McDonald, D. | bioRxiv Science

bioRxiv2018

Engineered Microbes to Sense and Respond to Enterotoxigenic Escherichia coli

Every year, Enterotoxigenic Escherichia coli (ETEC), the most common form of travelers diarrhea, affects thousands of military personnel deployed overseas. The goal of this research was to engineer non-pathogenic E. coli to sense ETEC, respond to its presence, and package the non-pathogenic E. coli in a cellulose matrix to enable environmental detection of ETEC. Two plasmids were created: sense-respond; and packaging. The sense-respond plasmid detected autoinducer 2 (AI-2), a quorum sensing molecule created by most ETEC strains, by expressing LsrR which switches on the Lsr promoter. Activation of the Lsr promoter expresses superfolder green fluorescent protein (sfGFP), indicating the presence of ETEC. The packaging plasmid expresses a fusion protein consisting of curli fibers and cellulose binding domains. These modified surface proteins permit the bacteria to bind to cellulose, encapsulating the sense-response module. This genetically engineered machine could be deployed in both the internal and external environment to detect ETEC.

synthetic biology↗

bioRxiv2018

American Gut: an Open Platform for Citizen-Science Microbiome Research

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as compared to environmental samples, demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations, uncover new molecules and kinds of molecular communities in the human stool metabolome, and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness, and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.\n\nImportanceWe show that a citizen-science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n=1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet which we confirm with untargeted metabolomics on hundreds of samples.

microbiology↗