Search

Innate lymphoid cells (ILCs) are a recently described population of innate immune cells that integrate into a complex matrix of cellular pathways that regulate mucosal immunity. Although they are less well represented in circulating blood, ILCs are abundant in intestinal, pulmonary, and oropharyngeal mucosal tissues. The development and organization of the mucosal immune system depend on ILCs as both inducers and regulators of lymphoid tissue. At these barrier sites, ILCs are well positioned to serve as the first responders in orchestrating mucosal immunity at steady state and in response to barrier disruption. In lieu of the rearranged receptors of conventional adaptive lymphocytes, mucosal ILCs utilize tissue-specific spatial organization and local cytokine cues to regulate barrier immunity and tissue repair. This chapter will review the development and heterogeneity of ILCs in the mucosal tissue and their contribution to barrier protection and tissue repair. In particular, we will focus on the organizational structure and environmental regulators that afford tight control of ILC-dependent mucosal immunity. This chapter will also review the role for mucosal ILCs in cross-regulation of adaptive and innate mucosal immune cells, which highlight a central role for ILCs in mucosal tissue homeostasis.

Summary Adherent-invasive E. coli (AIEC) are enriched in the intestinal microbiota of patients with Crohn’s disease (CD) and promote intestinal inflammation. Yet, how AIEC metabolism of nutrients impacts intestinal homeostasis is poorly defined. Here, we show that AIEC encoding the large subunit of propanediol dehydratase (PduC), which facilitates the utilization of fucose fermentation product 1,2-propanediol, are increased in the microbiome of CD patients and drive AIEC-induced intestinal T cell inflammation. In murine models, CX3CR1+ mononuclear phagocytes (MNP) are required for PduC-dependent induction of T helper 17 (Th17) cells and interleukin-1β (IL-1β) production that leads to AIEC-induced inflammatory colitis. Activation of this inflammatory cascade requires the catalytic activity of PduC to generate propionate, which synergizes with lipopolysaccharide (LPS) to induce IL-1β by MNPs. Disrupting fucose availability limits AIEC-induced propionate production and intestinal inflammation. These findings identify MNPs as metabolic sensors linking AIEC metabolism with intestinal inflammation and identify microbial metabolism as a potential therapeutic target in Crohn’s disease treatment.

Background Our lab has recently shown that adherent-invasive E. coli (AIEC), which is enriched in patients with Crohn’s disease, is sufficient to induce intestinal Th17 cell inflammation. Although AIEC lack pathogenic factors including type III secretion systems, virulence-associated metabolic enzymes, including propanediol dehydratase (PduC), enable AIEC to use fucose-derived propanediol as an alternate carbon source in the gut. We hypothesised that this propanediol utilisation pathway functionally modulates AIEC contribution to intestinal tissue immunity and inflammation. Methods We generated pduC-deficient (ΔpduC) and catalytically inactive pduC (pduC*) mutants of a patient-derived, AIEC isolate. Gnotobiotic and genetic mouse models were used to evaluate the cellular and metabolic contribution of pduC to mucosal Th17-cell inflammation. Results We found that pduC is enriched in the microbiome and within E. coli genomes in Crohn’s disease patients compared with healthy controls. Mono-colonisation of mice with pduC-deficient AIEC resulted in reduced, inflammatory Th17 cells and attenuated weight loss using a T-cell transfer colitis model. Using mouse models for inducible deletion of CX3CR1+mononuclear phagocytes (MNPs) or IL10-deficiency, we found that MNPs are required for AIEC-mediated induction of Th17 cells and that IL-10 is required to restrain pduC-dependent colitis. Using a catalytically inactive mutant in mono-colonised mice, we determined that PduC metabolic activity was required for this immune phenotype. Cell-free supernatants from WT AIEC (but not pduC-deficient AIEC) promoted ex vivo Th17 cell polarisation and LC-MS of these supernatants defined PduC-dependent metabolites capable of promoting Th17 polarisation. Conclusion These data reveal a link between AIEC microbial metabolism and inflammatory Th17 cells with the potential to serve as a therapeutic target for tissue inflammation in the treatment of Crohn’s disease.

While the molecular mechanisms by which the microbiome modulates mucosal immunity in Crohn’s disease (CD) are still largely unknown, recent data highlight the involvement of specific diet- and bacterial-derived metabolites in the regulation of intestinal immune cell activation and differentiation. We have recently shown that Adherent-Invasive E.coli (AIEC), which are enriched in CD patients, are sufficient to induce intestinal Th17 cells. Although AIEC lack pathogenic factors including type III secretion systems, many CD-derived isolates express virulence-associated metabolic enzymes including propanediol dehydratase (PduC), which enables AIEC to use fucose-derived propanediol as an alternate carbon source in the gut. We found that pduC is enriched in the microbiome and among E. coli genomes in CD patients compared to healthy controls. With fucosylated oligosaccharides on the surface of intestinal epithelial cells, we hypothesized that this propanediol utilization pathway provides AIEC a competitive advantage for epithelial cell adherence and intestinal immune cell activation. To evaluate the physiologic contribution of pduC to mucosal Th17 induction, we generated a pduC-deficient (ΔpduC) mutant of a CD-derived, AIEC isolate. Deletion of pduC resulted in reduced inflammatory Th17 cells and attenuated weight loss following T cell transfer colitis. Using genetic mouse models, we found that CX3CR1+ mononuclear phagocytes are required for this AIEC-mediated Th17 induction and IL-10 is required to restrain pduC-dependent dextran sodium sulfate (DSS)-induced colitis. Using a catalytically-inactive mutant, we determined that PduC metabolic activity was required for this immune phenotype. Cell-free supernatants from WT AIEC (but not the isogenic, pduC-deficient clone) promoted ex vivo Th17 cell polarization and metabolomics analysis (LC-MS) of these supernatants defined PduC-dependent metabolites capable of promoting Th17 polarization. These studies reveal a link between AIEC microbial metabolism and inflammatory Th17 cells with the potential to serve as a therapeutic target in the treatment of Crohn’s disease.

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001, eLife digest Viruses are unable to replicate independently. To generate copies of itself, a virus must instead invade a target cell and commandeer that cell's replication machinery. Different viruses are able to invade different types of cell, and a group of viruses known as bacteriophages (or phages for short) replicate within bacteria. The enormous number and diversity of phages in the world means that they play an important role in virtually every ecosystem. Despite their importance, relatively little is known about how different phage populations are related to each other and how they evolved. Many phages contain their genetic information in the form of strands of DNA. Using genetic sequencing to find out where and how different genes are encoded in the DNA can reveal information about how different viruses are related to each other. These relationships are particularly complicated in phages, as they can exchange genes with other viruses and microbes. Previous studies comparing the genomes—the complete DNA sequence—of reasonably small numbers of phages that infect the Mycobacterium group of bacteria have found that the phages can be sorted into ‘clusters’ based on similarities in their genes and where these are encoded in their DNA. However, the number of phages investigated so far has been too small to conclude how different clusters are related. Are the clusters separate, or do they form a ‘continuum’ with different genes and DNA sequences shared between different clusters? Here, Pope, Bowman, Russell et al. compare the individual genomes of 627 bacteriophages that infect the bacterial species Mycobacterium smegmatis. This is by far the largest number of phage genomes analyzed from a single host species. The large number of genomes analyzed allowed a much clearer understanding of the complexity and diversity of these phages to be obtained. The isolation, sequencing and analysis of the hundreds of M. smegmatis bacteriophage genomes was performed by an integrated research and education program, called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This enabled thousands of undergraduate students from different institutions to contribute to the phage discovery and sequencing project, and co-author the report. SEA-PHAGES therefore shows that it is possible to successfully incorporate genuine scientific research into an undergraduate course, and that doing so can benefit both the students and researchers involved. The results show that while the genomes could be categorized into 28 clusters, the genomes are not completely unrelated. Instead, a spread of diversity is seen, as genes and groups of genes are shared between different clusters. Pope, Bowman, Russell et al. further reveal that the phage population is in a constant state of change, and continuously acquires genes from other microorganisms and viruses. DOI: http://dx.doi.org/10.7554/eLife.06416.002