Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species.

Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.

Smartphone-based lateral flow imaging system for detection of food-borne bacteria E.coli O157:H7.

We report an application for the smartphone as an accurate and unbiased reading platform of a lateral flow immunoassays for food safety application. In particular, this report focuses on detection of food-borne bacteria in samples extracted from food matrices such as ground beef and spinach. The lateral flow assay is a widely accepted methodology owing to its on-site results, low-cost analysis, and ease of use with minimum user inputs, even though sensitivity is not quite equivalent to that of standard laboratory equipment. An antibody-antigen relationship is transduced into a color change on a nitrocellulose pad while visual interpretation of this color change can result in uncertainty, particularly near the detection limit of the assay. Employing the high resolution integrated camera, constant illumination from light source, and computing power of a smartphone, we provide an objective and accurate method to determine the bacterial cell concentration in a food matrix based on the regression model from the color intensity of test lines. A 3D-printed sample holder was designed for representative commercial lateral flow assays and an in-house application was developed in Android Studio to solve the inverse problem to provide cell concentration information from the color intensity. Test results with E.coli O157:H7 as a model organism suggests that smartphone-based reader can detect 104-105 CFU/ml from ground beef and spinach food matrices.