Diet leaves a genetic signature in a keystone member of the gut microbiota
Open accessAbstract
Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet causes microbiota imbalances that underlay many pathological conditions (i.e., dysbiosis). Although the effects of dietary changes on microbiota composition and functions are well documented, their impact in gut bacterial evolution remains unexplored. We followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly in the gut and Western-style diet selected for mutations that promote degradation of mucin-derived glycans. Periodic dietary changes caused fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intraspecies genetic diversity compared to constant dietary regimens. These results show that dietary changes leave a genetic signature in microbiome members and suggest that B. thetaiotaomicron genetic diversity could be a biomarker for dietary differences among individuals.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Consumption of a western-style diet drives the emergence of mutations in Bacteroides thetaiotaomicron that promote degradation of mucin O-glycans in the mouse gut.
“Consumption of a western-style diet also drives the emergence of mutations in Bacteroides thetaiotaomicron, an anaerobe specialized in fermenting complex polysaccharides. These mutations promote the degradation of mucin O-glycans in the mouse gut.”
From Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases (2024) · cites this paper as [642]
Cites
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742 · see citing works
Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012) · Fly · doi:10.4161/fly.19695 · Cited by 11,816 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · see citing works
The igraph software package for complex network research
Csárdi, G., & Nepusz, T. (2006) · Medical Entomology and Zoology · Cited by 10,078 · see citing works
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,633 · see citing works
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 8,994 · see citing works
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839 · see citing works
A 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 · see citing works
Vegan : community ecology package. R package version 1.17-9
Oksanen, J. (2007) · Medical Entomology and Zoology · Cited by 6,606 · see citing works
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986 · see citing works
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748 · see citing works
Richness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works
Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis
Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251 · see citing works
Interactions Between the Microbiota and the Immune System
Hooper, L. V., Littman, D. R., & Macpherson, A. J. (2012) · Science · doi:10.1126/science.1223490 · Cited by 4,173 · see citing works
mixOmics: An R package for ‘omics feature selection and multiple data integration
Rohart, F., Gautier, B., Singh, A., & Lê Cao, K.-A. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005752 · Cited by 4,056 · see citing works
Fast and accurate de novo genome assembly from long uncorrected readsPreprint
Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059 · see citing works
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · see citing works
Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805 · see citing works
Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609 · see citing works
Diet–microbiota interactions as moderators of human metabolism
Sonnenburg, J. L., & Bäckhed, F. (2016) · Nature · doi:10.1038/nature18846 · Cited by 2,257 · see citing works
The role of the gut microbiota in nutrition and health
Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.156 · Cited by 2,203 · see citing works
Dietary intervention impact on gut microbial gene richness
Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., et al. (2013) · Nature · doi:10.1038/nature12480 · Cited by 1,832 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
Kaoutari, A. E., Armougom, F., Gordon, J. I., Raoult, D., & Henrissat, B. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3050 · Cited by 1,683 · see citing works
The gastrointestinal mucus system in health and disease
Johansson, M. E. V., Sjövall, H., & Hansson, G. C. (2013) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2013.35 · Cited by 1,438 · see citing works
Interactions between the microbiota and pathogenic bacteria in the gut
Bäumler, A. J., & Sperandio, V. (2016) · Nature · doi:10.1038/nature18849 · Cited by 1,420 · see citing works
Gut microbial metabolites as multi-kingdom intermediates
Krautkramer, K. A., Fan, J., & Bäckhed, F. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0438-4 · Cited by 1,398 · see citing works
Png, C. W., Lindén, S. K., Gilshenan, K. S., Zoetendal, E. G., McSweeney, C. S., Sly, L. I., McGuckin, M. A., & Florin, T. H. J. (2010) · American Journal of Gastroenterology · doi:10.1038/ajg.2010.281 · Cited by 1,364 · see citing works
Fernandes, A. D., Reid, J. N., Macklaim, J. M., McMurrough, T. A., Edgell, D. R., & Gloor, G. B. (2014) · Microbiome · doi:10.1186/2049-2618-2-15 · Cited by 1,329 · see citing works
Genome evolution and adaptation in a long-term experiment with Escherichia coli
Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E., & Kim, J. F. (2009) · Nature · doi:10.1038/nature08480 · Cited by 1,184 · see citing works
Glycan foraging in vivo by an intestine-adapted bacterial symbiont
Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works
Diet dominates host genotype in shaping the murine gut microbiota
Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103 · see citing works
DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays
Singh, A., Shannon, C. P., Gautier, B., Rohart, F., Vacher, M. A., Tebbutt, S. J., & Cao, K. L. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty1054 · Cited by 1,079 · see citing works
Peres‐Neto, P. R., & Jackson, D. A. (2001) · Oecologia · doi:10.1007/s004420100720 · Cited by 981 · see citing works
Completing bacterial genome assemblies with multiplex MinION sequencing
Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017) · Microbial Genomics · doi:10.1099/mgen.0.000132 · Cited by 956 · see citing works
Martens, E. C., Chiang, H. C., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.007 · Cited by 919 · see citing works
Sonnenburg, E. D., & Sonnenburg, J. L. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.003 · Cited by 871 · see citing works
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Martens, E. C., Lowe, E. C., Chiang, H. C., Pudlo, N. A., Wu, M., McNulty, N. P., Abbott, D. W., Henrissat, B., Gilbert, H. J., Bolam, D. N., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001221 · Cited by 847 · see citing works
Health and disease markers correlate with gut microbiome composition across thousands of people
Manor, O., Dai, C. L., Kornilov, S. A., Smith, B., Price, N. D., Lovejoy, J. C., Gibbons, S. M., & Magis, A. T. (2020) · Nature Communications · doi:10.1038/s41467-020-18871-1 · Cited by 810 · see citing works
Role of the microbiome in human development
Domínguez-Bello, M. G., Godoy‐Vitorino, F., Knight, R. D., & Blaser, M. J. (2019) · Gut · doi:10.1136/gutjnl-2018-317503 · Cited by 786 · see citing works
Sonnenburg, E. D., Zheng, H., Joglekar, P., Higginbottom, S. K., Firbank, S. J., Bolam, D. N., & Sonnenburg, J. L. (2010) · Cell · doi:10.1016/j.cell.2010.05.005 · Cited by 745 · see citing works
Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon
Salyers, A. A., Vercellotti, J. R., West, S. E. H., & Wilkins, T. D. (1977) · Applied and Environmental Microbiology · doi:10.1128/aem.33.2.319-322.1977 · Cited by 691 · see citing works
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Baym, M., Kryazhimskiy, S., Lieberman, T. D., Chung, H., Desai, M. M., & Kishony, R. (2015) · PLOS ONE · doi:10.1371/journal.pone.0128036 · Cited by 685 · see citing works
Bacterial colonization factors control specificity and stability of the gut microbiota
Lee, S. M., Donaldson, G. P., Mikulski, Z., Boyajian, S., Ley, K. F., & Mazmanian, S. K. (2013) · Nature · doi:10.1038/nature12447 · Cited by 622 · see citing works
Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606 · see citing works
Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways
Marcobal, A., Barboza, M., Sonnenburg, E. D., Pudlo, N., Martens, E. C., Desai, P., Lebrilla, C. B., Weimer, B. C., Mills, D. A., German, J. B., et al. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.007 · Cited by 574 · see citing works
Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice
Faith, J. J., McNulty, N. P., Rey, F. E., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1206025 · Cited by 536 · see citing works
Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations
Zhang, C., Zhang, M. H., Pang, X., Zhao, Y., Wang, L., & Zhao, L. (2012) · The ISME Journal · doi:10.1038/ismej.2012.27 · Cited by 496 · see citing works
Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut
Giraud, A., Matić, I., Tenaillon, O., Clara, A., Radman, M., Fons, M., & Taddéi, F. (2001) · Science · doi:10.1126/science.1056421 · Cited by 482 · see citing works
PROTEST: A PROcrustean Randomization TEST of community environment concordance
Jackson, D. A. (1995) · Ecoscience · doi:10.1080/11956860.1995.11682297 · Cited by 473 · see citing works
Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon
Salyers, A. A., West, S. E. H., Vercellotti, J. R., & Wilkins, T. D. (1977) · Applied and Environmental Microbiology · doi:10.1128/aem.34.5.529-533.1977 · Cited by 471 · see citing works
Adaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works
Metabolic niche of a prominent sulfate-reducing human gut bacterium
Rey, F. E., Gonzalez, M. D., Cheng, J., Wu, M., Ahern, P. P., & Gordon, J. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1312524110 · Cited by 412 · see citing works
An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts
Rakoff-Nahoum, S., Coyne, M. J., & Comstock, L. E. (2013) · Current Biology · doi:10.1016/j.cub.2013.10.077 · Cited by 402 · see citing works
Filippis, F. D., Pasolli, E., Tett, A., Tarallo, S., Naccarati, A., Angelis, M. D., Neviani, E., Cocolin, L., Gobbetti, M., Segata, N., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.004 · Cited by 399 · see citing works
Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation
Cullen, T. W., Schofield, W. B., Barry, N. A., Putnam, E. E., Rundell, E. A., Trent, M. S., Degnan, P. H., Booth, C. J., Yu, H., & Goodman, A. L. (2015) · Science · doi:10.1126/science.1260580 · Cited by 395 · see citing works
Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota
Thompson, J. A., Oliveira, R. A., Djuković, A., Úbeda, C., & Xavier, K. B. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.049 · Cited by 390 · see citing works
Self-citationMimee, M., Tucker, A. C., Voigt, C. A., & Lu, T. K. (2015) · Cell Systems · doi:10.1016/j.cels.2015.06.001 · Cited by 387 · see citing works
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Garud, N. R., Good, B. H., Hallatschek, O., & Pollard, K. S. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000102 · Cited by 347 · see citing works
A field guide for the compositional analysis of any-omics data
Quinn, T. P., Erb, I., Gloor, G. B., Notredame, C., Richardson, M. F., & Crowley, T. M. (2019) · GigaScience · doi:10.1093/gigascience/giz107 · Cited by 345 · see citing works
Bjursell, M. K., Martens, E. C., & Gordon, J. I. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m606509200 · Cited by 338 · see citing works
Completing bacterial genome assemblies with multiplex MinION sequencingPreprint
Wick, R. R., Judd, L. M., Gorrie, C. L., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/160614 · Cited by 313 · see citing works
Commensal and Pathogenic Escherichia coli Metabolism in the Gut
Conway, T., & Cohen, P. S. (2015) · Microbiology Spectrum · doi:10.1128/microbiolspec.mbp-0006-2014 · Cited by 300 · see citing works
McNulty, N. P., Wu, M., Erickson, A. R., Pan, C., Erickson, B. K., Martens, E. C., Pudlo, N. A., Muegge, B. D., Henrissat, B., Hettich, R. L., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001637 · Cited by 290 · see citing works
Kashyap, P. C., Marcobal, A., Ursell, L. K., Smits, S. A., Sonnenburg, E. D., Costello, E. K., Higginbottom, S. K., Domino, S. E., Holmes, S. P., Relman, D. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306070110 · Cited by 285 · see citing works
Mucin Degradation in Human Colon Ecosystems
Hoskins, L. C., & Boulding, E. T. (1981) · Journal of Clinical Investigation · doi:10.1172/jci110009 · Cited by 277 · see citing works
Smith, E. A., & Macfarlane, G. T. (1998) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.1998.tb00487.x · Cited by 277 · see citing works
The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology
Porter, N. T., & Martens, E. C. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095316 · Cited by 251 · see citing works
An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations
Hegreness, M., Noam Shoresh, F., Hartl, D. L., & Kishony, R. (2006) · Science · doi:10.1126/science.1122469 · Cited by 250 · see citing works
Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model
Hryckowian, A. J., Treuren, W. V., Smits, S. A., Davis, N. M., Gardner, J. O., Bouley, D. M., & Sonnenburg, J. L. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0150-6 · Cited by 249 · see citing works
Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome
Whitaker, W. R., Shepherd, E. S., & Sonnenburg, J. L. (2017) · Cell · doi:10.1016/j.cell.2017.03.041 · Cited by 239 · see citing works
Poulsen, L. K., Licht, T. R., Rang, C. U., Krogfelt, K. A., & Molin, S. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.20.5840-5845.1995 · Cited by 202 · see citing works
Preparation of Genomic DNA from Bacteria
SURZYCKI, S. J. (2000) · Springer eBooks · doi:10.1007/978-3-642-56968-5_4 · Cited by 200 · see citing works
The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps
Barroso-Batista, J., Sousa, A., Lourenço, M., Bergman, M., Sobral, D., Demengeot, J., Xavier, K. B., & Gordo, I. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004182 · Cited by 188 · see citing works
Self-citationSymbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans
Pudlo, N. A., Urs, K., Kumar, S. S., German, J. B., Mills, D. A., & Martens, E. C. (2015) · mBio · doi:10.1128/mbio.01282-15 · Cited by 187 · see citing works
Roles of the intestinal microbiota in pathogen protection
Úbeda, C., Djuković, A., & Isaac, S. (2017) · Clinical & Translational Immunology · doi:10.1038/cti.2017.2 · Cited by 180 · see citing works
Santos-López, A., Marshall, C. W., Scribner, M. R., Snyder, D. J., & Cooper, V. S. (2019) · eLife · doi:10.7554/elife.47612 · Cited by 174 · see citing works
Liu, H., Shiver, A. L., Price, M. N., Carlson, H. K., Trotter, V. V., Chen, Y., Escalante, V., Ray, J., Hern, K. E., Petzold, C. J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108789 · Cited by 161 · see citing works
Wotzka, S. Y., Kreuzer, M., Maier, L., Arnoldini, M., Nguyen, B. D., Brachmann, A. O., Berthold, D. L., Zünd, M., Hausmann, A., Bakkeren, E., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0568-5 · Cited by 139 · see citing works
Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut
Crook, N., Ferreiro, A. L., Gasparrini, A. J., Pesesky, M. W., Gibson, M. K., Wang, B., Sun, X., Condiotte, Z. J., Dobrowolski, S., Peterson, D. A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.02.005 · Cited by 129 · see citing works
Porter, N. T., Canales-Herrerías, P., Peterson, D. A., & Martens, E. C. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.08.020 · Cited by 125 · see citing works
Parallel genetic adaptation across environments differing in mode of growth or resource availability
Turner, C. B., Marshall, C. W., & Cooper, V. S. (2018) · Evolution Letters · doi:10.1002/evl3.75 · Cited by 104 · see citing works
Dissecting the Genetic Components of Adaptation of Escherichia coli to the Mouse Gut
Giraud, A., Arous, S., Paepe, M. D., Gaboriau‐Routhiau, V., Bambou, J., Rakotobé, S., Lindner, A. B., Taddéi, F., & Cerf–Bensussan, N. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.0040002 · Cited by 98 · see citing works
Maharjan, R. P., & Ferenci, T. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2001477 · Cited by 98 · see citing works
Barroso-Batista, J., Demengeot, J., & Gordo, I. (2015) · Nature Communications · doi:10.1038/ncomms9945 · Cited by 94 · see citing works
Self-citationLeatham, M. P., Stevenson, S. J., Gauger, E. J., Krogfelt, K. A., Lins, J. J., Haddock, T. L., Autieri, S. M., Conway, T., & Cohen, P. S. (2005) · Infection and Immunity · doi:10.1128/iai.73.12.8039-8049.2005 · Cited by 93 · see citing works
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice
Yılmaz, B., Mooser, C., Keller, I., Li, H., Zimmermann, J., Bosshard, L., Fuhrer, T., de Agüero, M. G., Trigo, N. F., Lischer, H. E. L., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.001 · Cited by 87 · see citing works
Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility
Barroso-Batista, J., Pedro, M. F., Sales-Dias, J., Pinto, C., Thompson, J. A., Pereira, H., Demengeot, J., Gordo, I., & Xavier, K. B. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.050 · Cited by 86 · see citing works
Self-citationLescat, M., Launay, A., Ghalayini, M., Magnan, M., Glodt, J., Pintard, C., Dion, S., Denamur, É., & Tenaillon, O. (2016) · Molecular Ecology · doi:10.1111/mec.13851 · Cited by 81 · see citing works
Paepe, M. D., Gaboriau‐Routhiau, V., Rainteau, D. P., Rakotobé, S., Taddéi, F., & Cerf–Bensussan, N. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002107 · Cited by 73 · see citing works
Lynch, J. B., & Sonnenburg, J. L. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08123.x · Cited by 72 · see citing works
Radman, M., Matić, I., Halliday, J. A., & Taddéi, F. (1995) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1995.0015 · Cited by 71 · see citing works
Low mutational load and high mutation rate variation in gut commensal bacteria
Ramiro, R. S., Durão, P., Bank, C., & Gordo, I. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000617 · Cited by 68 · see citing works
Self-citationBiochemical Effects on Germ-free Mice of Association with Several Strains of Anaerobic Bacteria
Welling, G. W., Groen, G., Tuinte, J. H. M., Koopman, J. P., & Kennis, H. M. (1980) · Microbiology · doi:10.1099/00221287-117-1-57 · Cited by 61 · see citing works
The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice
Barreto, H. C., Sousa, A., & Gordo, I. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.037 · Cited by 52 · see citing works
Self-citationFabich, A. J., Leatham, M. P., Grissom, J. E., Wiley, G. B., Lai, H., Najar, F. Z., Roe, B. A., Cohen, P. S., & Conway, T. (2011) · Infection and Immunity · doi:10.1128/iai.01199-10 · Cited by 48 · see citing works
Lourenço, M., Ramiro, R. S., Güleresi, D., Barroso-Batista, J., Xavier, K. B., Gordo, I., & Sousa, A. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006420 · Cited by 43 · see citing works
Self-citationHow Food Affects Colonization Resistance Against Enteropathogenic Bacteria
Kreuzer, M., & Hardt, W. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-020420-013457 · Cited by 43 · see citing works
Evolution of commensal bacteria in the intestinal tract of mice
Sousa, A., Frazão, N., Ramiro, R. S., & Gordo, I. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.05.007 · Cited by 32 · see citing works
Self-citationDysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut
Cardoso, L. L., Durão, P., Amicone, M., & Gordo, I. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1235-1 · Cited by 31 · see citing works
Self-citationGhalayini, M., Magnan, M., Dion, S., Zatout, O., Bourguignon, L., Tenaillon, O., & Lescat, M. (2019) · Molecular Ecology · doi:10.1111/mec.15232 · Cited by 28 · see citing works
Relman, D. A. (2020) · Current Opinion in Microbiology · doi:10.1016/j.mib.2020.01.018 · Cited by 14 · see citing works
Mezouari, A., Nangia, R., & Gagnon, J. (2020) · Antioxidants · doi:10.3390/antiox9111038 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases
Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works
Intestinal mucus and their glycans: A habitat for thriving microbiota
Luis, A. S., & Hansson, G. C. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.05.026 · Cited by 295 · see citing works
Single-cell approaches in human microbiome research
Lloréns‐Rico, V., Simcock, J. A., Huys, G. R. B., & Raes, J. (2022) · Cell · doi:10.1016/j.cell.2022.06.040 · Cited by 139 · see citing works
Lopetuso, L. R., Deleu, S., Godny, L., Petito, V., Puca, P., Facciotti, F., Sokol, H., Ianiro, G., Masucci, L., Abreu, M., et al. (2023) · Gut · doi:10.1136/gutjnl-2023-329948 · Cited by 129 · see citing works
Arıkan, M., & Muth, T. (2023) · Molecular Omics · doi:10.1039/d3mo00089c · Cited by 128 · see citing works
Zhou, Y., Liu, M., & Yang, J. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127023 · Cited by 105 · see citing works
Weiß, A. S., Niedermeier, L., von Strempel, A., Burrichter, A. G., Ring, D., Meng, C., Kleigrewe, K., Lincetto, C., Hübner, J., & Stecher, B. (2023) · Nature Communications · doi:10.1038/s41467-023-40372-0 · Cited by 91 · see citing works
Lin, A., Xiong, M., Jiang, A., Huang, L., Wong, H. Z. H., Feng, S., Zhang, C., Yu, H., Chen, L., Chi, H., et al. (2025) · iMeta · doi:10.1002/imt2.70070 · Cited by 91 · see citing works
Intrahost evolution of the gut microbiota
Barreto, H. C., & Gordo, I. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00890-6 · Cited by 81 · see citing works
Self-citationMetabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Bakkeren, E., Piskovsky, V., & Foster, K. R. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.05.013 · Cited by 91 · see citing works
The role of animal hosts in shaping gut microbiome variation
Maritan, E., Quagliariello, A., Frago, E., Patarnello, T., & Martino, M. E. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0071 · Cited by 63 · see citing works
The role of ultra-processed food in obesity
Juul, F., Steele, E. M., Parekh, N., & Monteiro, C. A. (2025) · Nature Reviews Endocrinology · doi:10.1038/s41574-025-01143-7 · Cited by 65 · see citing works
Huang, Z., Boekhorst, J., Fogliano, V., Capuano, E., & Wells, J. M. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c08953 · Cited by 58 · see citing works
Liu, Z., Zhang, D., & Chen, S. (2024) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-024-03034-7 · Cited by 51 · see citing works
Zhang, Z. J., Cole, C. G., Coyne, M. J., Lin, H., Dylla, N. P., Smith, R. C., Pappas, T. E., Townson, S. A., Laliwala, N., Waligurski, E., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.08.016 · Cited by 48 · see citing works
Lv, Q., Li, Z., Sui, A., Yang, X., Han, Y., & Yao, R. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.977187 · Cited by 47 · see citing works
From microbiome composition to functional engineering, one step at a time
Burz, S. D., Čaušević, S., Co, A. D., Dmitrijeva, M., Engel, P., Garrido‐Sanz, D., Greub, G., Hapfelmeier, S., Hardt, W., Vassily Hatzimanikatis, A., et al. (2023) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00063-23 · Cited by 42 · see citing works
Ultra-processed foods: increasing the risk of inflammation and immune dysregulation?
Maki, K. A., Sack, M. N., & Hall, K. D. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01049-x · Cited by 42 · see citing works
Ndeh, D. A., Nakjang, S., Kwiatkowski, K. J., Sawyers, C., Koropatkin, N. M., Hirt, R. P., & Bolam, D. N. (2025) · Nature Communications · doi:10.1038/s41467-025-58660-2 · Cited by 36 · see citing works
Within-host evolution of the gut microbiome
Đapa, T., Wong, D. P. G. H., Vasquez, K. S., Xavier, K. B., Huang, K. C., & Good, B. H. (2023) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102258 · Cited by 36 · see citing works
Self-citationHost–pathobiont interactions in Crohn’s disease
Caruso, R., Lo, B. C., Chen, G., & Núñez, G. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00997-y · Cited by 35 · see citing works
Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization
Kennedy, M. S., Zhang, M., DeLeon, O., Bissell, J., Trigodet, F., Lolans, K., Temelkova, S., Carroll, K., Fiebig, A., Deutschbauer, A. M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113009 · Cited by 32 · see citing works
Hierarchical eco-evo dynamics mediated by the gut microbiome
Decaestecker, E., de Moortel, B. V., Mukherjee, S., Gurung, A., Stoks, R., & Meester, L. D. (2023) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2023.09.013 · Cited by 28 · see citing works
Infection leaves a genetic and functional mark on the gut population of a commensal bacterium
Tawk, C., Lim, B., Bencivenga-Barry, N. A., Lees, H., Ramos, R. J. F., Cross, J. R., & Goodman, A. L. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.04.005 · Cited by 28 · see citing works
Yakabe, K., Higashi, S., Akiyama, M., Mori, H., Murakami, T., Toyoda, A., Sugiyama, Y., Kishino, S., Okano, K., Hirayama, A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111332 · Cited by 24 · see citing works
Within-host bacterial evolution and the emergence of pathogenicity
Tonkin‐Hill, G. Q., Ruis, C., Bentley, S. D., Lythgoe, K., & Bryant, J. M. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02036-1 · Cited by 22 · see citing works
Effect of diet on the evolution of gut commensal bacteria
Đapa, T., & Xavier, K. B. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2369337 · Cited by 21 · see citing works
Self-citationMünch, P. C., Eberl, C., Woelfel, S., Ring, D., Fritz, A., Herp, S., Lade, I., Geffers, R., Franzosa, E. A., Huttenhower, C., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.05.013 · Cited by 21 · see citing works
Voogdt, C. G. P., Tripathi, S. M., Bassler, S. O., McKeithen-Mead, S. A., Guiberson, E. R., Koumoutsi, A., Bravo, A. M., Buie, C., Zimmermann, M., Sonnenburg, J. L., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113519 · Cited by 21 · see citing works
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking
Wong, D. P. G. H., & Good, B. H. (2024) · Nature Communications · doi:10.1038/s41467-024-45792-0 · Cited by 21 · see citing works
Tian, R., Yu, L., Tian, F., Zhao, J., Chen, W., & Zhai, Q. (2024) · Food & Function · doi:10.1039/d4fo00428k · Cited by 23 · see citing works
Hoces, D., Greter, G., Arnoldini, M., Stäubli, M. L., Moresi, C., Sintsova, A., Berent, S., Kolinko, I., Bansept, F., Woller, A., et al. (2023) · eLife · doi:10.7554/elife.81212 · Cited by 21 · see citing works
Phage-encoded carbohydrate-interacting proteins in the human gut
Rothschild-Rodriguez, D., Hedges, M., Kaplan, M., Karav, S., & Nóbrega, F. L. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1083208 · Cited by 18 · see citing works
Huang, K. D., Müller, M., Sivapornnukul, P., Bielecka, A. A., Amend, L., Tawk, C., Bruns, A., Lesker, T.-R., Hahn, A., & Strowig, T. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115067 · Cited by 17 · see citing works
Oh, S., & Li, R. W. (2024) · Advanced Science · doi:10.1002/advs.202400458 · Cited by 15 · see citing works
Mechanisms conferring multi-layered protection against intestinal Salmonella Typhimurium infection
Kroon, S., & Hardt, W. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf038 · Cited by 14 · see citing works
Ultra-Processed Foods and the Impact on Cardiometabolic Health: The Role of Diet Quality
Wang, X., & Sun, Q. (2024) · Diabetes & Metabolism Journal · doi:10.4093/dmj.2024.0659 · Cited by 13 · see citing works
Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis
Stevens, E. J., Li, J., Hector, T. E., Drew, G., Hoang, K. L., Greenrod, S. T. E., Paterson, S., & King, K. C. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf071 · Cited by 13 · see citing works
Huang, X., Tang, X., He, Q., Tadese, D. A., Cao, K., Gao, J., Xu, Q., Cheng, R., Lu, Q., Chen, Y., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.102260 · Cited by 13 · see citing works
Nondigestible carbohydrates and gut microbiota: A dynamic duo in host defense
Zong, X., Luo, S., Liu, S., Deehan, E. C., Wang, Y., & Jin, M. (2024) · Animal Nutriomics · doi:10.1017/anr.2024.8 · Cited by 13 · see citing works
Temporal response patterns of human gut microbiota to dietary fiber
Lin, X., Wang, C., Liu, B., Zhu, Y., Zhai, R., & Zhang, C. (2025) · iMeta · doi:10.1002/imt2.70046 · Cited by 12 · see citing works
Mucin-degrading gut bacteria: context-dependent roles in intestinal homeostasis and disease
Tiffany, E., Kim, K. S., Sittipo, P., Lee, D.-W., & Lee, Y. K. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2614054 · Cited by 15 · see citing works
Maritan, E., Gallo, M., Šrůtková, D., Jelinkova, A., Benada, O., Kofroňová, O., Silva-Soares, N. F., Hudcovic, T., Gifford, I., Barrick, J. E., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01477-y · Cited by 11 · see citing works
Unni, R., Andreani, N. A., Vallier, M., Heinzmann, S. S., Taubenheim, J., Guggeis, M. A., Tran, F., Vogler, O., Künzel, S., Hövener, J., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2286675 · Cited by 12 · see citing works
Liu, J., & Wong, S. S. C. (2022) · Anesthesia & Analgesia · doi:10.1213/ane.0000000000006289 · Cited by 12 · see citing works
From global to local: rethinking the design of probiotic intervention strategies
Vonaesch, P., Garneau, J. R., & Domínguez-Bello, M. G. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.11.009 · Cited by 14 · see citing works
Effects of Habitual Dietary Change on the Gut Microbiota and Health of Silkworms
Wang, G., Ding, X., Yang, J., Ma, L., Sun, X., Zhu, R., Lu, R., Xiao, Z., Xing, Z., Liu, J., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031722 · Cited by 10 · see citing works
Precision microbial regulation: Strategies for modulating GIT microbiota for host health
Pei, Z., Li, Q., Zhang, Y., Guo, C., Abdelsattar, M. M., & Bi, Y. (2025) · iMetaOmics. · doi:10.1002/imo2.54 · Cited by 11 · see citing works
Vasquez, K. S., Wong, D. P. G. H., Pedro, M. F., Yu, F. B., Jain, S., Meng, X., Higginbottom, S. K., DeFelice, B. C., Neff, N. F., Bhatt, A. S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.17.580834 · Cited by 9 · see citing works
Self-citationMandelbaum, N., Carasso, S., Kedem, A., Ziv, T., Keshet-David, R., Abboud, R., Zaatry, R., Gefen, T., & Geva‐Zatorsky, N. (2025) · Nature Communications · doi:10.1038/s41467-025-60202-9 · Cited by 8 · see citing works
Irizarry, H. G. L., & Brito, I. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1199640 · Cited by 8 · see citing works
The Lumenal Microbiota Varies Biogeographically in the Gastrointestinal Tract of Rhesus Macaques
Yan, Y., Wang, J., Qiu, S., Duan, Y., & Si, W. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00343-22 · Cited by 8 · see citing works
Pervasive selective sweeps across human gut microbiomesPreprint
Wolff, R., & Garud, N. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.22.573162 · Cited by 8 · see citing works
Distinguishing among evolutionary and ecological processes shaping microbiome dynamics
Batarseh, T. N., & Koskella, B. L. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf107 · Cited by 7 · see citing works
How nutrient starvation impacts the gut microbiome
Estrela, S., Long, J. Z., & Huang, K. C. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02139-9 · Cited by 7 · see citing works
Selenium alters the gene content but not the taxonomic composition of the soil microbiome
Bennett, A. E., Kelsey, S., Saup, C. M., Wilkins, M., & Malacrinò, A. (2024) · Environmental Microbiome · doi:10.1186/s40793-024-00641-x · Cited by 6 · see citing works
Preferential sugar utilization by bifidobacterial species
Murakami, R., Yoshida, K., Sakanaka, M., Urashima, T., Xiao, J., Katayama, T., & Odamaki, T. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2023.19 · Cited by 6 · see citing works
Tsukimi, T., Obana, N., Shigemori, S., Arakawa, K., Miyauchi, E., Yang, J., Song, I., Ashino, Y., Wakayama, M., Soga, T., et al. (2024) · mSystems · doi:10.1128/msystems.01123-23 · Cited by 8 · see citing works
Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution
Slack, E. M. C., & Diard, M. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00574-z · Cited by 6 · see citing works
Sharma, P., Singh, S., Das, K., Mahant, S., & Das, R. (2023) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-023-12470-y · Cited by 6 · see citing works
Microbial Evolution: An overlooked biomarker of host diet
Garud, N. R. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.01.009 · Cited by 5 · see citing works
Characterization of Mutational Signatures in Tumors from a Large Chinese Population
Chevalier, A. A., Guo, T., Gurevich, N. Q., Xu, J., Yajima, M., & Campbell, J. D. (2025) · Cancer Research Communications · doi:10.1158/2767-9764.crc-24-0496 · Cited by 4 · see citing works
Farmer, N. M., Benezra, A., Maki, K. A., Ishaq, S. L., & Kozik, A. J. (2025) · mSystems · doi:10.1128/msystems.00640-25 · Cited by 4 · see citing works
Impact of evolution on lifestyle in microbiome
González, A., Fullaondo, A., & Odriozola, A. (2024) · Advances in genetics · doi:10.1016/bs.adgen.2024.02.003 · Cited by 4 · see citing works
Uniform bacterial genetic diversity along the gut
Wasney, M., Briscoe, L., Wolff, R., Ghezzi, H., Tropini, C., & Garud, N. R. (2026) · Nature Communications · doi:10.1038/s41467-026-70705-8 · Cited by 3 · see citing works
Matsumoto, K., Noguchi, A., Miyamoto, F., Inoue, R., Hirai, H., Miwa, T., Nakagawa, Y., & Higashimura, Y. (2025) · Food Chemistry · doi:10.1016/j.foodchem.2025.144719 · Cited by 2 · see citing works
Saeed, N. K., Elbeltagi, Y. M., & Al‐Beltagi, M. (2026) · World Journal of Virology · doi:10.5501/wjv.v15.i1.118362 · Cited by 2 · see citing works
Liu, Z., Hu, Y., Li, J., Guo, X., Ai, C., Song, S., & Zhu, B. (2024) · Food Bioscience · doi:10.1016/j.fbio.2024.103701 · Cited by 2 · see citing works
Boatta, F., van Hal, J. R., Beukeboom, L. W., & Ellers, J. (2024) · Journal of Evolutionary Biology · doi:10.1093/jeb/voae122 · Cited by 2 · see citing works
Ecotype formation and prophage domestication during gut bacterial evolution
Frazão, N., & Gordo, I. (2023) · BioEssays · doi:10.1002/bies.202300063 · Cited by 2 · see citing works
Self-citationHoces, D., Greter, G., Arnoldini, M., Moresi, C., Berent, S., Kolinko, I., Bansept, F., Woller, A., Häfliger, J., Martens, E. C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.19.496708 · Cited by 2 · see citing works
Tryptophan catabolism by gut microbiota : A bridge connecting food science and human nutrition
Huang, Z. (2023) · doi:10.18174/583090 · Cited by 2 · see citing works
Within-host competition sparks pathogen molecular evolution and perpetual microbiota dysbiosisPreprint
Stevens, E. J., Li, J., Hector, T. E., Drew, G., Hoang, K. L., Greenrod, S. T. E., Paterson, S., & King, K. C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.03.610829 · Cited by 2 · see citing works
Hecht, A. L., Mahmud, N., Chaudhry, S., Cao, J. Y., Branigan, G. P., Lee, J., Theiller, E., Roggiani, M., Friedman, E. S., Herman, L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.26.645536 · Cited by 2 · see citing works
Shatova, O. P., Zabolotneva, A. A., Rumyantsev, S. A., & Shestopalov, A. V. (2025) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162025602101 · Cited by 1 · see citing works
Luo, J., Zhang, R., Wang, W., & Zhang, D. (2025) · European Journal of Nutrition · doi:10.1007/s00394-025-03843-2 · Cited by 1 · see citing works
Host diets drive microbiome evolution and functional divergence
Nguyen, K. L., Xia, J. S., & Mei, W. (2026) · Genes & Diseases · doi:10.1016/j.gendis.2026.102068 · Cited by 1 · see citing works
Antifungal therapy improves microbiome dynamics in inflammatory bowel disease
Pan, X.-Y., Conroy, A., Ngima, T. S., Mesko, M., Morzhanaeva, O., Li, A., Marino, J., Westblade, L. F., Grier, A., Bacher, P., et al. (2026) · Nature Medicine · doi:10.1038/s41591-026-04616-y · Cited by 2 · see citing works
Zioutis, C., Lang, M., Pereira, F. C., Bochkareva, O., Kolodyazhnaya, E., Osvatic, J., McCoy, K. D., Künzel, S., Fokt, H., Baines, J. F., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.24.661302 · Cited by 1 · see citing works
Maritan, E., Gallo, M., Šrůtková, D., Jelinkova, A., Benada, O., Kofroňová, O., Silva-Soares, N. F., Hudcovic, T., Gifford, I., Barrick, J. E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.04.482961
The Causal Relationship between Gut Microbiota and Acne: A Two-Sample Mendelian Randomization Study
顾, 昀. (2023) · Advances in Clinical Medicine · doi:10.12677/acm.2023.1361468
Aihetanmu, S., Liang, Z., Zhang, X., Luo, B., Zhang, H., Huang, J., Tian, F., Sun, H., & Ni, Y. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1399743
Les humains ont-ils coévolué avec le microbiote intestinal ?
Mazel, F. (2025) · médecine/sciences · doi:10.1051/medsci/2024190
The gut microbiota effect on obesity and associated metabolic disorders: A Review
Thamer, R. (2025) · Pharaonic Journal of Science · doi:10.71428/pjs.2025.0103
Walusimbi, B., Hayes, K. S., Lawson, M. A., Thompson, S., Bancroft, A. J., Elliott, A. M., & Grencis, R. K. (2026) · Parasite Immunology · doi:10.1111/pim.70060
Unrug-Bielawska, K., Dziełak, M., Sandowska-Markiewicz, Z., Piątkowska, M., Czarnowski, P., Goryca, K., Żeber‐Lubecka, N., Dąbrowska, M., Bałabas, A., Statkiewicz, M., et al. (2026) · BMC Gastroenterology · doi:10.1186/s12876-026-04647-2
Orchestrating life’s first community: molecular assembly by human milk oligosaccharides
Zhou, Y., Yang, B., Zhao, J., Ross, P. M., Stanton, C., & Chen, W. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2632973
Zeng, Z., Zhao, Y., Bi, J., Yan, Q., Zhang, W., Chen, F., & Wang, C. (2026) · Theoretical and Applied Genetics · doi:10.1007/s00122-026-05345-z
Within-host evolution and transmission of a human gut symbiont across ecological scales
Vasquez, K. S., Wong, D. P. G. H., Kotaka, K., McKeithen-Mead, S. A., Pedro, M. F., Yu, F. B., Jain, S., Meng, X., Higginbottom, S. K., DeFelice, B. C., et al. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.09.002
Self-citationFu, Y., 周剑敏, Zhang, H., Qi, G., Wang, J., & Wu, S. (2026) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2026.125943
- Authors
- Dapa, T., Ramiro, R. S., Pedro, M. F., Gordo, I., & Xavier, K. B.
- Affiliations
- Instituto Gulbenkian de Ciência (PT)
- Corresponding author
- Xavier, Karina Bivar
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2022-02
- Volume
- 30
- Issue
- 2
- Pages
- 183-199.e10
- ISSN
- 1931-3128 (ISSN-L)
- OpenAlex
- W4220756682
- Cited by
- 91
- References
- 108
- Citations by year
- 2026: 11 · 2025: 23 · 2024: 22 · 2023: 24 · 2022: 11
- FWCI
- 6.53
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 373 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell Host & Microbe (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- Bacteroides thetaiotaomicron, Western diet, high-fat high-sugar diet, fiber-degrading bacteria, intraspecies genetic diversity, dysbiosis, dietary change, intestinal colonization, metabolic switch
- MeSH terms
- Gastrointestinal Microbiome, Bacteroides thetaiotaomicron, Animals, Diet, Dietary Fiber, Humans, Mice, Diet, High-Fat, Dysbiosis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review