Imprinting of the immune system by the microbiota early in life

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

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

Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413

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

Cryan, J. F., & Dinan, T. G. (2012) · Nature Reviews Neuroscience · doi:10.1038/nrn3346 · Cited by 4,572

Gut Microbiota Metabolism of Dietary Fiber Influences Allergic Airway Disease and Hematopoiesis

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Trained immunity: A program of innate immune memory in health and– disease

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The Effect of Infections on Susceptibility to Autoimmune and Allergic Diseases

Bach, J. (2002) · New England Journal of Medicine · doi:10.1056/nejmra020100 · Cited by 2,723

The Placenta Harbors a Unique Microbiome

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How colonization by microbiota in early life shapes the immune system

Gensollen, T., Iyer, S. S., Kasper, D. L., & Blumberg, R. S. (2016) · Science · doi:10.1126/science.aad9378 · Cited by 2,044

Reciprocal T H 17 and Regulatory T Cell Differentiation Mediated by Retinoic Acid

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Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

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Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells

Wu, H.-J., Ivanov, I. I., Darce, J., Hattori, K., Shima, T., Umesaki, Y., Littman, D. R., Benoist, C., & Mathis, D. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.001 · Cited by 1,577

Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey

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Persistent gut microbiota immaturity in malnourished Bangladeshi children

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The maternal microbiota drives early postnatal innate immune development

Gomez de Agüero, M., Ganal-Vonarburg, S. C., Fuhrer, T., Rupp, S., Uchimura, Y., Li, H., Steinert, A., Heikenwalder, M., Hapfelmeier, S., Sauer, U., et al. (2016) · Science · doi:10.1126/science.aad2571 · Cited by 1,231

Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice

Bain, C. C., Bravo-Blas, A., Scott, C. L., Gomez Perdiguero, E., Geissmann, F., Henri, S., Malissen, B., Osborne, L. C., Artis, D., & Mowat, A. M. (2014) · Nature Immunology · doi:10.1038/ni.2967 · Cited by 1,178

Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity

Clarke, T. B., Davis, K. M., Lysenko, E. S., Zhou, A. Y., Yu, Y., & Weiser, J. N. (2010) · Nature Medicine · doi:10.1038/nm.2087 · Cited by 1,154

The Molecular and Systems Biology of Memory

Kandel, E. R., Dudai, Y., & Mayford, M. R. (2014) · Cell · doi:10.1016/j.cell.2014.03.001 · Cited by 1,134

Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis

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Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., Viale, A., Socci, N. D., van den Brink, M. R. M., Kamboj, M., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci43918 · Cited by 943

Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites

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The Aryl Hydrocarbon Receptor Regulates Gut Immunity through Modulation of Innate Lymphoid Cells

Qiu, J., Heller, J. J., Guo, X., Chen, Z. E., Fish, K., Fu, Y., & Zhou, L. (2011) · Immunity · doi:10.1016/j.immuni.2011.11.011 · Cited by 889

Early life antibiotic‐driven changes in microbiota enhance susceptibility to allergic asthma

Russell, S. L., Gold, M. J., Hartmann, M., Willing, B. P., Thorson, L., Wlodarska, M., Gill, N., Blanchet, M., Mohn, W. W., McNagny, K. M., et al. (2012) · The EMBO Reports · doi:10.1038/embor.2012.32 · Cited by 883

Individual intestinal symbionts induce a distinct population of RORγ + regulatory T cells

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The microbiota regulates type 2 immunity through RORγt + T cells

Ohnmacht, C., Park, J.-H., Cording, S., Wing, J. B., Atarashi, K., Obata, Y., Gaboriau-Routhiau, V., Marques, R., Dulauroy, S., Fedoseeva, M., et al. (2015) · Science · doi:10.1126/science.aac4263 · Cited by 863

Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles

Kiss, E. A., Vonarbourg, C., Kopfmann, S., Hobeika, E., Finke, D., Esser, C., & Diefenbach, A. (2011) · Science · doi:10.1126/science.1214914 · Cited by 801

Brain mechanisms in early language acquisition

Kuhl, P. K. (2010) · Neuron · doi:10.1016/j.neuron.2010.08.038 · Cited by 798

AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on and independent of Notch

Lee, J. S., Cella, M., McDonald, K. G., Garlanda, C., Kennedy, G. D., Nukaya, M., Mantovani, A., Kopan, R., Bradfield, C. A., Newberry, R. D., et al. (2012) · Nature Immunology · doi:10.1038/ni.2187 · Cited by 777

Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions.

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Inflammatory memory sensitizes skin epithelial stem cells to tissue damage

Naik, S., Larsen, S. B., Gomez, N. C., Alaverdyan, K., Sendoel, A., Yuan, S., Polak, L., Kulukian, A., Chai, S., & Fuchs, E. (2017) · Nature · doi:10.1038/nature24271 · Cited by 745

Human placenta has no microbiome but can contain potential pathogens

de Goffau, M. C., Lager, S., Sovio, U., Gaccioli, F., Cook, E., Peacock, S. J., Parkhill, J., Charnock-Jones, D. S., & Smith, G. C. S. (2019) · Nature · doi:10.1038/s41586-019-1451-5 · Cited by 691

A weaning reaction to microbiota is required for resistance to immunopathologies in the adult

Al Nabhani, Z., Dulauroy, S., Marques, R., Cousu, C., Al Bounny, S., Déjardin, F., Sparwasser, T., Bérard, M., Cerf-Bensussan, N., & Eberl, G. (2019) · Immunity · doi:10.1016/j.immuni.2019.02.014 · Cited by 679

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 668

Innate and Adaptive Immune Memory: an Evolutionary Continuum in the Host’s Response to Pathogens

Netea, M. G., Schlitzer, A., Placek, K., Joosten, L. A. B., & Schultze, J. L. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2018.12.006 · Cited by 644

Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

Cahenzli, J., Köller, Y., Wyss, M., Geuking, M. B., & McCoy, K. D. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.10.004 · Cited by 611

Lung microbiota promotes tolerance to allergens in neonates via PD-L1

Gollwitzer, E. S., Saglani, S., Trompette, A., Yadava, K., Sherburn, R., McCoy, K. D., Nicod, L. P., Lloyd, C. M., & Marsland, B. J. (2014) · Nature Medicine · doi:10.1038/nm.3568 · Cited by 596

A wave of regulatory T cells into neonatal skin mediates tolerance to commensal microbes

Scharschmidt, T. C., Vasquez, K. S., Truong, H.-A., Gearty, S. V., Pauli, M. L., Nosbaum, A., Gratz, I. K., Otto, M., Moon, J. J., Liese, J., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.10.016 · Cited by 586

Studies in Animal and Human Behaviour. Volume I

Lorenz, K. Z. (1970) · Harvard University Press eBooks · doi:10.4159/harvard.9780674430389 · Cited by 581

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

Farm dust and endotoxin protect against allergy through A20 induction in lung epithelial cells

Schuijs, M. J., Willart, M. A., Vergote, K., Gras, D., Deswarte, K., Ege, M. J., Madeira, F. B., Beyaert, R., van Loo, G., Bracher, F., et al. (2015) · Science · doi:10.1126/science.aac6623 · Cited by 576

MAIT cells are imprinted by the microbiota in early life and promote tissue repair

Constantinides, M. G., Link, V. M., Tamoutounour, S., Wong, A. C., Perez-Chaparro, P. J., Han, S.-J., Chen, Y. E., Li, K., Farhat, S., Weckel, A., et al. (2019) · Science · doi:10.1126/science.aax6624 · Cited by 567

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 527

Studies in animal and human behaviour

Lorenz, K. Z. (1970) · Virtual Defense Library (Ministerio de Defensa) · Cited by 502

Identification of Multiple Isolated Lymphoid Follicles on the Antimesenteric Wall of the Mouse Small Intestine

Hamada, H., Hiroi, T., Nishiyama, Y., Takahashi, H., Masunaga, Y., Hachimura, S., Kaminogawa, S., Takahashi‐Iwanaga, H., Iwanaga, T., Kiyono, H., et al. (2002) · The Journal of Immunology · doi:10.4049/jimmunol.168.1.57 · Cited by 481

Epigenetic programming and reprogramming during development

Cantone, I., & Fisher, A. G. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2489 · Cited by 459

High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model

Ma, J., Prince, A., Bader, D., Hu, M., Ganu, R., Baquero, K. C., Blundell, P., Harris, R. A., Frias, A. E., Grove, K. L., et al. (2014) · Nature Communications · doi:10.1038/ncomms4889 · Cited by 452

The microbiota regulate neuronal function and fear extinction learning

Chu, C., Murdock, M. H., Jing, D., Won, T. H., Chung, H., Kressel, A. M., Tsaava, T., Addorisio, M. E., Putzel, G. G., Zhou, L., et al. (2019) · Nature · doi:10.1038/s41586-019-1644-y · Cited by 421

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 419

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

Bashir, M. E. H., Louie, S., Shi, H. N., & Nagler‐Anderson, C. (2004) · The Journal of Immunology · doi:10.4049/jimmunol.172.11.6978 · Cited by 392

Microbial Factor-Mediated Development in a Host-Bacterial Mutualism

Koropatnick, T. A., Engle, J. T., Apicella, M. A., Stabb, E. V., Goldman, W. E., & McFall‐Ngai, M. (2004) · Science · doi:10.1126/science.1102218 · Cited by 379

How nutrition and the maternal microbiota shape the neonatal immune system

Macpherson, A. J., de Agüero, M. G., & Ganal-Vonarburg, S. C. (2017) · Nature Reviews Immunology · doi:10.1038/nri.2017.58 · Cited by 378

Microbial metabolites control the thymic development of mucosal-associated invariant T cells

Legoux, F., Bellet, D., Daviaud, C., El Morr, Y., Darbois, A., Niort, K., Procopio, E., Salou, M., Gilet, J., Ryffel, B., et al. (2019) · Science · doi:10.1126/science.aaw2719 · Cited by 320

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

Knoop, K. A., McDonald, K. G., McCrate, S., Mcdole, J. R., & Newberry, R. D. (2014) · Mucosal Immunology · doi:10.1038/mi.2014.58 · Cited by 276

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria

Knoop, K. A., Gustafsson, J. K., McDonald, K. G., Kulkarni, D. H., Coughlin, P. E., McCrate, S., Kim, D., Hsieh, C., Hogan, S. P., Elson, C. O., et al. (2017) · Science Immunology · doi:10.1126/sciimmunol.aao1314 · Cited by 270

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation

Osborne, L. C., Monticelli, L. A., Nice, T. J., Sutherland, T. E., Siracusa, M. C., Hepworth, M. R., Tomov, V. T., Kobuley, D. E., Tran, S. V., Bittinger, K. L., et al. (2014) · Science · doi:10.1126/science.1256942 · Cited by 268

Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice

Aidy, S. E., van Baarlen, P., Derrien, M., Lindenbergh-Kortleve, D. J., Hooiveld, G. J. E. J., Levenez, F., Dore, J. M., Dekker, J. P., Samsom, J. N., Nieuwenhuis, E. E. S., et al. (2012) · Mucosal Immunology · doi:10.1038/mi.2012.32 · Cited by 247

Retinoic Acid and Retinoic Acid Receptors as Pleiotropic Modulators of the Immune System

Larangé, A., & Cheroutre, H. (2016) · Annual Review of Immunology · doi:10.1146/annurev-immunol-041015-055427 · Cited by 243

miR-146a Mediates Protective Innate Immune Tolerance in the Neonate Intestine

Chassin, C., Kocur, M., Pott, J., Duerr, C. U., Gütle, D., Lotz, M., & Hornef, M. W. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.09.005 · Cited by 227

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

The theory of disappearing microbiota and the epidemics of chronic diseases

Blaser, M. J. (2017) · Nature reviews. Immunology · doi:10.1038/nri.2017.77 · Cited by 214

Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition

Fulde, M., Sommer, F., Chassaing, B., van Vorst, K., Dupont, A., Hensel, M., Basic, M., Klopfleisch, R., Rosenstiel, P., Bleich, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0395-5 · Cited by 206

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

Lynn, M. A., Tumes, D. J., Choo, J. M., Sribnaia, A., Blake, S. J., Leong, L. E. X., Young, G. P., Marshall, H. S., Wesselingh, S. L., Rogers, G. B., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.04.009 · Cited by 205

Adaptation and memory in immune responses

Natoli, G., & Ostuni, R. (2019) · Nature Immunology · doi:10.1038/s41590-019-0399-9 · Cited by 203

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche

Luo, Y., Chen, G., Hannemann, N., Ipseiz, N., Krönke, G., Bäuerle, T., Munos, L., Wirtz, S. J., Schett, G. A., & Bözec, A. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.08.020 · Cited by 201

Immunity by equilibrium

Eberl, G. (2016) · Nature reviews. Immunology · doi:10.1038/nri.2016.75 · Cited by 200

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota

Munyaka, P. M., Eissa, N., Bernstein, C. N., Khafipour, E., & Ghia, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142536 · Cited by 189

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study

Örtqvist, A. K., Lundholm, C., Halfvarson, J., Ludvigsson, J. F., & Almqvist, C. (2018) · Gut · doi:10.1136/gutjnl-2017-314352 · Cited by 178

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis

Zanvit, P., Konkel, J. E., Jiao, X., Kasagi, S., Zhang, D., Wu, R., Chia, C., Ajami, N. J., Smith, D. P., Petrosino, J. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9424 · Cited by 173

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice

Schulfer, A. F., Battaglia, T., Alvarez, Y., Bijnens, L., Ruiz, V. E., Ho, M. L., Robinson, S. L., Ward, T., Cox, L. M., Rogers, A. B., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0075-5 · Cited by 167

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring

Miyoshi, J., Bobe, A. M., Miyoshi, S., Huang, Y., Hubert, N., Delmont, T. O., Eren, A. M., Leone, V., & Chang, E. B. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.060 · Cited by 156

Perinatal Interactions between the Microbiome, Immunity, and Neurodevelopment

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Immunological memory: What's in a name?

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Mucosal immunity and allergic responses: lack of regulation and/or lack of microbial stimulation?

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Maternal High Fiber Diet during Pregnancy and Lactation Influences Regulatory T Cell Differentiation in Offspring in Mice

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Pacifier Cleaning Practices and Risk of Allergy Development

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Neonatal colonization of mice with LGG promotes intestinal development and decreases susceptibility to colitis in adulthood

Yan, F., Liu, L., Cao, H., Moore, D. J., Washington, M. K., Wang, B., Peek, R. M., Acra, S. A., & Polk, D. B. (2016) · Mucosal Immunology · doi:10.1038/mi.2016.43 · Cited by 106

Association between antibiotic treatment during pregnancy and infancy and the development of allergic diseases

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Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes

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Age‐associated increase in number of CD4+CD8+ intestinal intraepithelial lymphocytes in rats

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A20 is an early responding negative regulator of Toll-like receptor 5 signalling in intestinal epithelial cells during inflammation

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Excess calorie intake early in life increases susceptibility to colitis in adulthood

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Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin

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Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure

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Early-Life Antibiotic Exposure Causes Intestinal Dysbiosis and Exacerbates Skin and Lung Pathology in Experimental Systemic Sclerosis

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Early-Life Microbiota Exposure Restricts Myeloid-Derived Suppressor Cell–Driven Colonic Tumorigenesis

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