Inter-species interactions in microbial communities The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Hsu, Tiffany Yeong-Ting. 2018. Inter-species interactions in microbial communities. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42015251 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Inter-species interactions in microbial communities A dissertation presented by Tiffany Yeong-Ting Hsu to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts October 2017 © 2017 Tiffany Yeong-Ting Hsu All rights reserved. Dissertation Advisor: Professor Curtis Huttenhower Tiffany Yeong-Ting Hsu 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. iii 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. iv Table of Contents Abstract ...................................................................................................................................................iii Table of Contents ................................................................................................................................... v Acknowledgements ............................................................................................................................ vii List of Figures ......................................................................................................................................... x List of Tables ......................................................................................................................................... xii List of Abbreviations ......................................................................................................................... xiii Chapter 1: Introduction ............................................................................................................................. 1 Copyright Disclosure ............................................................................................................................. 2 Overview ................................................................................................................................................. 2 The significance of lateral gene transfer ............................................................................................. 3 Mechanisms and discovery of lateral gene transfer ......................................................... 3 Problems with the prokaryotic “species concept” ........................................................... 5 Methods for identifying species and LGT ......................................................................... 7 LGT in microbial communities ........................................................................................... 9 Transferred functions and their associated costs ........................................................... 11 Evolutionary legacy of LGT .............................................................................................. 12 Surveying microbial communities in the built-environment ........................................................ 13 Microbial composition of the built-environment ........................................................... 14 Applications for the built-environment ........................................................................... 16 Technical considerations for sampling the built-environment .................................... 17 The role of DNA sequencing for microbial profiling ...................................................................... 19 Amplicon Sequencing ........................................................................................................ 19 WMS Sequencing ................................................................................................................ 21 Contig Assembly ................................................................................................................. 23 Summary ............................................................................................................................................... 24 Chapter 2: Lateral Gene Transfer in the Human Microbiome .......................................................... 26 Attributions ........................................................................................................................................... 27 Introduction .......................................................................................................................................... 27 Results .................................................................................................................................................... 30 Identifying recent LGT events from metagenomic shotgun sequencing .................... 30 WAAFLE performance on synthetic data ....................................................................... 32 v Rates of novel LGT events across the human microbiome ........................................... 35 LGT frequency and pair formation are shaped by abundance and phylogeny ......... 41 Genera have preferred transfer partners that are shared across similar sites ............ 44 Mobile elements and TonB receptors are enriched in LGT contigs ............................. 49 Discussion ............................................................................................................................................. 54 Methods ................................................................................................................................................. 58 Chapter 3: Urban transit system microbial communities differ by surface type and interaction with humans and environment .............................................................................................................. 68 Copyright Disclosure ........................................................................................................................... 69 Attributions ........................................................................................................................................... 69 Abstract .................................................................................................................................................. 69 Importance ............................................................................................................................................ 70 Introduction .......................................................................................................................................... 71 Results ...................................................................................................................................................