Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works

UCHIME improves sensitivity and speed of chimera detection

Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114 · see citing works

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · 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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602 · see citing works

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Pluskal, T., Castillo, S., Villar‐Briones, A., & Orešič, M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-395 · Cited by 3,852 · 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

PyNAST: a flexible tool for aligning sequences to a template alignment

Caporaso, J. G., Bittinger, K. L., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R. D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp636 · Cited by 3,374 · 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

Human nutrition, the gut microbiome and the immune system

Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588 · see citing works

UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

Lozupone, C., Hamady, M., & Knight, R. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,454 · see citing works

The indigenous gastrointestinal microflora

Berg, R. (1996) · Trends in Microbiology · doi:10.1016/0966-842x(96)10057-3 · Cited by 1,153 · see citing works

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

Andersson, A. F., Lindberg, M., Jakobsson, H. E., Bäckhed, F., Nyrén, P., & Engstrand, L. G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002836 · Cited by 1,037 · see citing works

The core gut microbiome, energy balance and obesity

Turnbaugh, P. J., & Gordon, J. I. (2009) · The Journal of Physiology · doi:10.1113/jphysiol.2009.174136 · Cited by 993 · see citing works

Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity

Cani, P. D., Osto, M., Geurts, L., & Everard, A. (2012) · Gut Microbes · doi:10.4161/gmic.19625 · Cited by 864 · see citing works

Homeostasis and Inflammation in the Intestine

Garrett, W. S., Gordon, J. I., & Glimcher, L. H. (2010) · Cell · doi:10.1016/j.cell.2010.01.023 · Cited by 784 · see citing works

Targeting gut microbiota in obesity: effects of prebiotics and probiotics

Delzenne, N. M., Neyrinck, A. M., Bäckhed, F., & Cani, P. D. (2011) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2011.126 · Cited by 783 · see citing works

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 779 · see citing works

A novel inflammation‐related mouse colon carcinogenesis model induced by azoxymethane and dextran sodium sulfate

Tanaka, T., Kohno, H., Suzuki, R., Yamada, Y., Sugie, S., & Mori, H. (2003) · Cancer Science · doi:10.1111/j.1349-7006.2003.tb01386.x · Cited by 732 · see citing works

Differential effects of fat and sucrose on the development of obesity and diabetes in C57BL/6J and mice

Surwit, R. S., Feinglos, M. N., Rodin, J., Sutherland, A., Petro, A. E., Opara, E. C., Kuhn, C. M., & Rebuffe-Scrive, M. (1995) · Metabolism · doi:10.1016/0026-0495(95)90123-x · Cited by 618 · see citing works

Interactions Between Gut Microbiota and Host Metabolism Predisposing to Obesity and Diabetes

Musso, G., Gambino, R., & Cassader, M. (2011) · Annual Review of Medicine · doi:10.1146/annurev-med-012510-175505 · Cited by 598 · see citing works

Towards the Human Colorectal Cancer Microbiome

Marchesi, J. R., Dutilh, B. E., Hall, N., Peters, W. H. M., Roelofs, R., Boleij, A., & Tjalsma, H. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020447 · Cited by 552 · see citing works

Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression

Reikvam, D. H., Erofeev, A. S., Sandvik, A., Grcic, V., Jahnsen, F. L., Gaustad, P., McCoy, K. D., Macpherson, A. J., Meza‐Zepeda, L. A., & Johansen, F. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017996 · Cited by 531 · see citing works

Fusobacterium Is Associated with Colorectal Adenomas

McCoy, A. N., Araújo-Pérez, F., Azcárate-Peril, M. A., Yeh, J. J., Sandler, R. S., & Keku, T. O. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053653 · Cited by 516 · see citing works

The therapeutic potential of manipulating gut microbiota in obesity and type 2 diabetes mellitus

Kootte, R. S., Vrieze, A., Holleman, F., Dallinga‐Thie, G. M., Zoetendal, E. G., de Vos, W. M., Groen, A. K., Hoekstra, J. B. L., Stroes, E. S. G., & Nieuwdorp, M. (2011) · Diabetes Obesity and Metabolism · doi:10.1111/j.1463-1326.2011.01483.x · Cited by 348 · see citing works

Reshaping the gut microbiome with bacterial transplantation and antibiotic intakePreprint

Manichanh, C., Reeder, J., Gibert, P., Varela, E., Llopis, M., Antolı́n, M., Guigó, R., Knight, R. D., & Guarner, F. (2010) · Genome Research · doi:10.1101/gr.107987.110 · Cited by 332 · see citing works

Comparative evaluation of establishing a human gut microbial community within rodent models

Wos‐Oxley, M. L., Bleich, A., Oxley, A. P. A., Kahl, S., Janus, L. M., Smoczek, A., Nahrstedt, H., Pils, M. C., Taudien, S., Platzer, M., et al. (2012) · Gut Microbes · doi:10.4161/gmic.19934 · Cited by 155 · see citing works

The human gut microbiome: Implications for future health care

Kinross, J. M., von Roon, A. C., Holmes, E., Darzi, A., & Nicholson, J. K. (2008) · Current Gastroenterology Reports · doi:10.1007/s11894-008-0075-y · Cited by 137 · see citing works

The Role of the Gastrointestinal Microbiota in Colorectal Cancer

Rowland, I. (2009) · Current Pharmaceutical Design · doi:10.2174/138161209788168191 · Cited by 129 · see citing works

Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota

Li, F., Hullar, M. A. J., & Lampe, J. W. (2006) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2006.09.006 · Cited by 126 · see citing works

The complex interplay between inflammation, the microbiota and colorectal cancer

Arthur, J. C., & Jobin, C. (2013) · Gut Microbes · doi:10.4161/gmic.24220 · Cited by 95 · see citing works

Obesity and its associated disease: a role for microbiota?

Tehrani, A. B., Nezami, B. G., Gewirtz, A. T., & Srinivasan, S. (2012) · Neurogastroenterology & Motility · doi:10.1111/j.1365-2982.2012.01895.x · Cited by 82 · see citing works

COMPANION ANIMALS SYMPOSIUM: Humanized animal models of the microbiome1

Gootenberg, D. B., & Turnbaugh, P. J. (2010) · Journal of Animal Science · doi:10.2527/jas.2010-3371 · Cited by 69 · see citing works

Influence of Dietary Phytochemicals and Microbiota on Colon Cancer Risk

MacDonald, R. S., & Wagner, K. A. (2012) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf204230r · Cited by 68 · see citing works

Bacteria as Trigger for Chronic Gastrointestinal Disorders

Marteau, P. R., & Chaput, U. (2011) · Digestive Diseases · doi:10.1159/000323879 · Cited by 34 · see citing works

Microbiota and management of inflammatory bowel disease

Lawrance, I. C. (2012) · Journal of Gastroenterology and Hepatology · doi:10.1111/j.1440-1746.2012.07163.x · Cited by 5 · see citing works

Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior

Luczynski, P., McVey Neufeld, K.-A., Oriach, C. S., Clarke, G., Dinan, T. G., & Cryan, J. F. (2016) · International Journal of Neuropsychopharmacology · doi:10.1093/ijnp/pyw020 · Cited by 632 · see citing works

Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria

Kennedy, E. A., King, K. Y., & Baldridge, M. T. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01534 · Cited by 602 · see citing works

Microbial Ecology along the Gastrointestinal Tract

Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017) · Microbes and Environments · doi:10.1264/jsme2.me17017 · Cited by 586 · see citing works

Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice

Zhu, F., Guo, R., Wang, W., Ju, Y., Wang, Q., Ma, Q., Sun, Q., Fan, Y., Xie, Y., Yang, Z., et al. (2020) · Molecular Psychiatry · doi:10.1038/s41380-019-0475-4 · Cited by 323 · see citing works

Exploring the emerging role of the microbiome in cancer immunotherapy

Fessler, J. L., Matson, V. Z., & Gajewski, T. F. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0574-4 · Cited by 318 · see citing works

Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility

Ge, X., Ding, C., Zhao, W., Xu, L., Tian, H., Gong, J., Zhu, M., Li, J., & Li, N. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-016-1105-4 · Cited by 274 · see citing works

Immunoregulatory role of the gut microbiota in inflammatory depression

Liu, P., Liu, Z., Wang, J., Wang, J., Gao, M., Zhang, Y., Yang, C., Zhang, A., Li, G., Li, X., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47273-w · Cited by 253 · see citing works

Gut Microbiota and Their Metabolites in Stroke: A Double-Edged Sword

Peh, A., O’Donnell, J. A., Broughton, B. R. S., & Marques, F. Z. (2022) · Stroke · doi:10.1161/strokeaha.121.036800 · Cited by 259 · see citing works

Tumor-on-a-chip: from bioinspired design to biomedical application

Liu, X., Fang, J., Huang, S., Wu, X., Xie, X., Wang, J., Liu, F., Zhang, M., Peng, Z., & Hu, N. (2021) · Microsystems & Nanoengineering · doi:10.1038/s41378-021-00277-8 · Cited by 246 · 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

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

Animal models to study acute and chronic intestinal inflammation in mammals

Jiminez, J. A., Uwiera, T. C., Inglis, G. D., & Uwiera, R. R. E. (2015) · Gut Pathogens · doi:10.1186/s13099-015-0076-y · Cited by 210 · see citing works

Antibiotic therapy with metronidazole reduces endometriosis disease progression in mice: a potential role for gut microbiota

Chadchan, S. B., Cheng, M., Parnell, L. A., Yin, Y., Schriefer, A. E., Mysorekar, I. U., & Kommagani, R. (2019) · Human Reproduction · doi:10.1093/humrep/dez041 · Cited by 202 · see citing works

Metabolome analysis for investigating host-gut microbiota interactions

Chen, M. X., Wang, S., Kuo, C., & Tsai, I. (2018) · Journal of the Formosan Medical Association · doi:10.1016/j.jfma.2018.09.007 · Cited by 194 · see citing works

Procedures for Fecal Microbiota Transplantation in Murine Microbiome Studies

Bokoliya, S. C., Dorsett, Y., Panier, H. A., & Zhou, Y. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.711055 · Cited by 186 · see citing works

Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for “Precision Medicine and Pharmacometabolomics Task Group”—The Metabolomics Society Initiative)

Kirwan, J., Brennan, L., Broadhurst, D., Fiehn, O., Cascante, M., Dunn, W. B., Schmidt, M. A., & Velagapudi, V. (2018) · Clinical Chemistry · doi:10.1373/clinchem.2018.287045 · Cited by 171 · see citing works

Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls

Gheorghe, C. E., Ritz, N. L., Martin, J. A., Wardill, H. R., Cryan, J. F., & Clarke, G. A. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1941711 · Cited by 149 · see citing works

Dendrobium officinale Polysaccharide Alleviates Type 2 Diabetes Mellitus by Restoring Gut Microbiota and Repairing Intestinal Barrier via the LPS/TLR4/TRIF/NF-kB Axis

Chen, X., Chen, C., & Fu, X. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c02429 · Cited by 149 · see citing works

Comparative Evaluation of Microbiota Engraftment Following Fecal Microbiota Transfer in Mice Models: Age, Kinetic and Microbial Status Matter

Roy, T. L., Debédat, J., Marquet, F., Da-Cunha, C., Ichou, F., Guerre-Millo, M., Kapel, N., Aron‐Wisnewsky, J., & Clément, K. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03289 · Cited by 143 · see citing works

Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota

Wrzosek, L., Ciocan, D. M., Borentain, P., Spatz, M., Puchois, V., Hugot, C., Ferrere, G., Mayeur, C., Perlemuter, G., & Cassard, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-25300-3 · Cited by 143 · see citing works

Multi-compound and drug-combination pharmacokinetic research on Chinese herbal medicines

Li, C., Jia, W., Yang, J., Cheng, C., & Olaleye, O. E. (2022) · Acta Pharmacologica Sinica · doi:10.1038/s41401-022-00983-7 · Cited by 133 · see citing works

Gut Microbiome and Multiple Sclerosis

Bhargava, P., & Mowry, E. M. (2014) · Current Neurology and Neuroscience Reports · doi:10.1007/s11910-014-0492-2 · Cited by 129 · see citing works

Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications

van Leeuwen, P. T., Brul, S., Zhang, J., & Wortel, M. T. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad012 · Cited by 125 · see citing works

An overview of fecal sample preparation for global metabolic profiling

Deda, O., Gika, H., Wilson, I. D., & Theodoridis, G. A. (2015) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2015.02.006 · Cited by 120 · see citing works

Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in mice

Ogawa, Y., Miyoshi, C., Obana, N., Yajima, K., Hotta-Hirashima, N., Ikkyu, A., Kanno, S., Soga, T., Fukuda, S., & Yanagisawa, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-76562-9 · Cited by 120 · see citing works

<i>Akkermansia muciniphila</i> supplementation prevents cognitive impairment in sleep-deprived mice by modulating microglial engulfment of synapses

Li, N., Tan, S., Wang, Y., Deng, J., Wang, N., Zhu, S., Tian, W., Xu, J., & Wang, Q. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2252764 · Cited by 117 · see citing works

Comparison of different modes of antibiotic delivery on gut microbiota depletion efficiency and body composition in mouse

Tirelle, P., Breton, J., Riou, G., Déchelotte, P., Coëffier, M., & Ribet, D. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02018-9 · Cited by 113 · see citing works

Gut microbiota–derived short-chain fatty acids protect against the progression of endometriosis

Chadchan, S. B., Popli, P., Ambati, C. R., Tycksen, E., Han, S. J., Bulun, S. E., Putluri, N., Biest, S. W., & Kommagani, R. (2021) · Life Science Alliance · doi:10.26508/lsa.202101224 · Cited by 116 · see citing works

Fructus mori polysaccharide alleviates diabetic symptoms by regulating intestinal microbiota and intestinal barrier against TLR4/NF-κB pathway

Chen, X., Wu, J., Fu, X., Wang, P., & Chen, C. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.126038 · Cited by 108 · see citing works

Improving natural product research translation: From source to clinical trial

Sorkin, B. C., Kuszak, A. J., Bloss, G., Fukagawa, N. K., Hoffman, F. A., Jafari, M., Barrett, B. P., Brown, P. N., Bushman, F. D., Casper, S. J., et al. (2019) · The FASEB Journal · doi:10.1096/fj.201902143r · Cited by 104 · see citing works

Fecal microbiota transplantation as a tool to treat and reduce susceptibility to disease in animals

Niederwerder, M. C. (2018) · Veterinary Immunology and Immunopathology · doi:10.1016/j.vetimm.2018.11.002 · Cited by 89 · see citing works

In vitro vascularized liver and tumor tissue microenvironments on a chip for dynamic determination of nanoparticle transport and toxicity

Ozkan, A., Ghousifam, N., Hoopes, P. J., Yankeelov, T. E., & Rylander, M. N. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.26919 · Cited by 73 · see citing works

A guide to germ‐free and gnotobiotic mouse technology to study health and disease

Jans, M., & Vereecke, L. (2024) · FEBS Journal · doi:10.1111/febs.17124 · Cited by 65 · see citing works

The Role of the Gut Microbiota in Sustained Weight Loss Following Roux-en-Y Gastric Bypass Surgery

Fouladi, F., Brooks, A. E., Fodor, A. A., Carroll, I. M., Bulik‐Sullivan, E. C., Tsilimigras, M. C. B., Sioda, M., & Steffen, K. J. (2019) · Obesity Surgery · doi:10.1007/s11695-018-03653-y · Cited by 52 · see citing works

Experimental design considerations in microbiota/inflammation studies

Moore, R. J., & Stanley, D. (2016) · Clinical & Translational Immunology · doi:10.1038/cti.2016.41 · Cited by 53 · see citing works

Manual acupuncture benignly regulates blood-brain barrier disruption and reduces lipopolysaccharide loading and systemic inflammation, possibly by adjusting the gut microbiota

Zhang, Y., Ding, N., Hao, X., Zhao, J., Zhao, Y., Li, Y., & Li, Z. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.1018371 · Cited by 52 · see citing works

Use of Humanized Mice to Study the Pathogenesis of Autoimmune and Inflammatory Diseases

Koboziev, I., Jones‐Hall, Y., Valentine, J. F., Webb, C. R., Furr, K. L., & Grisham, M. B. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000446 · Cited by 50 · see citing works

Colonization Potential to Reconstitute a Microbe Community in Pseudo Germ-Free Mice After Fecal Microbe Transplant From Equol Producer

Liang, W., Zhao, L., Zhang, J., Fang, X., Zhong, Q., Liao, Z., Wang, J., Guo, Y., Liang, H., & Wang, L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01221 · Cited by 50 · see citing works

Gut metagenomic characteristics of ADHD reveal low Bacteroides ovatus -associated host cognitive impairment

Li, Y., Sun, H., Huang, Y., Yin, A., Zhang, L., Han, J., Lyu, Y., Xu, X., Zhai, Y., Sun, H., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2125747 · Cited by 44 · see citing works

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer

Fouladi, F., Glenny, E. M., Bulik‐Sullivan, E. C., Tsilimigras, M. C. B., Sioda, M., Thomas, S., Wang, Y., Djukic, Z., Tang, Q., Tarantino, L. M., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-0645-z · Cited by 42 · see citing works

The emerging potential ofmicrobiome transplantation on human health interventions

Junca, H., Pieper, D. H., & Medina, E. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.01.009 · Cited by 41 · see citing works

Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice

Wei, N., Ju, M., Su, X., Zhang, Y., Huang, Y., Rao, X., Cui, L., Lin, Z., & Dong, Y. W. (2024) · Schizophrenia · doi:10.1038/s41537-024-00460-6 · Cited by 45 · see citing works

Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems

Kang, T., & Kim, H. (2016) · Micromachines · doi:10.3390/mi7070107 · Cited by 40 · see citing works

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model

Libbey, J. E., Sanchez, J. M. S., Doty, D. J., Sim, J. T., Cusick, M. F., Cox, J. E., Fischer, K. F., Round, J. L., & Fujinami, R. S. (2018) · Beneficial Microbes · doi:10.3920/bm2017.0116 · Cited by 40 · see citing works

Benign regulation of the gut microbiota: The possible mechanism through which the beneficial effects of manual acupuncture on cognitive ability and intestinal mucosal barrier function occur in APP/PS1 mice

Hao, X., Ding, N., Zhang, Y., Yang, Y., Zhao, Y., Zhao, J. J., Li, Y., & Li, Z. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.960026 · Cited by 40 · see citing works

Refining a Protocol for Faecal Microbiota Engraftment in Animal Models After Successful Antibiotic-Induced Gut Decontamination

Amorim, N. M. L., McGovern, E., Raposo, A. E., Khatiwada, S., Shen, S., Koentgen, S., Hold, G. L., Behary, J., El-Omar, E. M., & Zekry, A. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.770017 · Cited by 38 · see citing works

Engraftment of Bacteria after Fecal Microbiota Transplantation Is Dependent on Both Frequency of Dosing and Duration of Preparative Antibiotic Regimen

Gopalakrishnan, V., Dozier, E. A., Glover, M. S., Novick, S. J., Ford, M. W., Morehouse, C. A., Warrener, P., Caceres, C. S., Hess, S. Y., Sellman, B. R., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9071399 · Cited by 37 · see citing works

Basal Diet Determined Long-Term Composition of the Gut Microbiome and Mouse Phenotype to a Greater Extent than Fecal Microbiome Transfer from Lean or Obese Human Donors

Rodriguez, D. M., Benninghoff, A. D., Aardema, N. D. J., Phatak, S., & Hintze, K. J. (2019) · Nutrients · doi:10.3390/nu11071630 · Cited by 36 · see citing works

An Introductory “How-to” Guide for Incorporating Microbiome Research into Integrative and Comparative Biology

Kohl, K. D. (2017) · Integrative and Comparative Biology · doi:10.1093/icb/icx013 · Cited by 31 · see citing works

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation

Johnson, K. V. ‐., & Burnet, P. W. J. (2020) · BMC Neuroscience · doi:10.1186/s12868-020-00583-3 · Cited by 31 · see citing works

Cow, Goat, and Mare Milk Diets Differentially Modulated the Immune System and Gut Microbiota of Mice Colonized by Healthy Infant Feces

Li, N., Xie, Q., Chen, Q., Evivie, S. E., Liu, D., Dong, J., Huo, G., & Li, B. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c06039 · Cited by 32 · see citing works

Humanizing the gut microbiota of mice: Opportunities and challenges

Lundberg, R. (2018) · Laboratory Animals · doi:10.1177/0023677218787554 · Cited by 28 · see citing works

What we need to know about the germ-free animal models

Aghighi, F., & Salami, M. (2024) · AIMS Microbiology · doi:10.3934/microbiol.2024007 · Cited by 26 · see citing works

A Double Humanized BLT-mice Model Featuring a Stable Human-Like Gut Microbiome and Human Immune System

Daharsh, L., Zhang, J., Ramer‐Tait, A. E., & Li, Q. (2019) · Journal of Visualized Experiments · doi:10.3791/59773 · Cited by 25 · see citing works

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects

Krigul, K. L., Feeney, R. H., Wongkuna, S., Aasmets, O., Holmberg, S. M., Andreson, R., Puértolas-Balint, F., Pantiukh, K., Sootak, L., Org, T., et al. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2377570 · Cited by 23 · see citing works

Oncologic outcome after completing or abandoning (radical) hysterectomy in patients with cervical cancer and intraoperative detection of lymph node positivity; ABRAX (ABandoning RAd hyst in cerviX cancer)

Dostálek, L., Runnebaum, I. B., Raspagliesi, F., Vergote, I. B., Dušek, L., Jarkovský, J., & Cibula, D. (2020) · International Journal of Gynecological Cancer · doi:10.1136/ijgc-2019-000890 · Cited by 24 · see citing works

A purified fraction of polysaccharides from the fruits of Lycium barbarum L. improves glucose homeostasis and intestinal barrier function in high-fat diet-fed mice

Zhou, W., Liu, P., Xu, W., Ran, L., Yan, Y., Lu, L., Zeng, X., Cao, Y., & Mi, J. D. (2023) · Food & Function · doi:10.1039/d3fo00262d · Cited by 23 · see citing works

Modeling microbiota-associated human diseases: from minimal models to complex systems

Aguanno, D., Metwaly, A., Coleman, O. I., & Haller, D. (2022) · Microbiome Research Reports · doi:10.20517/mrr.2022.01 · Cited by 22 · see citing works

Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Primer for Internists

Syal, G., Kashani, A., & Shih, D. Q. (2018) · The American Journal of Medicine · doi:10.1016/j.amjmed.2018.03.010 · Cited by 21 · see citing works

The gut microbiome is associated with susceptibility to febrile malaria in Malian children

Ham, K. M. V. D., Bower, L. K., Li, S., Lorenzi, H., Doumbo, S., Doumtabé, D., Kayentao, K., Ongoïba, A., Traoré, B., Crompton, P. D., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52953-8 · Cited by 22 · see citing works

Responses of the gut microbiota and metabolite profiles to sulfated polysaccharides from sea cucumber in humanized microbiota mice

Liu, Z., Yan, C., Lin, X., Ai, C., Dong, X., Shao, L., Wang, S., Song, S., & Zhu, B. (2022) · Food & Function · doi:10.1039/d1fo04443e · Cited by 19 · see citing works

Deprivation of dietary fiber enhances susceptibility of mice to cryptosporidiosis

Oliveira, B. C. M., Bresciani, K. D. S., & Widmer, G. (2019) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007411 · Cited by 19 · see citing works

Human microbiota-associated animal models: a review

Huang, X., Yu, Y., Tian, N., Huang, J., Zhang, X., & Yu, R. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1644187 · Cited by 19 · see citing works

Protective effect of gut microbiota restored by fecal microbiota transplantation in a sepsis model in juvenile mice

Han, Y. J., Kim, S., Shin, H., Kim, H. W., & Park, J. D. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1451356 · Cited by 17 · see citing works

Gut microbiota and host cytochrome P450 characteristics in the pseudo germ-free model: co-contributors to a diverse metabolic landscape

Wang, S., Wen, Q., Qin, Y., Xia, Q., Shen, C., & Song, S. (2023) · Gut Pathogens · doi:10.1186/s13099-023-00540-5 · Cited by 17 · see citing works

A high‐salt diet induces synaptic loss and memory impairment via gut microbiota and butyrate in mice

Lei, C., Liu, C., Peng, Y., Zhan, Y., Zhang, X., Liu, T., & Liu, Z. (2023) · iMeta · doi:10.1002/imt2.97 · Cited by 15 · see citing works

Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation

Greetatorn, T., Hashimoto, S., Maeda, T., Fukudome, M., Piromyou, P., Teamtisong, K., Tittabutr, P., Boonkerd, N., Kawaguchi, M., Uchiumi, T., et al. (2020) · Microbes and Environments · doi:10.1264/jsme2.me20049 · Cited by 14 · see citing works

Transfer of Human Microbiome to Drosophila Gut Model

Ji, D., Sun, H., Yang, W., Gao, M., & Xu, H. (2022) · Microorganisms · doi:10.3390/microorganisms10030553 · Cited by 14 · see citing works

Fecal microbiota transplantation derived from mild cognitive impairment individuals impairs cerebral glucose uptake and cognitive function in wild-type mice: Bacteroidetes and TXNIP-GLUT signaling pathway

Wang, T., Hao, L. Y., Yang, K., Feng, W., Guo, Z., Liu, M., & Xiao, R. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2395907 · Cited by 14 · see citing works

Potential of Establishing the Corresponding Human Microbial Community in Pseudo Germ-Free Mice through Fecal Microbe Transfer from Three Urolithin Metabotypes

Xian, W., Yang, S., Deng, Y., Yang, Y., Tan, Z., Li, W., & Yang, R. (2022) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c02796 · Cited by 14 · see citing works

Animal and human mucosal tissue models to study HIV biomedical interventions: can we predict success?

Dezzutti, C. S. (2015) · Journal of the International AIDS Society · doi:10.7448/ias.18.1.20301 · Cited by 13 · see citing works

Sheep fecal transplantation affects growth performance in mouse models by altering gut microbiota

Cheng, J., Zhang, X., Zhang, D., Zhang, Y., Li, X., Zhao, Y., Xu, D., Zhao, L., Li, W., Wang, J., et al. (2022) · Journal of Animal Science · doi:10.1093/jas/skac303 · Cited by 13 · see citing works

Donor Microbiota Composition and Housing Affect Recapitulation of Obese Phenotypes in a Human Microbiota-Associated Murine Model

Kaiser, T., Nalluri, H., Zhu, Z., & Staley, C. M. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.614218 · Cited by 13 · see citing works

Identification of sleep fragmentation-induced gut microbiota alteration and prediction of functional impact in Sprague Dawley rats harboring microbiome derived from multiple human donors

Triplett, J. C., Braddock, A., Roberts, E., Ellis, D. H., & Chan, V. (2022) · Sleep Science · doi:10.5935/1984-0063.20200116 · Cited by 12 · see citing works

Role of Phytochemicals in Treatment of Aging and Cancer: Focus on Mechanism of FOXO3 Activation

Park, S. (2024) · Antioxidants · doi:10.3390/antiox13091099 · Cited by 12 · see citing works

From the Dish to the Real World: Modeling Interactions between the Gut and Microorganisms in Gut Organoids by Tailoring the Gut Milieu

Park, N.-Y., & Koh, A. (2022) · International Journal of Stem Cells · doi:10.15283/ijsc21243 · Cited by 10 · see citing works

Chaihushugan powder regulates the gut microbiota to alleviate mitochondrial oxidative stress in the gastric tissues of rats with functional dyspepsia

Liu, X., Yang, K., Jia, Y., Yeertai, Y., Wu, C., Wang, X., Jia, Q., Gu, Z., Cong, J., & Ling, J. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1549554 · Cited by 10 · see citing works

Creation of a non-Western humanized gnotobiotic mouse model through the transplantation of rural African fecal microbiota

Ham, K. M. V. D., Little, M. R., Bednarski, O. J., Fusco, E. M., Mandal, R. K., Mitra, R., Li, S., Doumbo, S., Doumtabé, D., Kayentao, K., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.01554-23 · Cited by 9 · see citing works

Microbiome contributions to pain: a review of the preclinical literature

Pratt, M. L., Plumb, A. N., Manjrekar, A., Cardona, L. M., Chan, C. K., John, J. M., & Sadler, K. E. (2024) · Pain · doi:10.1097/j.pain.0000000000003376 · Cited by 9 · see citing works

Helminth Interactions with Bacteria in the Host Gut Are Essential for Its Immunomodulatory Effect

Jirků, M., Lhotská, Z., Frgelecová, L., Kadlecová, O., Petrželková, K. J., Morien, E., & Jirků‐Pomajbíková, K. (2021) · Microorganisms · doi:10.3390/microorganisms9020226 · Cited by 8 · see citing works

Investigating fecal microbiota transplants from individuals with anorexia nervosa in antibiotic-treated mice using a cross-over study design

Maschek, S., Østergaard, T. H., Krych, Ł., Zachariassen, L. F., Sørensen, D. B., Mentzel, C. M. J., Hansen, A. K., Sjögren, J. M., & Barfod, K. K. (2025) · Journal of Eating Disorders · doi:10.1186/s40337-025-01276-0 · Cited by 12 · see citing works

Human-fecal microbiota transplantation in relation to gut microbiome signatures in animal models for schizophrenia: A scoping review

Singh, R., Panganiban, K. J., Au, E., Ravikumar, R., Pereira, S., Prévot, T. D., Müller, D. J., Remington, G. J., Agarwal, S. M., Verdu, E. F., et al. (2024) · Asian Journal of Psychiatry · doi:10.1016/j.ajp.2024.104285 · Cited by 7 · see citing works

Antibiotic Conditioning Shapes Pseudosterile Mouse Models by Deleting Colonic Microbes Rather than Small Intestinal Microbes

Chen, Q., Xinming, M., Xing, Z., Zhao, X., Zu, H., Guo, Z., & Li, B. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.00814-23 · Cited by 7 · see citing works

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates

Taylor, J., Clarke, E., Baker, K. C., Lauder, A. P., Kim, D. J., Bailey, A., Wu, G. D., Collman, R. G., Doyle‐Meyers, L. A., Russell‐Lodrigue, K., et al. (2018) · PeerJ · doi:10.7717/peerj.4612 · Cited by 7 · see citing works

Intestinal microbiome dysbiosis increases Mycobacteria pulmonary colonization in mice by regulating the Nos2-associated pathwaysPreprint

Han, M., Wang, X., Su, L., Pan, S., Liu, N., Duan, L., Liu, L., Cui, J., Zhao, H., & Yang, F. (2024) · eLife · doi:10.7554/elife.99282 · Cited by 7 · see citing works

The Impacts of Microbiota on Animal Development and Physiology

Walsh, K. T., & Guillemin, K. J. (2022) · Progress in inflammation research · doi:10.1007/978-3-030-91051-8_6 · Cited by 6 · see citing works

Characterization of double humanized BLT-mice with stable engraftment of a human gut bacterial microbiome

Daharsh, L., Lohani, S. C., Ramer‐Tait, A. E., & Li, Q. (2024) · Frontiers in Microbiomes · doi:10.3389/frmbi.2024.1404353 · Cited by 5 · see citing works

Modified Xiaoyaosan rescues depression-like behavior via remodeling gut microbiota and leucine metabolism

Zhao, Y.-H., Wang, Q., Wu, Z., Zhou, Y., Gao, X., Gong, W., Qin, X., Ren, Y., & Tian, J. (2025) · Phytomedicine · doi:10.1016/j.phymed.2025.157241 · Cited by 5 · see citing works

The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles

Bayne, J. E., Charavaryamath, C., Hu, Y., Yousefi, F., Murphy, M., Law, A., Michael, A., Muyyarikkandy, M. S., Nibbering, B., Smits, W. K., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2568706 · Cited by 5 · see citing works

Modulating Bacteroides to boost anti-PD-1 immunotherapy in HCC

Qi, X., Yang, M. J., Liu, X., Ma, L., Kaifi, J. T., Ericsson, A. C., Kimchi, E. T., Staveley-O’Carroll, K. F., & Li, G. (2026) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2025-013755 · Cited by 5 · see citing works

Intestinal microbiome dysbiosis increases Mycobacteria pulmonary colonization in mice by regulating the Nos2-associated pathways

Han, M., Wang, X., Su, L., Pan, S., Liu, N., Duan, L., Liu, L., Cui, J., Zhao, H., & Yang, F. (2024) · eLife · doi:10.7554/elife.99282.3 · Cited by 5 · see citing works

Antibiotic Conditioning and Single Gavage Allows Stable Engraftment of Human Microbiota in Mice

Zhu, Z., Kaiser, T., & Staley, C. M. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1518-8_17 · Cited by 5 · see citing works

SigTree : A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Stevens, J. R., Jones, T. R., Lefevre, M., Ganesan, B., & Weimer, B. C. (2017) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2017.06.002 · Cited by 5 · see citing works

Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice

Pradhan, S., Ray, P., & Aich, P. (2021) · Life Sciences · doi:10.1016/j.lfs.2021.120201 · Cited by 5 · see citing works

Generation, Maintenance, and Identification of Germ-Free Zebrafish Models from Larvae to Juvenile Stages

Jia, P., Liu, X.-R., Wu, M., Li, Y., Zhang, L., & Pei, D. (2024) · Journal of Visualized Experiments · doi:10.3791/66512 · Cited by 6 · see citing works

Shenling Jianpiwei formula ameliorates metabolic associated fatty liver disease through modulation of the gut microbiota and attenuation of LPS-mediated inflammation

Chen, L., Pu, X., Li, L., Zhang, M., Liu, Y., Hu, K., Wang, J., Zhang, F., & Yu, J. (2025) · Fitoterapia · doi:10.1016/j.fitote.2025.106862 · Cited by 3 · see citing works

Efficacy of oral and rectal administration of human faecal microbiota transplant (FMT) in human microbiota-associated mouse models

Hradická, P., Holm, K., Bjørnholt, J. V., Melum, E., Hov, J. R., & Rasmussen, H. (2025) · Scientific Reports · doi:10.1038/s41598-025-32072-0 · Cited by 3 · see citing works

Fecal microbiota transplantation from psychiatric patients to mice - systematic review of methodologies and a call for standardization

D’Onofrio, A. M., Gomez-Nguyen, A., Camardese, G., Scaldaferri, F., Burberry, A., & Cominelli, F. (2026) · Translational Psychiatry · doi:10.1038/s41398-026-03847-4 · Cited by 4 · see citing works

Effect of Caging on Cryptosporidium parvum Proliferation in Mice

Creasey, H. N., Zhang, W., & Widmer, G. (2022) · Microorganisms · doi:10.3390/microorganisms10061242 · Cited by 3 · see citing works

Basal Diet Fed to Recipient Mice Was the Driving Factor for Colitis and Colon Tumorigenesis, despite Fecal Microbiota Transfer from Mice with Severe or Mild Disease

Rodriguez, D. M., Hintze, K. J., Rompato, G., Stewart, E. C., Barton, A. H., Mortensen, E., Green, P. A., Wettere, A. J. V., Thomas, A. J., & Benninghoff, A. D. (2023) · Nutrients · doi:10.3390/nu15061338 · Cited by 3 · see citing works

Feasibility study on construction of humanized mice with antibiotics combined with fecal bacteria transplantation

Xu, M.-L., & Wang, P. (2021) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 1 · see citing works

Of men in mice: the development and application of a humanized gnotobiotic mouse model for microbiome therapeutics

Park, J. C., & Im, S. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0473-2 · Cited by 217 · see citing works

Cross-species engraftment biases and metabolic divergence in gnotobiotic mice humanized with ulcerative colitis microbiota

Guggeis, M. A., Andreani, N. A., López-Agudelo, V. A., Tran, F., Kadibalban, A. S., Moors, K. A., Μαρίνος, Γ., Saboukh, A., Harris, D. M. M., Falk‐Paulsen, M., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2581445 · Cited by 15 · see citing works

Stable Engraftment of a Human Gut Bacterial Microbiome in Double Humanized BLT-micePreprint

Daharsh, L., Ramer‐Tait, A. E., & Li, Q. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/749093 · Cited by 3 · see citing works

Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route

Yang, Y., Tan, X., Zhang, Z., Liang, L. Y., Wu, Z., He, J., Wang, Y., Dong, M., Zheng, J., Zhang, H. S., et al. (2026) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2400495