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

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T _reg Cell Homeostasis

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Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

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Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis

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Induction of Colonic Regulatory T Cells by Indigenous <i>Clostridium</i> Species

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An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System

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Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis

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Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist

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Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works

Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function

Kelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., Wilson, K. E., Glover, L. E., Kominsky, D. J., Magnuson, A., et al. (2015) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2015.03.005 · Cited by 1,716 · see citing works

Microbiota regulates immune defense against respiratory tract influenza A virus infection

Ichinohe, T., Pang, I. K., Kumamoto, Y., Peaper, D. R., Ho, J. H., Murray, T. S., & Iwasaki, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019378108 · Cited by 1,502 · see citing works

Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis

Lee, Y. K., Menezes, J. S., Umesaki, Y., & Mazmanian, S. K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000082107 · Cited by 1,323 · see citing works

Compartmentalized Control of Skin Immunity by Resident Commensals

Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., et al. (2012) · Science · doi:10.1126/science.1225152 · Cited by 1,092 · see citing works

ATP drives lamina propria TH17 cell differentiation

Atarashi, K., Nishimura, J., Shima, T., Umesaki, Y., Yamamoto, M., Onoue, M., Yagita, H., Ishii, N., Evans, R., Honda, K., et al. (2008) · Nature · doi:10.1038/nature07240 · Cited by 1,089 · see citing works

Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface

Vaishnava, S., Behrendt, C. L., Ismail, A. S., Eckmann, L., & Hooper, L. V. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808723105 · Cited by 1,019 · see citing works

Commensal bacteria calibrate the activation threshold of innate antiviral immunity

Abt, M. C., Osborne, L. C., Monticelli, L. A., Doering, T. A., Alenghat, T., Sonnenberg, G. F., Paley, M. A., Antenus, M., Williams, K. L., Erikson, J., et al. (2012) · Immunity · doi:10.1016/j.immuni.2012.04.011 · Cited by 993 · see citing works

Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling

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<i>Lactobacillus reuteri</i> induces gut intraepithelial CD4 ⁺ CD8αα ⁺ T cells

Cervantes-Barragan, L., Chai, J. N., Tianero, M. D., Di Luccia, B., Ahern, P. P., Merriman, J., Cortez, V. S., Caparon, M. G., Donia, M. S., Gilfillan, S., et al. (2017) · Science · doi:10.1126/science.aah5825 · Cited by 896 · see citing works

The microbiota regulates type 2 immunity through RORγt ⁺ T cells

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Neutrophil ageing is regulated by the microbiome

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The gut microbiota regulates bone mass in mice

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Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis

Mortha, A., Chudnovskiy, A., Hashimoto, D., Bogunovic, M., Spencer, S. P., Belkaid, Y., & Merad, M. (2014) · Science · doi:10.1126/science.1249288 · Cited by 820 · see citing works

Commensal bacteria protect against food allergen sensitization

Stefka, A. T., Feehley, T., Tripathi, P., Qiu, J., McCoy, K. D., Mazmanian, S. K., Tjota, M. Y., Seo, G., Cao, S. Z., Theriault, B. R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412008111 · Cited by 795 · see citing works

Gut microbiota induce IGF-1 and promote bone formation and growth

Yan, J., Herzog, J. W., Tsang, K., Brennan, C. A., Bower, M. A., Garrett, W. S., Sartor, B. R., Aliprantis, A. O., & Charles, J. F. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1607235113 · Cited by 750 · see citing works

Gut Microbiota Promote Hematopoiesis to Control Bacterial Infection

Khosravi, A., Yáñez, A., Price, J. G., Chow, A. T., Mérad, M., Goodridge, H. S., & Mazmanian, S. K. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.006 · Cited by 651 · see citing works

Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis

Kuss-Duerkop, S. K., Best, G. T., Etheredge, C. A., Pruijssers, A. J. P., Frierson, J. M., Hooper, L. V., Dermody, T. S., & Pfeiffer, J. K. (2011) · Science · doi:10.1126/science.1211057 · Cited by 631 · see citing works

Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits

Brandl, K., Plitas, G., Mihu, C. N., Ubeda, C., Jia, T., Fleisher, M., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2008) · Nature · doi:10.1038/nature07250 · Cited by 631 · see citing works

Innate immune recognition of the microbiota promotes host-microbial symbiosis

Chu, H., & Mazmanian, S. K. (2013) · Nature Immunology · doi:10.1038/ni.2635 · Cited by 630 · see citing works

Role of Gut Commensal Microflora in the Development of Experimental Autoimmune Encephalomyelitis

Ochoa-Repáraz, J., Mielcarz, D. W., Ditrio, L. E., Burroughs, A. R., Foureau, D. M., Haque-Begum, S., & Kasper, L. H. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900747 · Cited by 590 · see citing works

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

Gury-BenAri, M., Thaiss, C. A., Serafini, N., Winter, D. R., Giladi, A., Lara-Astiaso, D., Levy, M., Salame, T. M., Weiner, A., David, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.043 · Cited by 587 · see citing works

The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice

Deshmukh, H. S., Liu, Y., Menkiti, O. R., Mei, J., Dai, N., O'Leary, C. E., Oliver, P. M., Kolls, J. K., Weiser, J. N., & Worthen, G. S. (2014) · Nature Medicine · doi:10.1038/nm.3542 · Cited by 579 · see citing works

The microbial metabolite desaminotyrosine protects from influenza through type I interferon

Steed, A. L., Christophi, G. P., Kaiko, G. E., Sun, L., Goodwin, V. M., Jain, U., Esaulova, E., Artyomov, M. N., Morales, D. J., Holtzman, M. J., et al. (2017) · Science · doi:10.1126/science.aam5336 · Cited by 569 · see citing works

RORγt+ innate lymphoid cells regulate intestinal homeostasis by integrating negative signals from the symbiotic microbiota

Sawa, S., Lochner, M., Satoh‐Takayama, N., Dulauroy, S., Berard, M., Kleinschek, M. A., Cua, D., Santo, J. P. D., & Eberl, G. (2011) · Nature Immunology · doi:10.1038/ni.2002 · Cited by 568 · see citing works

Normalization of host intestinal mucus layers requires long-term microbial colonization

Johansson, M. E. V., Jakobsson, H. E., Holmén-Larsson, J., Schütte, A., Ermund, A., Rodríguez-Piñeiro, A. M., Arike, L., Wising, C., Svensson, F., Bäckhed, F., et al. (2015) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2015.10.007 · Cited by 549 · see citing works

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013) · Nature · doi:10.1038/nature12212 · Cited by 542 · see citing works

TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination

Oh, J. Z., Ravindran, R., Chassaing, B., Carvalho, F. A., Maddur, M. S., Bower, M., Hakimpour, P., Gill, K. P., Nakaya, H. I., Yarovinsky, F., et al. (2014) · Immunity · doi:10.1016/j.immuni.2014.08.009 · Cited by 541 · see citing works

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

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An enteric virus can replace the beneficial function of commensal bacteria

Kernbauer, E., Ding, Y., & Cadwell, K. (2014) · Nature · doi:10.1038/nature13960 · Cited by 513 · see citing works

Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota

Ganal, S. C., Sanos, S. L., Kallfass, C., Oberle, K., Johner, C., Kirschning, C., Lienenklaus, S., Weiss, S., Staeheli, P., Aichele, P., et al. (2012) · Immunity · doi:10.1016/j.immuni.2012.05.020 · Cited by 484 · see citing works

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine

Theriot, C. M., Bowman, A. A., & Young, V. B. (2016) · mSphere · doi:10.1128/msphere.00045-15 · Cited by 481 · see citing works

A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling

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Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX3CR1hi cells

Diehl, G. E., Longman, R., Zhang, J.-X., Bréart, B., Galan, C., Cuesta, A., Schwab, S. R., & Littman, D. R. (2013) · Nature · doi:10.1038/nature11809 · Cited by 472 · see citing works

Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation

Hill, D. A., Siracusa, M. C., Abt, M. C., Kim, B. S., Kobuley, D., Kubo, M., Kambayashi, T., LaRosa, D. F., Renner, E. D., Orange, J. S., et al. (2012) · Nature Medicine · doi:10.1038/nm.2657 · Cited by 468 · see citing works

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

Enault, F., Briet, A., Bouteille, L., Roux, S., Sullivan, M. B., & Petit, M. (2016) · The ISME Journal · doi:10.1038/ismej.2016.90 · Cited by 432 · see citing works

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice

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Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

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Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection

Baldridge, M. T., Nice, T. J., McCune, B. T., Yokoyama, C. C., Kambal, A., Wheadon, M. J., Diamond, M., Ivanova, Y., Artyomov, M. N., & Virgin, H. W. (2014) · Science · doi:10.1126/science.1258025 · Cited by 413 · see citing works

Microbiota depletion promotes browning of white adipose tissue and reduces obesity

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Toll-Like Receptor 4 Signaling by Intestinal Microbes Influences Susceptibility to Food Allergy

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Microbial Modulation of Energy Availability in the Colon Regulates Intestinal Transit

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The microbiota protects against respiratory infection via GM-CSF signaling

Brown, R. L., Sequeira, R. P., & Clarke, T. B. (2017) · Nature Communications · doi:10.1038/s41467-017-01803-x · Cited by 378 · see citing works

Gut Dysbiosis Promotes M2 Macrophage Polarization and Allergic Airway Inflammation via Fungi-Induced PGE2

Kim, Y.-G., Udayanga, K. G. S., Totsuka, N., Weinberg, J. B., Núñez, G., & Shibuya, A. (2014) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2013.12.010 · Cited by 366 · see citing works

Antibiotics impair murine hematopoiesis by depleting the intestinal microbiota

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Impact of intestinal microbiota on intestinal luminal metabolome

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Microbiota-induced IL-1β, but not IL-6, is critical for the development of steady-state TH17 cells in the intestine

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Gut-derived lipopolysaccharide augments adipose macrophage accumulation but is not essential for impaired glucose or insulin tolerance in mice

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Role of Antibiotics and Fungal Microbiota in Driving Pulmonary Allergic Responses

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Immune-microbiota interactions in health and disease

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Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

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γδ intraepithelial lymphocytes are essential mediators of host–microbial homeostasis at the intestinal mucosal surface

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Commensal-dependent expression of IL-25 regulates the IL-23–IL-17 axis in the intestine

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Promotion of Intestinal Epithelial Cell Turnover by Commensal Bacteria: Role of Short-Chain Fatty Acids

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Localization of gamma/delta T cells to the intestinal epithelium is independent of normal microbial colonization.

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Microbial sensing by goblet cells controls immune surveillance of luminal antigens in the colon

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Microbiota-Derived Compounds Drive Steady-State Granulopoiesis via MyD88/TICAM Signaling

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

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Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

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The response of the lymphatic tissue to the microbial flora. Studies on germfree mice.

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Transient TLR Activation Restores Inflammatory Response and Ability To Control Pulmonary Bacterial Infection in Germfree Mice

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Use of Germ-Free Animal Models in Microbiota-Related Research

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Bacterial Flagellin Stimulates Toll‐Like Receptor 5–Dependent Defense against Vancomycin‐Resistant <i>Enterococcus</i> Infection

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

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Tropism for tuft cells determines immune promotion of norovirus pathogenesis

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Antibiotic Administration Routes Significantly Influence the Levels of Antibiotic Resistance in Gut Microbiota

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Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses

Kim, M., Galan, C., Hill, A. A., Wu, W.-J., Fehlner-Peach, H., Song, H. W., Schady, D., Bettini, M. L., Simpson, K. W., Longman, R. S., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.05.009 · Cited by 202 · cited 4× · see citing works

Reciprocal Interactions between Commensal Bacteria and γδ Intraepithelial Lymphocytes during Mucosal Injury

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Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice

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Antibiotic Treatment Suppresses Rotavirus Infection and Enhances Specific Humoral Immunity

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