PT  - JOURNAL ARTICLE
AU  - Joshua J. Hamilton
AU  - Sarahi L. Garcia
AU  - Brittany S. Brown
AU  - Ben O. Oyserman
AU  - Francisco Moya-Flores
AU  - Stefan Bertilsson
AU  - Rex R. Malmstrom
AU  - Katrina T. Forest
AU  - Katherine D. McMahon
TI  - High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Microbial Lineage
AID  - 10.1101/106856
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 106856
4099  - http://biorxiv.org/content/early/2017/02/20/106856.short
4100  - http://biorxiv.org/content/early/2017/02/20/106856.full
AB  - An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework”, which computes the set of compounds that an organism must acquire from its environment (Borenstein et al., 2008), enables high-throughput, computational analysis of metabolic reconstructions, while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater Actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, featuring high expression of transport proteins and the light-harvesting protein actinorhodopsin, and confirming predictions of nutrients and essential metabolites while providing additional support to the hypothesis that members of the acI are photoheterotrophs.