1155/2017/7585989 · Cited by 156
Autoimmune host–microbiota interactions at barrier sites and beyond
Ruff, W. E., & Kriegel, M. A. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2015.02.006 · Cited by 122
“Diet and antibiotic use, for instance, are well established to profoundly alter the gut microbiota, leading to longlasting changes in metabolic profiles [32,33].”
BackgroundThe nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota
Cox, L. M., Cho, I., Young, S. A., Anderson, W. H. K., Waters, B. J., Hung, S., Gao, Z., Mahana, D., Bihan, M., Alekseyenko, A. V., et al. (2012) · The FASEB Journal · doi:10.1096/fj.12-219477 · Cited by 123
Cheng, M., Zhang, X., Zhu, J., Cheng, L., Cao, J., Wu, Z., Weng, P., & Zheng, X. (2018) · Food & Function · doi:10.1039/c7fo01570d · Cited by 121
Analysis and correction of compositional bias in sparse sequencing count data
Kumar, M. S. B., SLUD, E. V., Okrah, K., Hicks, S. C., Hannenhalli, S. S., & Bravo, H. C. (2018) · BMC Genomics · doi:10.1186/s12864-018-5160-5 · Cited by 123
“A diet study in which the gut microbiomes ( n = 139) of carefully controlled laboratory mice fed plant-based or western diets were sequenced [35].”
BackgroundMethodIndoles as essential mediators in the gut-brain axis. Their role in Alzheimer's disease
Pappolla, M. A., Perry, G. L., Fang, X., Zagorski, M. G., Sambamurti, K., & Pöeggeler, B. (2021) · Neurobiology of Disease · doi:10.1016/j.nbd.2021.105403 · Cited by 124
“(Roager and Licht, 2018) A number of cell-protective indoles can be derived from cruciferous vegetables (Verhoeven et al., 1996; Fuentes et al., 2015) and may also have neuroprotective activity,(El-Naga et al., 2014) which overlaps with microbiota-derived indoles (see below).”
BackgroundBamberger, C., Rossmeier, A., Lechner, K., Li-ya, W., Waldmann, E., Fischer, S. E., Stark, R. G., Altenhofer, J., Henze, K., & Parhofer, K. G. (2018) · Nutrients · doi:10.3390/nu10020244 · Cited by 128
“On the other hand, a high-fat Western-type diet in mice resulted in an increased abundance of Firmicutes and a decrease in Bacteroidetes [19,24,25].”
BackgroundImpaired Intestinal Barrier and Tissue Bacteria: Pathomechanisms for Metabolic Diseases
Massier, L., Blüher, M., Kovacs, P. L., & Chakaroun, R. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.616506 · Cited by 130
“A high caloric “western” diet, in particular due to high-fat/low-fiber content (48) and food additives (49), is associated with adverse changes in the microbiome (50) and both are independently important factors in the development of metabolic diseases.”
BackgroundIdentification of Allobaculum mucolyticum as a novel human intestinal mucin degrader
van Muijlwijk, G. H., van Mierlo, G., Jansen, P. W. T. C., Vermeulen, M., Bleumink‐Pluym, N. M. C., Palm, N. W., van Putten, J. P. M., & de Zoete, M. R. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1966278 · Cited by 119
Comparison of the gut microbiota of people in France and Saudi Arabia
Yasir, M., Angelakis, E., Bibi, F., Azhar, E. I., Bachar, D., Lagier, J., Gaborit, B., Hassan, A. M., Jiman-Fatani, A. A., Alshali, K. Z., et al. (2015) · Nutrition and Diabetes · doi:10.1038/nutd.2015.3 · Cited by 118
Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis
Chen, P. B., Black, A. S., Sobel, A. L., Zhao, Y., Mukherjee, P., Molparia, B., Moore, N. E., Muench, G. R. A., Wu, J., Chen, W., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0549-5 · Cited by 121
Cao, Y., Zou, L., Li, W., Yu, S., Zhao, G., & Hu, Y. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.06.241 · Cited by 125
Using ecological coexistence theory to understand antibiotic resistance and microbial competition
Letten, A. D., Hall, A. R., & Levine, J. M. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01385-w · Cited by 120
Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing
Tun, H. M., Brar, M. S., Khin, N., Li, J., Hui, R. K.-H., Dowd, S. E., & Leung, F. C.-C. (2012) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2012.01.001 · Cited by 118
“Recent studies have demonstrated that dietary components affect intestinal microbiota of cats (Lubbs et al., 2009), and also reported by the experiment done in mice, rats and human (Lubbs et al., 2009; Turnbaugh et al., 2009).”
BackgroundTakagi, R., Sasaki, K., Sasaki, D., Fukuda, I., Tanaka, K., Yoshida, K., Kondo, A., & Osawa, R. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160533 · Cited by 120
“Usually, the functionality of such food components has been evaluated by human intervention trials or animal-feeding trials [3,9].”
Gut Microbiome: A Promising Biomarker for Immunotherapy in Colorectal Cancer
Temraz, S. N., Nassar, F. J., Nasr, R., Charafeddine, M., Mukherji, D., & Shamseddine, A. I. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20174155 · Cited by 125
Gut microbiota and old age: Modulating factors and interventions for healthy longevity
Coman, V., & Vodnar, D. C. (2020) · Experimental Gerontology · doi:10.1016/j.exger.2020.111095 · Cited by 129
Multi-omics microsampling for the profiling of lifestyle-associated changes in health
Shen, X., Kellogg, R., Panyard, D. J., Bararpour, N., Castillo, K. P. E., Lee‐McMullen, B., Delfarah, A., Ubellacker, J. M., Ahadi, S., Rosenberg‐Hasson, Y., et al. (2023) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00999-8 · Cited by 126
“We have revised the text to say that this method enables frequent sampling on the order of minutes or hours and the collection of a large number of samples from a single individual.”
Food allergy: an enigmatic epidemic
Berin, M. C., & Sampson, H. A. (2013) · Trends in Immunology · doi:10.1016/j.it.2013.04.003 · Cited by 120
“Such a finding could be followed up with mechanistic studies in mice as it has been shown that germ-free mice can be colonized with defined human flora [77, 78].”
BackgroundCani, P. D. (2012) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2012.03866.x · Cited by 117
“of obesity and related metabolic disorders are convincing [5,6]; however, this theory does not help to unravel the interplay between obesity-related metabolic disorders and the development of a low grade inflammation.”
BackgroundGut microbiota and obesity: lessons from the microbiome
Cani, P. D. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt014 · Cited by 123
Hoggard, M., Mackenzie, B. W., Jain, R., Taylor, M. W., Biswas, K., & Douglas, R. G. (2016) · Clinical Microbiology Reviews · doi:10.1128/cmr.00060-16 · Cited by 122
Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice
Harada, N., Hanaoka, R., Horiuchi, H., Kitakaze, T., Mitani, T., Inui, H., & Yamaji, R. (2016) · Scientific Reports · doi:10.1038/srep23001 · Cited by 110
Respondek, F., Gérard, P., Bossis, M., Boschat, L., Bruneau, A., Rabot, S., Wagner, A., & Martin, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071026 · Cited by 119
“Conversely, the introduction of more fat and sugars in the diet had been previously found to increase the proportion of Erysipelotrichi in humanized gnotobiotic mice [37].”
BackgroundHuman intestinal microbiota: cross-talk with the host and its potential role in colorectal cancer
Candela, M., Guidotti, M., Fabbri, A., Brigidi, P., Franceschi, C., & Fiorentini, C. (2010) · Critical Reviews in Microbiology · doi:10.3109/1040841x.2010.501760 · Cited by 117
“%) belongs to five bacterial phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria.”
BackgroundInfluentialFoley, S. E., Tuohy, C. A., Dunford, M., Grey, M. J., Luca, H. E. D., Cawley, C., Szabady, R. L., Maldonado‐Contreras, A., Houghton, J. M., Ward, D. V., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01137-3 · Cited by 121
Effects of caloric restriction on the gut microbiome are linked with immune senescence
Sbierski‐Kind, J., Grenkowitz, S., Schlickeiser, S., Sandforth, A., Friedrich, M., Kunkel, D., Glauben, R., Brachs, S., Mai, K., Thürmer, A., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01249-4 · Cited by 116
“Additionally, these data demonstrate that one week is sufficient for a human microbiota to mature in a previously GF mouse gut, replicating, as shown previously [34, 49].”
BackgroundSelf-citationMetagenomic Surveys of Gut Microbiota
Mandal, R. S., Saha, S., & Das, S. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.02.005 · Cited by 123
“Mouse Cecum 16S rRNA-based sequencing 5088 16S rRNA sequences DQ014552 DQ015671; AY989911 AY993908 [20] Mouse Cecum and feces 16S rRNA-based sequencing 2878 16S rRNA sequences GQ491120 GQ493997 [3] Mouse Feces 16S rRNA-based sequencing 4172 16S rRNA sequences FJ032696 FJ036849 ; EU584214 EU584231 [23] Mouse and zebraf…”
BackgroundInfluentialBeilharz, J. E., Kaakoush, N. O., Maniam, J., & Morris, M. J. (2018) · Molecular Psychiatry · doi:10.1038/mp.2017.38 · Cited by 116
Crosstalk between the microbiome and cancer cells by quorum sensing peptides
Wynendaele, E., Verbeke, F., D’Hondt, M., Hendrix, A., de Wiele, C. V., Burvenich, C., Peremans, K. Y., Wever, O. D., Bracke, M., & Spiegeleer, B. M. J. D. (2015) · Peptides · doi:10.1016/j.peptides.2014.12.009 · Cited by 116
“switching from a low-fat, plant (non- or limited digestible) polysaccharide-rich diet to a high-fat, high-sugar diet can shift the structure of the gut microbiota within a single day [52,53].”
Comparative Analysis of Intestinal Tract Models
Williams, C. F., Walton, G., Jiang, L., Plummer, S. F., Garaiová, I., & Gibson, G. R. (2015) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-022814-015429 · Cited by 123
Diet, microbiota, and dysbiosis: a ‘recipe’ for colorectal cancer
Vipperla, K., & O’Keefe, S. J. (2016) · Food & Function · doi:10.1039/c5fo01276g · Cited by 117
Crosstalk between Bile Acids and Gut Microbiota and Its Impact on Farnesoid X Receptor Signalling
Wahlstrom, A. M., Kovatcheva‐Datchary, P., Ståhlman, M., Bäckhed, F., & Marschall, H. (2017) · Digestive Diseases · doi:10.1159/000450982 · Cited by 119
Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome
Boling, L., Cuevas, D., Grasis, J. A., Kang, H. S., Knowles, B., Levi, K., Maughan, H., McNair, K. A., Rojas, M. I., Sanchez, S. E., et al. (2020) · Gut Microbes · doi:10.1080/19490976.2019.1701353 · Cited by 112
“gut community composition.(3,21,22) Thus, there is strong evidence that many common food and/or environmental compounds alter gut community composition, sometimes through prophage activation.”
BackgroundDiet Effects in Gut Microbiome and Obesity
Chen, J., He, X., & Huang, J. (2014) · Journal of Food Science · doi:10.1111/1750-3841.12397 · Cited by 121
Carbohydrate Intake in the Etiology of Crohnʼs Disease and Ulcerative Colitis
Chan, S. S. M., Luben, R., van Schaik, F. D. M., Oldenburg, B., Bueno-de-Mesquita, H. B., Hallmans, G., Karling, P., Lindgren, S. C., Grip, O., Key, T. J., et al. (2014) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000168 · Cited by 118
“induced dysbiosis of the gut microbiota may disrupt immune regulatory mechanisms leading to IBD susceptibility(39, 40), although the exact mechanism by which dysbiosis contributes to IBD has yet to be fully defined.”
Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose
Zhang, W., Liu, W., Hou, R., Zhang, L., Schmitz‐Esser, S., Sun, H., Xie, J., Zhang, Y., Wang, C., Li, L., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0051-y · Cited by 113
Intestinal Sensing by Gut Microbiota: Targeting Gut Peptides
Covașă, M., Stephens, R. W., Toderean, R., & Cobuz, C. (2019) · Frontiers in Endocrinology · doi:10.3389/fendo.2019.00082 · Cited by 117
“Indeed, HF-feeding of humanized gnotobiotic mice results in a rapid shift in microbiome and its metabolic pathways preceding increased adiposity (168) suggesting that direct microbe host crosstalk influences intestinal signaling mechanism.”
BackgroundMicrobiome-mediated plasticity directs host evolution along several distinct time scales
Kolodny, O., & Schulenburg, H. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0589 · Cited by 116
Gut and Root Microbiota Commonalities
Ramírez-Puebla, S. T., Servín-Garcidueñas, L. E., Jiménez‐Marín, B., Bolaños, L. M., Rosenblueth, M., Martínez, J., Rogel, M. A., Ormeño‐Orrillo, E., & Martínez‐Romero, E. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.02553-12 · Cited by 119
The role of the gut microbiota in the metabolism of polyphenols as characterized by gnotobiotic mice
Pasinetti, G. M., Singh, R., Westfall, S., Herman, F., Faith, J., & Ho, L. (2018) · Journal of Alzheimer s Disease · doi:10.3233/jad-171151 · Cited by 112
“One germ free mouse model found that consistent with in vitro evidence supporting the relevance of gut microbiota in the bioconversion and bioavailability of phenolic metabolites from botanical polyphenol components [85–87], germ-free mice or antibiotictreated mice had decreased bioconversion of orally consumed polyph…”
ResultSelf-citationMasanta, W. O., Heimesaat, M. M., Bereswill, S., Tareen, A. M., Lugert, R., Groß, U., & Zautner, A. E. (2013) · Clinical and Developmental Immunology · doi:10.1155/2013/526860 · Cited by 112
Ejtahed, H., Soroush, A. R., Angoorani, P., Larijani, B. A., & Hasani‐Ranjbar, S. (2016) · Hormone and Metabolic Research · doi:10.1055/s-0042-107792 · Cited by 115
Kumari, M., & Kozyrskyj, A. L. (2016) · Obesity Reviews · doi:10.1111/obr.12484 · Cited by 111
“Dietary fibre, however, is passed into the large intestine undigested because humans lack enzymatic machinery for its breakdown (11) and is instead broken down by microbial enzymes to generate ATP (energy) and metabolites such as SCFAs (12).”
BackgroundHelminth-induced alterations of the gut microbiota exacerbate bacterial colitis
Su, C., Su, L., Li, Y., Long, S. R., Chang, J. H., Zhang, W., Walker, W. A., Xavier, R. J., Cherayil, B. J., & Shi, H. N. (2017) · Mucosal Immunology · doi:10.1038/mi.2017.20 · Cited by 111
Exercise prevents high fat diet-induced bone loss, marrow adiposity and dysbiosis in male mice
McCabe, L. R., Irwin, R., Tekalur, A., Evans, C. C., Schepper, J. D., Parameswaran, N., & Ciancio, M. J. (2018) · Bone · doi:10.1016/j.bone.2018.03.024 · Cited by 117
Fuirst, M., Veit, R. R., Hahn, M. A., Dheilly, N. M., & Thorne, L. H. (2018) · PLoS ONE · doi:10.1371/journal.pone.0209200 · Cited by 108
Newman, T. M., Shively, C. A., Register, T. C., Appt, S. E., Yadav, H., Colwell, R. R., Fanelli, B. C., Dadlani, M., Graubics, K., Nguyen, U. T., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01069-y · Cited by 113
“Bacterial abundance is modulated by dietary macronutrient consumption, including proteins, carbohydrates, and fats [6, 8, 9].”
BackgroundGut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention
Cani, P. D., de Hase, E. M., & Hul, M. V. (2021) · Microorganisms · doi:10.3390/microorganisms9061302 · Cited by 116
“However, despite the differences between the donor and recipient mice, several studies showed that there is a remarkable proportion (±85%) of the human microbiota that can be successfully transferred into GF rodents [61], although others reports are challenging this number [64].”
BackgroundEffects of anti-aging interventions on intestinal microbiota
Du, Y., Gao, Y., Zeng, B., Fan, X., Yang, D., & Yang, M. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1994835 · Cited by 118
“The balance between Firmicutes and Bacteroidetes varies with obesity and the proportion of lean body mass.(68) Enrichment of Firmicutes or a reduction in Bacteroidetes is considered an obesity-inducing trait that is commonly seen in obese children.”
BackgroundThe nature of nutrition: a unifying framework
Simpson, S. J., & Raubenheimer, D. (2012) · Australian Journal of Zoology · doi:10.1071/zo11068 · Cited by 122
Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice
Chaplin, A. M. L., Parra, P., Laraichi, S., Serra, F. A., & Palou, A. (2015) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500480 · Cited by 115
Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons
Grieneisen, L., Livermore, J. A., Alberts, S. C., Tung, J., & Archie, E. A. (2017) · Integrative and Comparative Biology · doi:10.1093/icb/icx046 · Cited by 117
“Dietary shifts in gut microbiome composition tend to occur rapidly, over hours or days (Turnbaugh et al. 2009b; Fernando et al. 2010; David et al. 2014), whereas our data suggest that males’ microbiomes continue to converge with their new social group years after emigration.”
BackgroundConserved and variable responses of the gut microbiome to resistant starch type 2
Bendiks, Z. A., Knudsen, K. E. B., Keenan, M. J., & Marco, M. L. (2020) · Nutrition Research · doi:10.1016/j.nutres.2020.02.009 · Cited by 116
Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases
Thomas, C., Minty, M., Vinel, A., Canceill, T., Loubières, P., Burcelin, R., Kaddech, M., Blasco‐Baqué, V., & Laurencin‐Dalicieux, S. (2021) · Diagnostics · doi:10.3390/diagnostics11081376 · Cited by 122
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Hansen, M. E. B., Rubel, M. A., Bailey, A. G., Ranciaro, A., Thompson, S. R., Campbell, M. C., Beggs, W., Dave, J. R., Mokone, G. G., Mpoloka, S. W., et al. (2019) · Genome Biology · doi:10.1186/s13059-018-1616-9 · Cited by 110
Healthy hosts rule within: ecological forces shaping the gut microbiota
Byndloss, M. X., Pernitzsch, S. R., & Bäumler, A. J. (2018) · Mucosal Immunology · doi:10.1038/s41385-018-0010-y · Cited by 109
Impact of prebiotics on metabolic and behavioral alterations in a mouse model of metabolic syndrome
de Cossío, L. F., Fourrier, C., Sauvant, J., Everard, A., Capuron, L., Cani, P. D., Layé, S., & Castanon, N. (2016) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2016.12.022 · Cited by 108
Pröbstel, A.-K., & Baranzini, S. E. (2018) · Neurotherapeutics · doi:10.1007/s13311-017-0587-y · Cited by 110
“Another major potential confounder for studies on the gut microbiome is diet, whose influence on the gut bacterial composition is arguably stronger than that of genetics [60].”
Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome
Lang, J. M., Pan, C., Cantor, R. M., Tang, W. H. W., Garcı́a-Garcı́a, J. C., Kurtz, I., Hazen, S. L., Bergeron, N., Krauss, R. M., & Lusis, A. J. (2018) · mBio · doi:10.1128/mbio.01604-18 · Cited by 112
Fan, Y., Qin, Y., Chen, M., Li, X., Wang, R., Huang, Z., Xu, Q., Yu, M., Zhang, Y., Han, X., et al. (2019) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2019.121534 · Cited by 109
Can diet modulate trimethylamine N-oxide (TMAO) production? What do we know so far?
Coutinho‐Wolino, K. S., Cardozo, L., Leal, V. D. O., Mafra, D., & Stockler‐Pinto, M. B. (2021) · European Journal of Nutrition · doi:10.1007/s00394-021-02491-6 · Cited by 116
Taschuk, R., & Griebel, P. J. (2012) · Animal Health Research Reviews · doi:10.1017/s1466252312000096 · Cited by 116
“Amazingly, fecal transplants from humanized mice with ‘westernized’ microbiomes were transmissible to gnotobiotes (Turnbaugh et al., 2009).”
BackgroundThe Gut Microbiome and Individual-Specific Responses to Diet
Leshem, A., Segal, E., & Elinav, E. (2020) · mSystems · doi:10.1128/msystems.00665-20 · Cited by 109
The modulatory role of high fat feeding on gastrointestinal signals in obesity
Duca, F. A., Sakar, Y., & Covașă, M. (2013) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2013.05.005 · Cited by 112
Collins, B., Hoffman, J. B., Martinez, K., Grace, M. H., Lila, M. A., Cockrell, C., Nadimpalli, A., Chang, E. B., Chuang, C., Wei, Z., et al. (2016) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2015.12.021 · Cited by 109
“For example, fecal microbiota transplant from lean donors improved insulin sensitivity in humans with metabolic syndrome [72].”
BackgroundCox, L. M., Sohn, J., Tyrrell, K. L., Citron, D. M., Lawson, P. A., Patel, N. B., Iizumi, T., Perez-Perez, G. I., Goldstein, E. J. C., & Blaser, M. J. (2017) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001793 · Cited by 110
Oral bacteria colonize and compete with gut microbiota in gnotobiotic mice
Li, B., Yang, G., Cheng, L., Zeng, B., Yu, J., Peng, X., Zhao, J., Li, W., Ren, B., Li, M., et al. (2019) · International Journal of Oral Science · doi:10.1038/s41368-018-0043-9 · Cited by 116
Luche, É., Cousin, B., Garidou, L., Sérino, M., Waget, A., Barreau, C., André, M., Valet, P., Courtney, M., Casteilla, L., et al. (2013) · Molecular Metabolism · doi:10.1016/j.molmet.2013.06.005 · Cited by 115
“A substantial number of publications have demonstrated the important role of intestinal microbiota in the control of adipose tissue development [6,8,35,36] and metabolic inflammation [13,27,35,37,38].”
BackgroundZhang, F., Ma, T., Cui, P., Tamadon, A., He, S., Huo, C., Yierfulati, G., Xu, X., Hu, W., Li, X., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00175 · Cited by 108
Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation
Richards, A. L., Muehlbauer, A. L., Alazizi, A., Burns, M. B., Findley, A. S., Messina, F., Gould, T. J., Cascardo, C. A., Piqué-Regi, R., Blekhman, R., et al. (2019) · mSystems · doi:10.1128/msystems.00323-18 · Cited by 110
“Variability in gut microbiota composition is related to many factors, including medication, diet and genetics [4, 5, 13, 15, 23, 30, 33, 35, 49, 53, 55, 56, 58].”
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine
Preidis, G. A., Saulnier, D. M. A., Blutt, S. E., Mistretta, T., Riehle, K. P., Major, A. M., Venable, S. F., Finegold, M. J., Petrosino, J. F., Conner, M. E., et al. (2012) · The FASEB Journal · doi:10.1096/fj.10-177980 · Cited by 111
“In neonatal mice, stool is not available in adequate amounts for individual sampling until the third week of life (25); thus, samples were pooled from 20 8-d-old pups/group.”
MethodResultHost-Microbe Interactions in the Neonatal Intestine: Role of Human Milk Oligosaccharides
Donovan, S. M., Wang, M., Li, M., Friedberg, I., Schwartz, S., & Chapkin, R. S. (2012) · Advances in Nutrition · doi:10.3945/an.112.001859 · Cited by 116
Factors Determining Colorectal Cancer: The Role of the Intestinal Microbiota
Nistal, E., Fernández-Fernández, N., Vivas, S., & Olcoz, J. L. (2015) · Frontiers in Oncology · doi:10.3389/fonc.2015.00220 · Cited by 111
“Associated with these metabolic functions, the intestinal TABLe 1 | Gut bacteria associated with dysbiosis in CRC. Microorganism Changes in microbiota Sampling Reference Fusobacterium ↑ Feces/Mucosa (56, 60, 70) Enterococcaceae ↑ Feces (60, 71) Campylobacter ↑ Feces (60) Erysipelotrichaceae ↑ Feces (60, 72) Collinsell…”
Background
Metadata
- Authors
- Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- University of Colorado Boulder (US)
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Science Translational Medicine
- Published
- 2009-11-11
- Volume
- 1
- Issue
- 6
- Pages
- 6ra14-6ra14
- ISSN
- 1946-6234 (ISSN-L)
- 1946-6242
- PMC
- PMC2894525
- OpenAlex
- W2136552678
- Cited by
- 3,058
- References
- 27
- Citations by year
- 2026: 71 · 2025: 112 · 2024: 140 · 2023: 158 · 2022: 201 · 2021: 251 · 2020: 269 · 2019: 288 · 2018: 248 · 2017: 246 · 2016: 237 · 2015: 198 · 2014: 183 · 2013: 173 · 2012: 131
- FWCI
- 37.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science Translational Medicine (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Crohn's and Colitis Foundation
- National Institute of Diabetes and Digestive and Kidney Diseases (DK 70977, R01DK070977)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- gut microbiota, diet, fecal microbiota transplantation, Western diet, high-fat high-sugar diet, bacterial colonization, intergenerational transmission, adiposity, metabolic pathways, germ-free mice, 16S rRNA gene sequences
- MeSH terms
- Animals, Bacteria, Diet, Energy Metabolism, Germ-Free Life, Humans, Intestines, Male, Mice, Inbred C57BL, Molecular Sequence Data, RNA, Ribosomal, 16S, Genomics, Adiposity, Mice
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