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Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.

Mammals are defined by their metagenome, a combination of host and microbiome genes. This knowledge presents opportunities to further basic biology with translation to human diseases. However, the now-documented influence of the metagenome on experimental results and the reproducibility of in vivo mammalian models present new challenges. Here we provide the scientific basis for calling on all investigators, editors and funding agencies to embrace changes that will enhance reproducible and interpretable experiments by accounting for metagenomic effects. Implementation of new reporting and experimental design principles will improve experimental work, speed discovery and translation, and properly use substantial investments in biomedical research., Recent studies highlight that differences in human genetics explain only a fraction of observed human phenotypic variation (1,2). Another well-recognized source of variation is the microbiome, which is the collection [...]

The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control (1-5). In many cases, the microbiota is the presumed cause of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice (6,7). In conventionally raised mice, the microbiome is transmitted from the dam (2,8,9). Here we show that microbially driven dichotomous faecal immunoglobulinA (IgA) levels in wild-type mice within the same facility mimic the effects of chromosomal mutations. We observe in multiple facilities that vertically transmissible bacteria in IgA-low mice dominantly lower faecal IgA levels in IgA-high mice after co-housing or faecal transplantation. In response to injury, IgA-low mice show increased damage that is transferable by faecal transplantation and driven by faecal IgA differences. We find that bacteria from IgA-low mice degrade the secretory component of secretory IgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose faecal IgA as one marker of microbial variability and conclude that co-housing and/or faecal transplantation enables analysis of progeny from different dams., We chose to study the role of secretory immunoglobulin A (SIgA), which is a critical intersection between the host immune system and the microbiota (10). While interrogating baseline intestinal IgA [...]

The instruction of the immune system to be tolerant of self, thereby preventing autoimmunity, is facilitated by the education of T cells in a specialized organ, the thymus, in which self-reactive cells are either eliminated or differentiated into tolerogenic [Foxp3.sup.+] regulatory T ([T.sub.reg]) cells (1). However, it is unknown whether T cells are also educated to be tolerant of foreign antigens, such as those from commensal bacteria, to prevent immunopathology such as inflammatory bowel disease (2-4). Here we show that encounter with commensal microbiota results in the peripheral generation of [T.sub.reg] cells rather than pathogenic effectors. We observed that colonic [T.sub.reg] cells used T-cell antigen receptors (TCRs) different from those used by [T.sub.reg] cells in other locations, implying an important role for local antigens in shaping the colonic [T.sub.reg]-cell population. Many of the local antigens seemed to be derived from commensal bacteria, on the basis of the in vitro reactivity of common colon [T.sub.reg] TCRs. These TCRs did not facilitate thymic [T.sub.reg]-cell development, implying that many colonic [T.sub.reg] cells arise instead by means of antigen-driven peripheral [T.sub.reg]-cell development. Further analysis of two of these TCRs by the creation of retroviral bone marrow chimaeras and a TCR transgenic line revealed that microbiota indigenous to our mouse colony was required for the generation of colonic [T.sub.reg] cells from otherwise naive T cells. If T cells expressing these TCRs fail to undergo [T.sub.reg]-cell development and instead become effector cells, they have the potential to induce colitis, as evidenced by adoptive transfer studies. These results suggest that the efficient peripheral generation of antigen-specific populations of [T.sub.reg] cells in response to an individual's microbiota provides important post-thymic education of the immune system to foreign antigens, thereby providing tolerance to commensal microbiota., Although [T.sub.reg] cells are required for the maintainenance of gut tolerance (3), commensal bacteria are not necessary for colonic [T.sub.reg]-cell generation (5,6 ) (Supplementary Fig. 1). Moreover, [T.sub.reg] cells from [...]

Susceptibility to Crohn's disease, a complex inflammatory disease involving the small intestine, is controlled by over 30 loci (1). One Crohn's disease risk allele is in ATG16L1, a gene homologous [...]