Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection

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

The gut microbiota as an environmental factor that regulates fat storage

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245

Obesity 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

Host-Bacterial Mutualism in the Human Intestine

Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277

Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine

Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358

A Genomic View of the Human- Bacteroides thetaiotaomicron Symbiosis

Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C., Hooper, L. V., & Gordon, J. I. (2003) · Science · doi:10.1126/science.1080029 · Cited by 1,353

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

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

Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785

The human microbiome project

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

Gut microbiota in health and disease

Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182

Evolution of mammals and their gut microbes

Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747

Bacterial Community Variation in Human Body Habitats Across Space and Time

Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231

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

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200

The microbiome and innate immunity

Thaiss, C. A., Zmora, N., Levy, M., & Elinav, E. (2016) · Nature · doi:10.1038/nature18847 · Cited by 2,012

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

Wen, L., Ley, R. E., Volchkov, P. Y., Stranges, P. B., Avanesyan, L., Stonebraker, A. C., Hu, C., Wong, F. S., Szot, G. L., Bluestone, J. A., et al. (2008) · Nature · doi:10.1038/nature07336 · Cited by 1,921

The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43

Kimura, I., Ozawa, K., Inoue, D., Imamura, T., Kimura, K., Maeda, T., Terasawa, K., Kashihara, D., Hirano, K., Tani, T., et al. (2013) · Nature Communications · doi:10.1038/ncomms2852 · Cited by 1,512

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

Gut immune maturation depends on colonization with a host-specific microbiota

Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241

Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis

Bevins, C. L., & Salzman, N. H. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2546 · Cited by 1,238

Enteric defensins are essential regulators of intestinal microbial ecology

Salzman, N. H., Hung, K., Haribhai, D., Chu, H., Karlsson-Sjöberg, J., Amir, E., Teggatz, P., Barman, M., Hayward, M., Eastwood, D., et al. (2010) · Nature Immunology · doi:10.1038/ni.1825 · Cited by 1,156

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

Jones, B. V., Begley, M., Hill, C., Gahan, C. G. M., & Marchesi, J. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804437105 · Cited by 1,098

Role of gastrointestinal microbiota in fish

Nayak, S. K. (2010) · Aquaculture Research · doi:10.1111/j.1365-2109.2010.02546.x · Cited by 1,073

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048

Immunological aspects of intestinal mucus and mucins

Johansson, M. E. V., & Hansson, G. C. (2016) · Nature Reviews Immunology · doi:10.1038/nri.2016.88 · Cited by 1,007

The host shapes the gut microbiota via fecal microRNA

Liu, S., da Cunha, A. P., Rezende, R. M., Cialic, R., Wei, Z., Bry, L., Comstock, L. E., Gandhi, R., & Weiner, H. L. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2015.12.005 · Cited by 808

The human gut microbiome: ecology and recent evolutionary changes

Walter, J., & Ley, R. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102830 · Cited by 720

Conducting a microbiome study

Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R., & Ley, R. E. (2014) · Cell · doi:10.1016/j.cell.2014.06.037 · Cited by 714

A new view of the fish gut microbiome: advances from next-generation sequencing

Ghanbari, M., Kneifel, W., & Domig, K. J. (2015) · Aquaculture · doi:10.1016/j.aquaculture.2015.06.033 · Cited by 669

The gut microbiota modulates host energy and lipid metabolism in mice

Velagapudi, V. R., Hezaveh, R., Reigstad, C. S., Gopalacharyulu, P., Yetukuri, L., Islam, S., Felin, J., Perkins, R., Borén, J., Orešič, M., et al. (2010) · Journal of Lipid Research · doi:10.1194/jlr.m002774 · Cited by 589

Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

Peterson, D. A., Frank, D. N., Pace, N. R., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.05.001 · Cited by 503

Chapter 12: Human Microbiome Analysis

Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496

Microbiota and metabolic diseases

Pascale, A., Marchesi, N., Marelli, C., Coppola, A., Luzi, L., Govoni, S., Giustina, A., & Gazzaruso, C. (2018) · Endocrine · doi:10.1007/s12020-018-1605-5 · Cited by 423

Paneth cells, defensins, and the commensal microbiota: A hypothesis on intimate interplay at the intestinal mucosa

Salzman, N. H., Underwood, M. A., & Bevins, C. L. (2007) · Seminars in Immunology · doi:10.1016/j.smim.2007.04.002 · Cited by 414

Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota

Espey, M. G. (2013) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2012.10.554 · Cited by 396

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden

Baxter, N. T., Zackular, J. P., Chen, G. Y., & Schloss, P. D. (2014) · Microbiome · doi:10.1186/2049-2618-2-20 · Cited by 299

Untitled work

(2016) · PubMed · Cited by 287

Microbes, immunity, and behavior: psychoneuroimmunology meets the microbiome

Dinan, T. G., & Cryan, J. F. (2017) · Neuropsychopharmacology · doi:10.1038/npp.2016.103 · Cited by 246

Unique and shared responses of the gut microbiota to prolonged fasting: A comparative study across five classes of vertebrate hosts

Kohl, K. D., Amaya, J., Passement, C. A., Dearing, M. D., & McCue, M. D. (2014) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12442 · Cited by 249

Non-alcoholic fatty liver and the gut microbiota

Bashiardes, S., Shapiro, H., Rozin, S., Shibolet, O., & Elinav, E. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.06.003 · Cited by 241

Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice

Friswell, M. K., Gika, H., Stratford, I. J., Theodoridis, G., Telfer, B., Wilson, I. D., & McBain, A. J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008584 · Cited by 207

The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus

Jašarević, E., Howard, C. D., Morrison, K., Misic, A., Weinkopff, T., Scott, P., Hunter, C., Beiting, D., & Bale, T. L. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0182-5 · Cited by 189

Genetics and Environmental Interactions Shape the Intestinal Microbiome to Promote Inflammatory Bowel Disease Versus Mucosal Homeostasis

Sartor, R. B. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.10.036 · Cited by 164

Community-Wide Response of the Gut Microbiota to Enteropathogenic Citrobacter rodentium Infection Revealed by Deep Sequencing

Hoffmann, C., Hill, D. A., Minkah, N., Kirn, T., Troy, A., Artis, D., & Bushman, F. (2009) · Infection and Immunity · doi:10.1128/iai.00493-09 · Cited by 142

Fostering of advanced mutualism with gut microbiota by Immunoglobulin A

Sutherland, D. B., Suzuki, K., & Fagarasan, S. (2016) · Immunological Reviews · doi:10.1111/imr.12384 · Cited by 115

The Metabolic and Ecological Interactions of Oxalate-Degrading Bacteria in the Mammalian Gut

Miller, A., & Dearing, D. (2013) · Pathogens · doi:10.3390/pathogens2040636 · Cited by 101

The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs

Yáñez-Ruiz, D. R., Macías, B., Pinloche, E., & Newbold, C. J. (2010) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2010.00852.x · Cited by 92

Interpreting infective microbiota: the importance of an ecological perspective

Rogers, G. B., Hoffman, L. R., Carroll, M. P., & Bruce, K. D. (2013) · Trends in Microbiology · doi:10.1016/j.tim.2013.03.004 · Cited by 76

Nutrients and Microbiota in Lung Diseases of Prematurity: The Placenta-Gut-Lung Triangle

Piersigilli, F., Van Grambezen, B., Hocq, C., & Danhaive, O. (2020) · Nutrients · doi:10.3390/nu12020469 · Cited by 64

Comprehensive understanding the impacts of dietary exposure to polyethylene microplastics on genetically improved farmed tilapia (Oreochromis niloticus): tracking from growth, microbiota, metabolism to gene expressions

Lu, X., Zhang, J.-X., Zhang, L., Wu, D., Tian, J., Yu, L.-J., He, L., Zhong, S., Du, H., Deng, D.-F., et al. (2022) · Science of The Total Environment · doi:10.1016/j.scitotenv.2022.156571 · Cited by 65

Evaluating the capacity of human gut microorganisms to colonize the zebrafish larvae (Danio rerio)

Valenzuela, M.-J., Caruffo, M., Herrera, Y., Medina, D. A., Coronado, M., Feijóo, C. G., Muñoz, S., Garrido, D., Troncoso, M., Figueroa, G., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01032 · Cited by 39

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism

Lee, J.-G., Lee, S., Jeon, J., Kong, H. G., Cho, H.-J., Kim, J.-H., Kim, S.-Y., Oh, M. J., Lee, D., Seo, N., et al. (2022) · Microbiome · doi:10.1186/s40168-021-01191-x · Cited by 26

The role of host molecules in communication with the resident and pathogenic microbiota: A review

White, J. R., Dauros-Singorenko, P., Hong, J., Vanholsbeeck, F., Phillips, A., & Swift, S. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100005 · Cited by 21