Inter-species interactions in microbial communities

Abstract

Microorganisms are omnipresent and exist as communities within and around the human body. These communities, regardless of location, may cause disease: dysbioses within the gut microbiota are associated with obesity and inflammatory bowel disease, while differences in immune development and environmental exposures are linked to atopy and diabetes. It is thus crucial to characterize microbial communities and their interactions to better understand how they are formed, maintained, and manipulated. To better understand the ecology of communities on and around the human body, my work has explored lateral gene transfer (LGT) within human-associated microbial communities and the transfer of microbes between the human body and environmental surfaces. I developed the first method for detection of de novo LGT events from metagenomes termed WAAFLE, a Workflow to Annotate Assemblies and Find LGT Events. I applied WAAFLE to the Human Microbiome Project: LGT frequencies were highest in the gut and oral sites, and lowest in the vaginal and skin microbiomes. High frequency pairs corresponded with increased taxon abundances and close phylogenetic distances. Taxa found in multiple LGT pairs had strong partner preferences, and several had biases in transfer directionality. Enriched functions in LGT contigs included transposases, phage, and TonB membrane receptors. Taxa in high frequency LGT pairs may preferentially use LGT as a tool to maintain or change their community status. I examined cross-talk between human-associated and built-environment microbial communities in heavily trafficked environments, specifically the Boston subway. These areas may facilitate microbial transmission and are ripe for public health interventions such as sanitation or architecture. We used 16S rRNA gene and metagenomics shotgun sequencing to profile microbes on multiple surface types in trains along the red, green, and orange lines, as well as ticketing machines at four train stations. Community structure was dictated by surface type, rather than train line. Common taxa included human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. Enriched functions were often from Propionibacterium acnes pathways, and few antibiotic resistance genes were observed. Overall, microbial communities on the Boston subway are likely derived from the rider population and influenced by rider interactions and environmental biochemistry.