Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

Stanford Encyclopedia of Philosophy

(2015) · Choice Reviews Online · doi:10.5860/choice.187763 · Cited by 5,364 · see citing works

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) · Nature Genetics · doi:10.1038/ng1201-365 · Cited by 4,109 · see citing works

Helicobacter pylori Infection and the Risk of Gastric Carcinoma

Parsonnet, J., FRIEDMAN, G. D., Vandersteen, D. P., Chang, Y., Vogelman∥, J. H., Orentreich∥, N., & Sibley, R. K. (1991) · New England Journal of Medicine · doi:10.1056/nejm199110173251603 · Cited by 3,893 · see citing works

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works

Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease

Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan, Z. E., Challis, C., Schretter, C. E., Rocha, S., Gradinaru, V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.018 · Cited by 3,622 · see citing works

Human Genetics Shape the Gut Microbiome

Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · see citing works

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143 · 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

CONJECTURES AND REFUTATIONS

Alexander, P. F. (1963) · Philosophical Books · doi:10.1111/j.1468-0149.1963.tb00798.x · Cited by 2,864 · see citing works

Environment dominates over host genetics in shaping human gut microbiota

Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works

Population-level analysis of gut microbiome variation

Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400 · see citing works

Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: A proof-of-concept exploratory study

Depommier, C., Everard, A., Druart, C., Plovier, H., Van Hul, M., Vieira-Silva, S., Falony, G., Raes, J., Maiter, D., Delzenne, N. M., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0495-2 · Cited by 2,357 · see citing works

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

Koren, O., Goodrich, J. K., Cullender, T. C., Spor, A., Laitinen, K., Kling Bäckhed, H., Gonzalez, A., Werner, J. J., Angenent, L. T., Knight, R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.008 · Cited by 2,165 · see citing works

Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism

Zheng, P., Zeng, B., Zhou, C., Liu, M., Fang, Z., Xu, X., Zeng, L., Chen, J., Fan, S., Du, X., et al. (2016) · Molecular Psychiatry · doi:10.1038/mp.2016.44 · Cited by 2,023 · see citing works

Early infancy microbial and metabolic alterations affect risk of childhood asthma

Arrieta, M., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist‐Doutsch, S., Kuzeljevic, B., Gold, M. J., Britton, H. M., Lefebvre, D. L., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aab2271 · Cited by 1,783 · see citing works

Gut microbiota and IBD: causation or correlation?

Ni, J., Wu, G. D., Albenberg, L., & Tomov, V. T. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.88 · Cited by 1,778 · see citing works

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella

Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., Hallen, A., Martens, E., Björck, I., & Bäckhed, F. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.10.001 · Cited by 1,731 · see citing works

Gut microbiota dysbiosis contributes to the development of hypertension

Li, J., Zhao, F., Wang, Y., Chen, J., Tao, J., Tian, G., Wu, S., Liu, W., Cui, Q., Geng, B., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0222-x · Cited by 1,685 · see citing works

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat

Kelly, J. R., Borre, Y., O' Brien, C., Patterson, E., El Aidy, S., Deane, J., Kennedy, P. J., Beers, S., Scott, K., Moloney, G., et al. (2016) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2016.07.019 · Cited by 1,683 · see citing works

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

Sanna, S., van Zuydam, N. R., Mahajan, A., Kurilshikov, A., Vich Vila, A., Võsa, U., Mujagic, Z., Masclee, A. A. M., Jonkers, D. M. A. E., Oosting, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0350-x · Cited by 1,539 · see citing works

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention

Liu, R., Hong, J., Xu, X., Feng, Q., Zhang, D., Gu, Y., Shi, J., Zhao, S., Liu, W., Wang, X., et al. (2017) · Nature Medicine · doi:10.1038/nm.4358 · Cited by 1,501 · see citing works

Gut microbes promote colonic serotonin production through an effect of short-chain fatty acids on enterochromaffin cells

Reigstad, C. S., Salmonson, C. E., III, J. F. R., Szurszewski, J. H., Linden, D. R., Sonnenburg, J. L., Farrugia, G., & Kashyap, P. C. (2015) · The FASEB Journal · doi:10.1096/fj.14-259598 · Cited by 1,335 · see citing works

Negative results are disappearing from most disciplines and countries

Fanelli, D. (2012) · Scientometrics · doi:10.1007/s11192-011-0494-7 · Cited by 1,248 · see citing works

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 · see citing works

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Sharon, G., Cruz, N. J., Kang, D.-W., Gandal, M. J., Wang, B., Kim, Y.-M., Zink, E. M., Casey, C. P., Taylor, B. C., Lane, C. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.05.004 · Cited by 1,182 · see citing works

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173 · see citing works

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

Cekanaviciute, E., Yoo, B. B., Runia, T. F., Debelius, J. W., Singh, S., Nelson, C., Kanner, R., Bencosme, Y., Lee, Y. K., Hauser, S. L., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711235114 · Cited by 1,040 · see citing works

Reproducibility in Science: Improving the Standard for Basic and Preclinical Research

Begley, C. G., & Ioannidis, J. P. A. (2015) · Circulation Research · doi:10.1161/circresaha.114.303819 · Cited by 1,035 · see citing works

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) · doi:10.1038/s41467-017-01973-8 · Cited by 986 · see citing works

Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice

Berer, K., Gerdes, L. A., Cekanaviciute, E., Jia, X., Xiao, L., Xia, Z., Liu, C., Klotz, L., Stauffer, U., Baranzini, S. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711233114 · Cited by 933 · see citing works

The Human Gut Microbiome: From Association to Modulation

Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845 · see citing works

The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice

Zheng, P., Zeng, B., Liu, M., Chen, J., Pan, J., Han, Y., Liu, Y., Cheng, K., Zhou, C., Wang, H., et al. (2019) · Science Advances · doi:10.1126/sciadv.aau8317 · Cited by 704 · see citing works

Dysbiosis Contributes to Arthritis Development via Activation of Autoreactive T Cells in the Intestine

Maeda, Y., Kurakawa, T., Umemoto, E., Motooka, D., Ito, Y., Gotoh, K., Hirota, K., Matsushita, M., Furuta, Y., Narazaki, M., et al. (2016) · Arthritis & Rheumatology · doi:10.1002/art.39783 · Cited by 686 · see citing works

Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice

Wong, S. H., Zhao, L., Zhang, X., Nakatsu, G., Han, J., Xu, W., Xiao, X., Kwong, T. N. Y., Tsoi, H., Wu, W. K. K., et al. (2017) · Gastroenterology · doi:10.1053/j.gastro.2017.08.022 · Cited by 634 · see citing works

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

Wang, J., Thingholm, L. B., Skiecevičienė, J., Rausch, P., Kummen, M., Hov, J. R., Degenhardt, F., Heinsen, F.-A., Rühlemann, M. C., Szymczak, S., et al. (2016) · Nature Genetics · doi:10.1038/ng.3695 · Cited by 625 · see citing works

Humanized Mouse Models of Clinical Disease

Walsh, N. C., Kenney, L. L., Jangalwe, S., Aryee, K., Greiner, D. L., Brehm, M. A., & Shultz, L. D. (2016) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-052016-100332 · Cited by 565 · see citing works

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

Britton, G. J., Contijoch, E. J., Mogno, I., Vennaro, O. H., Llewellyn, S. R., Ng, R., Li, Z., Mortha, A., Merad, M., Das, A., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.015 · Cited by 549 · see citing works

Citrobacter rodentium: infection, inflammation and the microbiota

Collins, J. W., Keeney, K. M., Crepin, V. F., Rathinam, V. A. K., Fitzgerald, K. A., Finlay, B. B., & Frankel, G. M. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3315 · Cited by 508 · see citing works

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice

De Palma, G., Lynch, M. D. J., Lu, J., Dang, V. T., Deng, Y., Jury, J., Umeh, G., Miranda, P. M., Pigrau Pastor, M., Sidani, S., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf6397 · Cited by 505 · see citing works

Fecal microbiota transplantation: in perspective

Gupta, S., Allen‐Vercoe, E., & Petrof, E. O. (2015) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x15607414 · Cited by 484 · see citing works

Causation in biology: stability, specificity, and the choice of levels of explanation

Woodward, J. (2010) · Biology & Philosophy · doi:10.1007/s10539-010-9200-z · Cited by 475 · see citing works

Healthy infants harbor intestinal bacteria that protect against food allergy

Feehley, T., Plunkett, C. H., Bao, R., Hong, S. M. C., Culleen, E., Belda‐Ferre, P., Campbell, E., Aitoro, R., Nocerino, R., Paparo, L., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0324-z · Cited by 474 · see citing works

The Human Microbiome and Obesity: Moving beyond Associations

Maruvada, P., Leone, V., Kaplan, L. M., & Chang, E. B. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.10.005 · Cited by 468 · see citing works

Use of pigs as a potential model for research into dietary modulation of the human gut microbiota

Heinritz, S. N., Mosenthin, R., & Weiss, E. (2013) · Nutrition Research Reviews · doi:10.1017/s0954422413000152 · Cited by 421 · see citing works

Dysbiosis and Its Discontents

Hooks, K. B., & O’Malley, M. A. (2017) · mBio · doi:10.1128/mbio.01492-17 · Cited by 386 · see citing works

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy

Kau, A. L., Planer, J. D., Liu, J., Rao, S. M., Yatsunenko, T., Trehan, I., MANARY, M. J., Liu, T., Stappenbeck, T. S., Maleta, K. M., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa4877 · Cited by 373 · see citing works

A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

Marcobal, A. M., Kashyap, P., Nelson, T. A., Aronov, P. A., Donia, M. S., Spormann, A. M., Fischbach, M. A., & Sonnenburg, J. L. (2013) · The ISME Journal · doi:10.1038/ismej.2013.89 · Cited by 351 · see citing works

Inflammatory Bowel Disease as a Model for Translating the Microbiome

Huttenhower, C., Kostic, A. D., & Xavier, R. J. (2014) · Immunity · doi:10.1016/j.immuni.2014.05.013 · Cited by 332 · see citing works

Fecal microbiota transplantation in metabolic syndrome: History, present and future

de Groot, P. F., Frissen, M. N., de Clercq, N. C., & Nieuwdorp, M. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1293224 · Cited by 322 · see citing works

Publication Bias (The "File-Drawer Problem") in Scientific Inference

Scargle, J. D. (1999) · arXiv · doi:10.48550/arxiv.physics/9909033 · Cited by 313 · see citing works

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 · see citing works

The microbiome beyond the horizon of ecological and evolutionary theory

Koskella, B. L., Hall, L. J., & Metcalf, C. J. E. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0340-2 · Cited by 292 · see citing works

What exactly is ‘N’ in cell culture and animal experiments?

Lazic, S. E., Clarke-Williams, C. J., & Munafò, M. R. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2005282 · Cited by 291 · see citing works

The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD

Soderborg, T. K., Clark, S. E., Mulligan, C. E., Janssen, R. C., Babcock, L. R., Ir, D., Young, B. E., Krebs, N. F., Lemas, D. J., Johnson, L. K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06929-0 · Cited by 288 · see citing works

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

Yassour, M., Lim, M. Y., Yun, H. S., Tickle, T. L., Sung, J., Song, Y., Lee, K., Franzosa, E. A., Morgan, X. C., Gevers, D., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0271-6 · Cited by 286 · see citing works

Parasutterella, in association with irritable bowel syndrome and intestinal chronic inflammation

Chen, Y., Wu, H., Wu, S., Lü, N., Wang, Y., Liu, H., Dong, L., Liu, T., & Shen, X. (2018) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.14281 · Cited by 285 · see citing works

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions

McBurney, M. I., Davis, C. D., Fraser, C. M., Schneeman, B. O., Huttenhower, C., Verbeke, K., Walter, J., & Latulippe, M. E. (2019) · Journal of Nutrition · doi:10.1093/jn/nxz154 · Cited by 283 · see citing works

Publication bias and the canonization of false facts

Nissen, S. B., Magidson, T., Gross, K., & Bergstrom, C. T. (2016) · eLife · doi:10.7554/elife.21451 · Cited by 266 · see citing works

Disbiome database: linking the microbiome to disease

Janssens, Y., Nielandt, J., Bronselaer, A., Debunne, N., Verbeke, F., Wynendaele, E., Immerseel, F. V., Vandewynckel, Y., Tré, G. D., & Spiegeleer, B. D. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1197-5 · Cited by 250 · see citing works

Problems with the concept of gut microbiota dysbiosis

Brüssow, H. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13479 · Cited by 250 · see citing works

HIV persists throughout deep tissues with repopulation from multiple anatomical sources

Chaillon, A., Gianella, S., Dellicour, S., Rawlings, S. A., Schlub, T. E., De Oliveira, M. F., Ignacio, C., Porrachia, M., Vrancken, B., & Smith, D. M. (2020) · Journal of Clinical Investigation · doi:10.1172/jci134815 · Cited by 250 · see citing works

Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice

Nagao‐Kitamoto, H., Shreiner, A. B., Gillilland, M. G., Kitamoto, S., Ishii, C., Hirayama, A., Kuffa, P., Zaatari, M. E., Grasberger, H., Seekatz, A. M., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.02.003 · Cited by 248 · see citing works

Microbiome: Focus on Causation and Mechanism

Fischbach, M. A. (2018) · Cell · doi:10.1016/j.cell.2018.07.038 · Cited by 248 · see citing works

Animal models of anxiety disorders in rats and mice: some conceptual issues

Steimer, T. J. (2011) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2011.13.4/tsteimer · Cited by 242 · see citing works

Practical considerations for large-scale gut microbiome studies

Vandeputte, D., Tito, R. Y., Vanleeuwen, R., Falony, G., & Raes, J. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux027 · Cited by 237 · see citing works

Human Microbiota-Associated Mice: A Model with Challenges

Arrieta, M., Walter, J., & Finlay, B. B. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.014 · Cited by 236 · see citing works

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

Staley, C. M., Kaiser, T., Beura, L. K., Hamilton, M. J., Weingarden, A. R., Bobr, A., Kang, J., Masopust, D., Sadowsky, M. J., & Khoruts, A. (2017) · Microbiome · doi:10.1186/s40168-017-0306-2 · Cited by 236 · see citing works

Microbiota and reproducibility of rodent models

Franklin, C. L., & Ericsson, A. C. (2017) · Lab Animal · doi:10.1038/laban.1222 · Cited by 235 · see citing works

Inferring causal molecular networks: empirical assessment through a community-based effort

Hill, S. M., Heiser, L. M., Cokelaer, T., Unger, M., Nesser, N. K., Carlin, D. E., Zhang, Y., Sokolov, A., Paull, E., Wong, C., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3773 · Cited by 232 · see citing works

Potential role of fecal microbiota from patients with slow transit constipation in the regulation of gastrointestinal motility

Ge, X., Zhao, W., Ding, C., Tian, H., Xu, L., Wang, H., Ni, L., Jiang, J., Gong, J., Zhu, W., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-00612-y · Cited by 232 · see citing works

Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice

Torres, J., Hu, J., Seki, A., Eisele, C., Nair, N., Huang, R., Tarassishin, L., Jharap, B., Cote-Daigneault, J., Mao, Q., et al. (2020) · Gut · doi:10.1136/gutjnl-2018-317855 · Cited by 218 · see citing works

Negativity towards negative results: a discussion of the disconnect between scientific worth and scientific culture

Matosin, N., Frank, E., Engel, M., Lum, J., & Newell, K. (2014) · Disease Models & Mechanisms · doi:10.1242/dmm.015123 · Cited by 209 · see citing works

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic

Tomkovich, S., Dejea, C. M., Winglee, K., Drewes, J. L., Chung, L., Housseau, F., Pope, J. L., Gauthier, J., Sun, X., Mühlbauer, M., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124196 · Cited by 209 · see citing works

Adapting Koch's postulates

Byrd, A. L., & Segre, J. A. (2016) · Science · doi:10.1126/science.aad6753 · Cited by 207 · see citing works

Microbiology: Microbiome science needs a healthy dose of scepticism

Hanage, W. P. (2014) · Nature · doi:10.1038/512247a · Cited by 200 · see citing works

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

Martínez, I., Maldonado-Gomez, M. X., Gomes-Neto, J. C., Kittana, H., Ding, H., Schmaltz, R., Joglekar, P., Cardona, R. J., Marsteller, N. L., Kembel, S. W., et al. (2018) · eLife · doi:10.7554/elife.36521 · Cited by 199 · see citing works

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes

Walter, J., Maldonado-Gómez, M. X., & Martínez, I. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.08.008 · Cited by 198 · see citing works

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

Battaglioli, E. J., Hale, V. L., Chen, J., Jeraldo, P., Ruiz-Mojica, C. A., Schmidt, B. A., Rekdal, V. M., Till, L. M., Huq, L., Smits, S. A., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aam7019 · Cited by 173 · see citing works

Translational Mouse Models of Autism: Advancing Toward Pharmacological Therapeutics

Kazdoba, T. M., Leach, P. T., Yang, M., Silverman, J. L., Solomon, M., & Crawley, J. N. (2015) · Current topics in behavioral neurosciences · doi:10.1007/7854_2015_5003 · Cited by 172 · see citing works

Analysis of the Contribution of Salmonella Pathogenicity Islands 1 and 2 to Enteric Disease Progression Using a Novel Bovine Ileal Loop Model and a Murine Model of Infectious Enterocolitis

Coombes, B. K., Coburn, B. A., Potter, A. A., Gomis, S. M., Mirakhur, K. K., Li, Y., & Finlay, B. B. (2005) · Infection and Immunity · doi:10.1128/iai.73.11.7161-7169.2005 · Cited by 168 · see citing works

Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults

Fielding, R. A., Reeves, A. R., Jasuja, R., Liu, C. K., Barrett, B. B., & Lustgarten, M. S. (2019) · Experimental Gerontology · doi:10.1016/j.exger.2019.110722 · Cited by 163 · see citing works

Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis

Chiu, C.-C., Ching, Y.-H., Li, Y.-P., Liu, J.-Y., Huang, Y.-T., Huang, Y.-W., Yang, S.-S., Huang, W.-C., & Chuang, H.-L. (2017) · Nutrients · doi:10.3390/nu9111220 · Cited by 160 · see citing works

Mediation Analysis: A Retrospective Snapshot of Practice and More Recent Directions

Gelfand, L. A., Mensinger, J. L., & TenHave, T. R. (2009) · The Journal of General Psychology · doi:10.3200/genp.136.2.153-178 · Cited by 152 · see citing works

Medicines from microbiota

Olle, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2548 · Cited by 140 · see citing works

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes

Poole, A. C., Goodrich, J. K., Youngblut, N. D., Luque, G. G., Ruaud, A., Sutter, J. L., Waters, J. L., Shi, Q., El-Hadidi, M. S., Johnson, L. M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.001 · Cited by 139 · see citing works

Fecal metabolite of a gnotobiotic mouse transplanted with gut microbiota from a patient with Alzheimer’s disease

Fujii, Y., Nguyen, T. T. T., Fujimura, Y., Kameya, N., Nakamura, S., Arakawa, K., & Morita, H. (2019) · Bioscience Biotechnology and Biochemistry · doi:10.1080/09168451.2019.1644149 · Cited by 133 · see citing works

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 124 · see citing works

Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model

Natividad, J. M., Pinto-Sánchez, M. I., Galipeau, H. J., Jury, J., Jordana, M., Reinisch, W., Collins, S. M., Bercik, P., Surette, M. G., Allen‐Vercoe, E., et al. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000422 · Cited by 119 · see citing works

Compositional mediation analysis for microbiome studies

Sohn, M. B., & Li, H. (2019) · The Annals of Applied Statistics · doi:10.1214/18-aoas1210 · Cited by 113 · see citing works

Innovative Drugs to Treat Depression: Did Animal Models Fail to Be Predictive or Did Clinical Trials Fail to Detect Effects?

Belzung, C. (2014) · Neuropsychopharmacology · doi:10.1038/npp.2013.342 · Cited by 106 · see citing works

Commensal Koch's postulates: establishing causation in human microbiota research

Neville, B. A., Forster, S. C., & Lawley, T. D. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.001 · Cited by 102 · see citing works

Neuroinflammation in Murine Cirrhosis Is Dependent on the Gut Microbiome and Is Attenuated by Fecal Transplant

Liu, R., Kang, J. D., Sartor, R. B., Sikaroodi, M., Fagan, A., Gavis, E. A., Zhou, H., Hylemon, P. B., Herzog, J., Li, X., et al. (2019) · Hepatology · doi:10.1002/hep.30827 · Cited by 101 · see citing works

Does the gut microbiota have a role in type 1 diabetes? Early evidence from humans and animal models of the disease

Atkinson, M. A., & Chervonsky, A. V. (2012) · Diabetologia · doi:10.1007/s00125-012-2672-4 · Cited by 90 · see citing works

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

Zhang, L., Bahl, M. I., Roager, H. M., Fonvig, C. E., Hellgren, L. I., Frandsen, H. L., Pedersen, O. B., Holm, J., Hansen, T. F., & Licht, T. R. (2016) · The ISME Journal · doi:10.1038/ismej.2016.151 · Cited by 85 · see citing works

A great-ape view of the gut microbiome

Nishida, A. H., & Ochman, H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0085-z · Cited by 82 · see citing works

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection

Li, S. X., Sen, S., Schneider, J. M., Xiong, K.-N., Nusbacher, N. M., Moreno-Huizar, N., Shaffer, M., Armstrong, A. J. S., Severs, E., Kuhn, K. A., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007611 · Cited by 75 · see citing works

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models

Touw, K., Ringus, D. L., Hubert, N., Wang, Y., Leone, V. A., Nadimpalli, A., Theriault, B. R., Huang, Y. E., Tune, J. D., Herring, P. B., et al. (2017) · Physiological Reports · doi:10.14814/phy2.13182 · Cited by 68 · see citing works

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition

Wagner, V. E., Dey, N., Guruge, J. L., Hsiao, A., Ahern, P. P., Semenkovich, N. P., Blanton, L. V., Cheng, J., Griffin, N. W., Stappenbeck, T. S., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aah4669 · Cited by 64 · see citing works

Mediation Analysis as a Means of Identifying Dietary Components That Differentially Affect the Fecal Microbiota of Infants Weaned by Modified Baby-Led and Traditional Approaches

Leong, C. S.-F., Haszard, J. J., Lawley, B., Otal, A., Taylor, R. W., Szymlek‐Gay, E. A., Fleming, E., Daniels, L., Fangupo, L. J., Tannock, G. W., et al. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.00914-18 · Cited by 61 · see citing works

How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers

Lynch, K. E., Parke, E. C., & O’Malley, M. A. (2019) · Biology & Philosophy · doi:10.1007/s10539-019-9702-2 · Cited by 60 · see citing works

Humanized mice: Current states and perspectives

Garcia, S., & Freitas, A. A. (2012) · Immunology Letters · doi:10.1016/j.imlet.2012.03.009 · Cited by 53 · see citing works

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice

Quach, D., Collins, F. L., Parameswaran, N., McCabe, L. R., & Britton, R. A. (2018) · mSphere · doi:10.1128/mspheredirect.00545-17 · Cited by 53 · see citing works

An Adult Mouse Model of Vibrio cholerae-induced Diarrhea for Studying Pathogenesis and Potential Therapy of Cholera

Sawasvirojwong, S., Srimanote, P., Chatsudthipong, V., et al. (2013) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0002293 · Cited by 50 · see citing works

Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques

Namasivayam, S., Kauffman, K. D., McCulloch, J. A., Yuan, W., Thovarai, V., Mittereder, L. R., Trinchieri, G., Barber, D. L., & Sher, A. (2019) · mBio · doi:10.1128/mbio.01018-19 · Cited by 49 · see citing works

Severe obesity and gut microbiota: does bariatric surgery really reset the system?

Cani, P. D. (2018) · Gut · doi:10.1136/gutjnl-2018-316815 · Cited by 45 · see citing works

An Extensively Humanized Mouse Model to Predict Pathways of Drug Disposition and Drug/Drug Interactions, and to Facilitate Design of Clinical Trials

Henderson, C. J., Kapelyukh, Y., Scheer, N., Rode, A., McLaren, A. W., MacLeod, A. K., Lin, D., Wright, J., Stanley, L. A., & Wolf, C. R. (2019) · Drug Metabolism and Disposition · doi:10.1124/dmd.119.086397 · Cited by 44 · see citing works

Language, numeracy and logic in microbiome science

Shanahan, F., & Hill, C. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0163-5 · Cited by 41 · see citing works

Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model

Dhakal, S., Wang, L., Antony, L., Rank, J., Bernardo, P., Ghimire, S., Bondra, K., Siems, C., Lakshmanappa, Y. S., Renu, S., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01509 · Cited by 40 · see citing works

Akkermansia muciniphila is permissive to arthritis in the K/BxN mouse model of arthritis

Stoll, M. L., Pierce, M. K., Watkins, J. A., Zhang, M., Weiss, P. F., Weiss, J. E., Elson, C. O., Cron, R. Q., Kumar, R., Morrow, C. D., et al. (2018) · Genes and Immunity · doi:10.1038/s41435-018-0024-1 · Cited by 38 · see citing works

Which experimental systems should we use for human microbiome science?

Douglas, A. E. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005245 · Cited by 30 · see citing works

Challenges with modelling anxiety disorders: a possible hindrance for drug discovery

Freudenberg, F., O’Leary, A., de Aguiar, D. C., & Slattery, D. A. (2017) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1418321 · Cited by 19 · see citing works

Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice

Petursdottír, D. H., Nordlander, S., Qazi, K. R., Carvalho‐Queiroz, C., Osman, O. A., Hell, É., Björkander, S., Haileselassie, Y., Navis, M., Kokkinou, E., et al. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01699 · Cited by 19 · see citing works

Rewarding negative results keeps science on track

(2017) · Nature · doi:10.1038/d41586-017-07325-2 · Cited by 15 · see citing works

Have Causal Claims About the Gut Microbiome Been Over‐Hyped?

Bourrat, P. (2018) · BioEssays · doi:10.1002/bies.201800178 · Cited by 14 · see citing works

Separating the microbiome from the hyperbolome

Shanahan, F. (2015) · Genome Medicine · doi:10.1186/s13073-015-0143-5 · Cited by 12 · see citing works

The gut microbiota–brain axis in behaviour and brain disorders

Morais, L. H., Schreiber, H. L., & Mazmanian, S. K. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00460-0 · Cited by 2,149 · see citing works

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics

Swanson, K. S., Gibson, G. R., Hutkins, R., Reimer, R. A., Reid, G., Verbeke, K., Scott, K. P., Holscher, H. D., Azad, M. B., Delzenne, N. M., et al. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0344-2 · Cited by 2,196 · see citing works

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

The microbiota-gut-brain axis: from motility to mood

Margolis, K. G., Cryan, J. F., & Mayer, E. A. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.10.066 · Cited by 999 · see citing works

Inflammatory bowel diseases (IBD) and the microbiome-searching the crime scene for clues

Lee, M., & Chang, E. B. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.056 · Cited by 645 · see citing works

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial

Routy, B., Lenehan, J. G., Miller, W. H., Jamal, R., Messaoudene, M., Daisley, B. A., Hes, C., Al, K. F., Martinez-Gili, L., Punčochář, M., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02453-x · Cited by 526 · see citing works

Hallmarks of Health

López-Otín, C., & Kroemer, G. (2021) · Cell · doi:10.1016/j.cell.2020.11.034 · Cited by 499 · see citing works

Next-generation sequencing: insights to advance clinical investigations of the microbiome

Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154944 · Cited by 437 · see citing works

The microbiome–gut–brain axis in Parkinson disease — from basic research to the clinic

Tan, A. H., Lim, S. Y., & Lang, A. E. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00681-2 · Cited by 392 · see citing works

Gut microbial molecules in behavioural and neurodegenerative conditions

Needham, B. D., Kaddurah-Daouk, R., & Mazmanian, S. K. (2020) · Nature Reviews Neuroscience · doi:10.1038/s41583-020-00381-0 · Cited by 379 · see citing works

Rethinking healthy eating in light of the gut microbiome

Armet, A. M., Deehan, E. C., O’Sullivan, A. F., Mota, J. F., Field, C. J., Prado, C. M., Lucey, A. J., & Walter, J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.016 · Cited by 252 · see citing works

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities

Iliev, I. D., Ananthakrishnan, A. N., & Guo, C.-J. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01163-0 · Cited by 249 · see citing works

Gut microbiota-induced changes in β-hydroxybutyrate metabolism are linked to altered sociability and depression in alcohol use disorder

Leclercq, S., Le Roy, T., Furgiuele, S., Coste, V., Bindels, L. B., Leyrolle, Q., Neyrinck, A. M., Quoilin, C., Amadieu, C., Petit, G., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108238 · Cited by 178 · see citing works

Mining microbes for mental health: determining the role of microbial metabolic pathways in human brain health and disease

Spichak, S., Bastiaanssen, T. F. S., Berding, K., Vlckova, K., Clarke, G., Dinan, T. G., & Cryan, J. F. (2021) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2021.02.044 · Cited by 127 · see citing works

Live Biotherapeutic Products, A Road Map for Safety Assessment

Rouanet, A., Bolca, S., Bru, A., Claes, I., Cvejic, H., Girgis, H., Harper, A., Lavergne, S. N., Mathys, S., Pane, M., et al. (2020) · Frontiers in Medicine · doi:10.3389/fmed.2020.00237 · Cited by 120 · see citing works

Metabolic independence drives gut microbial colonization and resilience in health and disease

Watson, A. R., Füssel, J., Veseli, I., DeLongchamp, J. Z., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J. M., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02924-x · Cited by 92 · see citing works

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics

Podlesny, D., Durdevic, M., Paramsothy, S., Kaakoush, N. O., Högenauer, C., Gorkiewicz, G., Walter, J., & Fricke, W. F. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100711 · Cited by 111 · see citing works

Autism Spectrum Disorders and the Gastrointestinal Tract: Insights into Mechanisms and Clinical Relevance

Hung, L. Y., & Margolis, K. G. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-023-00857-1 · Cited by 96 · see citing works

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

Han, D., Gao, P., Li, R., Tan, P., Xie, J., Zhang, R., & Li, J. (2020) · Journal of Advanced Research · doi:10.1016/j.jare.2020.07.010 · Cited by 93 · see citing works

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

Djukovic, A., Garzón, M. J., Canlet, C., Cabral, V., Lalaoui, R., García-Garcerá, M., Rechenberger, J., Tremblay-Franco, M., Peñaranda, I., Puchades-Carrasco, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33313-w · Cited by 85 · see citing works

Geographic Differences in Gut Microbiota Composition Impact Susceptibility to Enteric Infection

Porras, A. M., Shi, Q., Zhou, H., Callahan, R., Montenegro-Bethancourt, G., Solomons, N., & Brito, I. L. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109457 · Cited by 74 · see citing works

New technologies for developing phage-based tools to manipulate the human microbiome

Khan Mirzaei, M., & Deng, L. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2021.04.007 · Cited by 53 · see citing works

Regulation of microglial physiology by the microbiota

Cook, J., & Prinz, M. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2125739 · Cited by 49 · see citing works

Gut microbiome and amyotrophic lateral sclerosis: a systematic review of current evidence

Sun, J., Huang, T., Debelius, J. W., & Fang, F. (2021) · Journal of Internal Medicine · doi:10.1111/joim.13336 · Cited by 43 · see citing works

Quercetin improves gut dysbiosis in antibiotic-treated mice

Shi, T., Bian, X., Yao, Z., Wang, Y., Gao, W., & Guo, C. (2020) · Food & Function · doi:10.1039/d0fo01439g · Cited by 130 · see citing works

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients

Cui, X., Ye, L., Li, J., Jin, L., Wang, W., Li, S., Bao, M., Wu, S., Li, L., Geng, B., et al. (2018) · Scientific Reports · doi:10.1038/s41598-017-18756-2 · Cited by 373 · see citing works

Traumatic Brain Injury Induces Gastrointestinal Dysfunction and Dysbiosis of Gut Microbiota Accompanied by Alterations of Bile Acid Profile

You, W., Zhu, Y., Wei, A., Du, J., Wang, Y., Zheng, P., Tu, M., Wang, H., Wen, L., & Yang, X. (2021) · Journal of Neurotrauma · doi:10.1089/neu.2020.7526 · Cited by 87 · see citing works

Gut microbiota dysbiosis in rats with LPS-induced liver diseases affected by Aronia melanocarpa polyphenols

Kong, Y., Li, D., & Meng, X. (2023) · Food Science and Technology · doi:10.5327/fst.130622 · Cited by 1 · see citing works

Gut dysbiosis correction contributes to the hepatoprotective effects of Thymus quinquecostatus Celak extract against alcohol through the gut–liver axis

Yan, X., Wang, Y., Ren, X., et al. (2021) · Food & Function · doi:10.1039/d1fo01117k · Cited by 24 · see citing works