1. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.

    Science 352(6289):1116 (2016) PMID 27230380

    Inflammatory bowel disease (IBD) is associated with risk variants in the human genome and dysbiosis of the gut microbiome, though unifying principles for these findings remain largely undescribed. The human commensal Bacteroides fragilis delivers immunomodulatory molecules to immune cells via se...
  2. Gut biogeography of the bacterial microbiota.

    Nature Reviews: Microbiology 14(1):20 (2016) PMID 26499895 PMCID PMC4837114

    Animals assemble and maintain a diverse but host-specific gut microbial community. In addition to characteristic microbial compositions along the longitudinal axis of the intestines, discrete bacterial communities form in microhabitats, such as the gut lumen, colonic mucus layers and colonic cry...
  3. Winning the Microbial Battle, but Not the War.

    Cell 163(2):271 (2015) PMID 26451475

    An effective immune response leads to rapid elimination of infectious agents, with seemingly little long-term impairment to the host. New findings by Morais da Fonseca et al. reveal that acute infections may result in permanent disruption of tissue homeostasis and immune dysfunction, long after ...
  4. Control of brain development, function, and behavior by the microbiome.

    Cell Host & Microbe 17(5):565 (2015) PMID 25974299 PMCID PMC4442490

    Animals share an intimate and life-long partnership with a myriad of resident microbial species, collectively referred to as the microbiota. Symbiotic microbes have been shown to regulate nutrition and metabolism and are critical for the development and function of the immune system. More recent...
  5. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.

    Cell 161(2):264 (2015) PMID 25860609 PMCID PMC4393509

    The gastrointestinal (GI) tract contains much of the body's serotonin (5-hydroxytryptamine, 5-HT), but mechanisms controlling the metabolism of gut-derived 5-HT remain unclear. Here, we demonstrate that the microbiota plays a critical role in regulating host 5-HT. Indigenous spore-forming bacter...
  6. Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires.

    eLife 4:e09083 (2015) PMID 26422511 PMCID PMC4714975

    Processes that define immunoglobulin repertoires are commonly presumed to be the same for all murine B cells. However, studies here that couple high-dimensional FACS sorting with large-scale quantitative IgH deep-sequencing demonstrate that B-1a IgH repertoire differs dramatically from the folli...
  7. Gut microbes and the brain: paradigm shift in neuroscience.

    Journal of Neuroscience 34(46):15490 (2014) PMID 25392516 PMCID PMC4228144

    The discovery of the size and complexity of the human microbiome has resulted in an ongoing reevaluation of many concepts of health and disease, including diseases affecting the CNS. A growing body of preclinical literature has demonstrated bidirectional signaling between the brain and the gut m...
  8. Specialized metabolites from the microbiome in health and disease.

    Cell Metabolism 20(5):719 (2014) PMID 25440054 PMCID PMC4337795

    The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with vario...
  9. Commensal bacteria protect against food allergen sensitization.

    PNAS 111(36):13145 (2014) PMID 25157157 PMCID PMC4246970

    Environmentally induced alterations in the commensal microbiota have been implicated in the increasing prevalence of food allergy. We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota. By selective...
  10. Finding the missing links among metabolites, microbes, and the host.

    Immunity 40(6):824 (2014) PMID 24950202 PMCID PMC4503329

    The unexpected diversity of the human microbiome and metabolome far exceeds the complexity of the human genome. Although we now understand microbial taxonomic and genetic repertoires in some populations, we are just beginning to assemble the necessary computational and experimental tools to unde...
  11. Microbial learning lessons: SFB educate the immune system.

    Immunity 40(4):457 (2014) PMID 24745329

    Segmented filamentous bacteria (SFB) contribute to immune-system maturation. In this issue of Immunity, Goto et al. (2014) and Lécuyer et al. (2014) provide evidence for how SFB induce antigen-specific T helper 17 cells and promote development of adaptive immunity at discrete mucosal sites. Copy...
  12. Gut microbiota promote hematopoiesis to control bacterial infection.

    Cell Host & Microbe 15(3):374 (2014) PMID 24629343 PMCID PMC4144825

    The commensal microbiota impacts specific immune cell populations and their functions at peripheral sites, such as gut mucosal tissues. However, it remains unknown whether gut microbiota control immunity through regulation of hematopoiesis at primary immune sites. We reveal that germ-free mice d...
  13. Identification of secreted bacterial proteins by noncanonical amino acid tagging.

    PNAS 111(1):433 (2014) PMID 24347637 PMCID PMC3890788

    Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted patho...
  14. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders.

    Cell 155(7):1451 (2013) PMID 24315484 PMCID PMC3897394

    Neurodevelopmental disorders, including autism spectrum disorder (ASD), are defined by core behavioral impairments; however, subsets of individuals display a spectrum of gastrointestinal (GI) abnormalities. We demonstrate GI barrier defects and microbiota alterations in the maternal immune activ...
  15. Bacterial colonization factors control specificity and stability of the gut microbiota.

    Nature 501(7467):426 (2013) PMID 23955152 PMCID PMC3893107

    Mammals harbour a complex gut microbiome, comprising bacteria that confer immunological, metabolic and neurological benefits. Despite advances in sequence-based microbial profiling and myriad studies defining microbiome composition during health and disease, little is known about the molecular p...
  16. Innate immune recognition of the microbiota promotes host-microbial symbiosis.

    Nature Immunology 14(7):668 (2013) PMID 23778794 PMCID PMC4109969

    Pattern-recognition receptors (PRRs) are traditionally known to sense microbial molecules during infection to initiate inflammatory responses. However, ligands for PRRs are not exclusive to pathogens and are abundantly produced by the resident microbiota during normal colonization. Mechanism(s) ...
  17. Disruption of the gut microbiome as a risk factor for microbial infections

    Current Opinion in Microbiology 16(2):221 (2013) PMID 23597788

    • Commensal microbes are critical in promoting host resistance against infectious disease. • Protection by the microbiota from infection can be achieved through di...
  18. Animals in a bacterial world, a new imperative for the life sciences.

    PNAS 110(9):3229 (2013) PMID 23391737 PMCID PMC3587249

    In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimat...
  19. A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis.

    Journal of Allergy and Clinical Immunology 131(1):201 (2013) PMID 23201093 PMCID PMC3860814

    Commensal microbiota play a critical role in maintaining oral tolerance. The effect of food allergy on the gut microbial ecology remains unknown. We sought to establish the composition of the gut microbiota in experimental food allergy and its role in disease pathogenesis. Food allergy-prone mic...
  20. Outer membrane vesicles of a human commensal mediate immune regulation and disease protection.

    Cell Host & Microbe 12(4):509 (2012) PMID 22999859 PMCID PMC3895402

    Commensal bacteria impact host health and immunity through various mechanisms, including the production of immunomodulatory molecules. Bacteroides fragilis produces a capsular polysaccharide (PSA), which induces regulatory T cells and mucosal tolerance. However, unlike pathogens, which employ se...