Full Title: Growth-Altering Microbial Interactions Are Highly Sensitive to Environmental Context

13 Microbial interactions are ubiquitous in nature, and equally as relevant to human wellbeing as the 14 identities of the interacting microbes. However, microbial interactions are difficult to measure and 15 characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on 16 environmental context. We present a novel workflow for inferring microbial interactions that integrates 17 semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving 18 throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions 19 among bacterial species associated with the normal lung microbiome, and how those interactions are 20 altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that 21 the presence of this single compound changed the interaction network, demonstrating that microbial 22 interactions are indeed highly dynamic and responsive to environmental context. 23