Philip P. Ahern

Human nutrition, the gut microbiome and the immune system

Marked changes in socio-economic status, cultural traditions, population growth and agriculture are affecting diets worldwide. Understanding how our diet and nutritional status influence the composition and dynamic operations of our gut microbial communities, and the innate and adaptive arms of our immune system, represents an area of scientific need, opportunity and challenge. The insights gleaned should help to address several pressing global health problems.

Identifying Gut Microbe–Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

Identifying human gut bacterial strains that affect three diverse biological responses should facilitate discovery of next-generation probiotics and realization of the microbiota’s diagnostic potential. Mining the Microbiota for Next Generation Probiotics Our human guts are populated by a mind-boggling number of microbial cells. Identifying members of this vast microbial community that produce specific effects on physiology, metabolism, or immunity is extremely challenging, given the large number of combinations of organisms that could tested. Now, Faith et al. have developed a way to address this challenge. They transplanted intact uncultured microbiota from different human donors into germ-free mice to identify features (phenotypes) of the donor that are transmissible to recipient animals. They then ascertained the ability of the culturable component of a microbiota to transmit these phenotypes. The culture collection was randomly divided into subsets of different sizes, and each subset was introduced into a sterile mouse. By assaying subsets with overlapping bacterial strains, the effect of each strain could be assayed in the context of different community memberships and sizes. Follow-up colonizations with single strains of interest were used to validate those whose presence or absence best explained a phenotype. Screening 94 strain combinations from a single adult’s microbiota revealed strains that modulated the number of regulatory T cells in the colon’s immune system, adiposity, and several facets of metabolism. This approach should facilitate mechanistic studies of how bacterial strains influence health and the discovery of therapeutic probiotics. Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic, and immunologic phenotypes remains a challenge. We describe a method in which a clonally arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (Tregs) and expansion of Nrp1lo/− peripheral Tregs, as well as strains that modulated mouse adiposity and cecal metabolite concentrations, using feature selection algorithms and follow-up monocolonizations. This combinatorial approach enables a systems-level understanding of microbial contributions to human biology.

Metabolic niche of a prominent sulfate-reducing human gut bacterium

Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage’s substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.

Mining the Human Gut Microbiota for Effector Strains that Shape the Immune System

The gut microbiota codevelops with the immune system beginning at birth. Mining the microbiota for bacterial strains responsible for shaping the structure and dynamic operations of the innate and adaptive arms of the immune system represents a formidable combinatorial problem but one that needs to be overcome to advance mechanistic understanding of microbial community and immune system coregulation and to develop new diagnostic and therapeutic approaches that promote health. Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice. Clonally arrayed sequenced collections of bacterial strains are constructed from representative donor microbiota. If the collection transmits phenotypes, effector strains are identified by testing randomly generated subsets with overlapping membership in individually housed germ-free animals. Detailed mechanistic studies of effector strain-host interactions can then be performed.

Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells

Tolerogenic T cells need probiotics CD4+CD8αα+ double-positive intraepithelial lymphocytes (DP IELs) are a recently discovered class of intestinal T cells believed to take part in a variety of immune responses, including oral tolerance. These cells are absent in germ-free mice, but the mechanisms driving their development are unclear. Cervantes-Barragan et al. found that a particular species of probiotic bacteria, Lactobacillus reuteri, induces DP IELs. This does not occur by stimulating the immune system directly. Instead, L. reuteri generates a specific derivative of dietary tryptophan that promotes differentiation of DP IEL precursors. These findings underscore the delicate interplay between benign bacteria, diet, and gut health. Science, this issue p. 806 Lactobacillus reuteri induces a specific type of gut intraepithelial T cell via tryptophan catabolites that activate the aryl hydrocarbon receptor. The small intestine contains CD4+CD8αα+ double-positive intraepithelial lymphocytes (DP IELs), which originate from intestinal CD4+ T cells through down-regulation of the transcription factor Thpok and have regulatory functions. DP IELs are absent in germ-free mice, which suggests that their differentiation depends on microbial factors. We found that DP IEL numbers in mice varied in different vivaria, correlating with the presence of Lactobacillus reuteri. This species induced DP IELs in germ-free mice and conventionally-raised mice lacking these cells. L. reuteri did not shape the DP-IEL-TCR (TCR, T cell receptor) repertoire but generated indole derivatives of tryptophan that activated the aryl-hydrocarbon receptor in CD4+ T cells, allowing Thpok down-regulation and differentiation into DP IELs. Thus, L. reuteri, together with a tryptophan-rich diet, can reprogram intraepithelial CD4+ T cells into immunoregulatory T cells.

Analysis of gene-environment interactions in postnatal development of the mammalian intestine.

Significance The mammalian intestine provides a key interface with several essential environmental factors, including nutrients, toxins, resident microbiota, and pathogens. Consequently, the intestine undergoes major developmental transitions that correspond to dramatic changes in the environment: one at birth and the other at weaning. These transitions reflect both developmental and environmentally induced changes in intestinal gene expression. Here, we performed a systematic analysis of global gene expression that is associated with developmental timing versus the changes that are due to the innate immune signaling pathways mediated by toll-like receptor (TLR) and IL-1 receptor families. The results reveal distinct roles of these pathways in intestinal adaptation throughout postnatal development. Unlike mammalian embryogenesis, which takes place in the relatively predictable and stable environment of the uterus, postnatal development can be affected by a multitude of highly variable environmental factors, including diet, exposure to noxious substances, and microorganisms. Microbial colonization of the intestine is thought to play a particularly important role in postnatal development of the gastrointestinal, metabolic, and immune systems. Major changes in environmental exposure occur right after birth, upon weaning, and during pubertal maturation into adulthood. These transitions include dramatic changes in intestinal contents and require appropriate adaptations to meet changes in functional demands. Here, we attempt to both characterize and provide mechanistic insights into postnatal intestinal ontogeny. We investigated changes in global intestinal gene expression through postnatal developmental transitions. We report profound alterations in small and large intestinal transcriptional programs that accompany both weaning and puberty in WT mice. Using myeloid differentiation factor 88 (MyD88)/TIR-domain-containing adapter-inducing interferon-β (TRIF) double knockout littermates, we define the role of toll-like receptors (TLRs) and interleukin (IL)-1 receptor family member signaling in postnatal gene expression programs and select ontogeny-specific phenotypes, such as vascular and smooth muscle development and neonatal epithelial and mast cell homeostasis. Metaanalysis of the effect of the microbiota on intestinal gene expression allowed for mechanistic classification of developmentally regulated genes by TLR/IL-1R (TIR) signaling and/or indigenous microbes. We find that practically every aspect of intestinal physiology is affected by postnatal transitions. Developmental timing, microbial colonization, and TIR signaling seem to play distinct and specific roles in regulation of gene-expression programs throughout postnatal development.

An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome

The Sackler Institute for Nutrition Science and the World Health Organization (WHO) have worked together to formulate a research agenda for nutrition science. Undernutrition of children has profound effects on health, development, and achievement of full human capacity. Undernutrition is not simply caused by a lack of food, but results from a complex interplay of intra‐ and intergenerational factors. Representative preclinical models and comprehensive well‐controlled longitudinal clinical studies are needed to further understand the contributions and the interrelationships among these factors and to develop interventions that are effective and durable. This paper summarizes work on mechanisms underlying the varied manifestations of childhood undernutrition and discusses current gaps in knowledge and challenges to our understanding of undernutrition and infection/immunity throughout the human life cycle, focusing on early childhood growth. It proposes a series of basic and clinical studies to address this global health challenge.

T-bet is a key modulator of IL-23-driven pathogenic CD4+ T cell responses in the intestine

IL-23 is a key driver of pathogenic Th17 cell responses. It has been suggested that the transcription factor T-bet is required to facilitate IL-23-driven pathogenic effector functions; however, the precise role of T-bet in intestinal T cell responses remains elusive. Here, we show that T-bet expression by T cells is not required for the induction of colitis or the differentiation of pathogenic Th17 cells but modifies qualitative features of the IL-23-driven colitogenic response by negatively regulating IL-23R expression. Consequently, absence of T-bet leads to unrestrained Th17 cell differentiation and activation characterized by high amounts of IL-17A and IL-22. The combined increase in IL-17A/IL-22 results in enhanced epithelial cell activation and inhibition of either IL-17A or IL-22 leads to disease amelioration. Our study identifies T-bet as a key modulator of IL-23-driven colitogenic responses in the intestine and has important implications for understanding of heterogeneity among inflammatory bowel disease patients.

The absence of a microbiota enhances TSLP expression in mice with defective skin barrier but does not affect the severity of their allergic inflammation

Evidence is accumulating to suggest that our indigenous microbial communities (microbiota) may play a role in modulating allergic and immune disorders of the skin (Gallo and Nakatsuji, 2011; Macia et al., 2012). To examine the link between the microbiota and atopic dermatitis, we examined a mouse model of defective cutaneous barrier function with an atopic dermatitis-like disease due to loss of Notch signaling. Comparisons of conventionally-raised (CONV-R) and germ-free (GF) mice revealed a similar degree of allergic skin inflammation, systemic atopy, and airway hypersensitivity. GF mutant animals expressed significantly higher levels of thymic stromal lymphopoietin (TSLP), a major proinflammatory cytokine released by skin with defective barrier function, resulting in a more severe B-lymphoproliferative disorder that persisted into adulthood. These findings suggest a role for the microbiota in ameliorating stress signals released by keratinocytes in response to perturbation in cutaneous barrier function.

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

Pathobiont-associated cachexia in a gnotobiotic model of childhood undernutrition is determined by strain-level interactions within the gut microbiota. Neighbors matter A big unanswered question is what determines the effects of enteropathogen burden in children who are undernourished or at risk for undernutrition. In a new study, Wagner and colleagues introduce collections of sequenced gut bacterial strains cultured from healthy or underweight Bangladeshi children into germfree mice fed diets resembling those consumed by the children. The gut bacterial strains were transplanted with or without nontoxigenic or enterotoxigenic Bacteroides fragilis strains. Addition of enterotoxigenic B. fragilis induced cachexia in the transplanted mice, and altered gene expression and metabolic activity of the transplanted bacterial strains. These effects were mitigated by cocolonization with nontoxigenic B. fragilis, illustrating the influence of intra- and interspecies interactions in determining the impact of an enteropathogen on its host. To model how interactions among enteropathogens and gut microbial community members contribute to undernutrition, we colonized gnotobiotic mice fed representative Bangladeshi diets with sequenced bacterial strains cultured from the fecal microbiota of two 24-month-old Bangladeshi children: one healthy and the other underweight. The undernourished donor’s bacterial collection contained an enterotoxigenic Bacteroides fragilis strain (ETBF), whereas the healthy donor’s bacterial collection contained two nontoxigenic strains of B. fragilis (NTBF). Analyses of mice harboring either the unmanipulated culture collections or systematically manipulated versions revealed that ETBF was causally related to weight loss in the context of its native community but not when introduced into the healthy donor’s community. This phenotype was transmissible from the dams to their offspring and was associated with derangements in host energy metabolism manifested by impaired tricarboxylic acid cycle activity and decreased acyl–coenzyme A utilization. NTBF reduced ETBF’s expression of its enterotoxin and mitigated the effects of ETBF on the transcriptomes of other healthy donor community members. These results illustrate how intraspecific (ETBF-NTBF) and interspecific interactions influence the effects of harboring B. fragilis.