Person:

Franzosa, Eric

Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analyzed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously-produced signaling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species overrepresented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota toward an IBD-like composition.

Human microbiome science has advanced rapidly and reached a scale at which basic biology, clinical translation, and population health are increasingly integrated. It is thus now possible for public health researchers, practitioners, and policymakers to take specific action leveraging current and future microbiome-based opportunities and best practices. Here, we provide an outline of considerations for research, education, interpretation, and scientific communication of the human microbiome and public health. This includes guidelines for population-scale microbiome study design; necessary physical platforms and analysis methods; integration into public health areas such as epidemiology, nutrition, chronic disease, and global and environmental health; entrepreneurship and technology transfer; and educational curricula. Particularly in the near future, there are opportunities both for the incorporation of microbiome-based technologies into public health practice, and a growing need for policymaking and regulation around related areas such as prebiotic and probiotic supplements, novel live cell therapies, and fecal microbiota transplants.

A mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate with highly adapted and evolved microbial consortia. The microbial residents within these organ systems are increasingly well characterized, yielding a good understanding of human microbiome composition. However, we have yet to elucidate the full chemical impact the microbiome exerts on an animal and the breadth of the chemical diversity it contributes. A number of molecular families are known to be shaped by the microbiome including short-chain fatty acids, indoles, complex polysaccharides, host sphingolipids and bile acids. These metabolites profoundly affect host physiology and are being explored for their roles in both health and disease. Considering the diversity of the human microbiome, numbering over 40,000 operational taxonomic units, a plethora of molecular diversity remains to be discovered. In this study we used novel mass spectrometry informatics and visualization approaches to provide an untargeted assessment of the chemical contributions of the microbiome to an entire mammal by comparing germ-free (GF) and specific-pathogen free (SPF) animals. We found that the microbiome affected the chemistry of all murine organs. These affects were highlighted by novel amino acid conjugations of host bile acids that have evaded characterization despite the extensive research on bile acid chemistry. These new bile acid conjugates were enriched in dysbiotic disease states and directly agonized the farnesoid X receptor (FXR) resulting in changes in host bile acid metabolism.