RT Journal Article
SR Electronic
T1 High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Microbial Lineage
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 106856
DO 10.1101/106856
A1 Joshua J. Hamilton
A1 Sarahi L. Garcia
A1 Brittany S. Brown
A1 Ben O. Oyserman
A1 Francisco Moya-Flores
A1 Stefan Bertilsson
A1 Rex R. Malmstrom
A1 Katrina T. Forest
A1 Katherine D. McMahon
YR 2017
UL http://biorxiv.org/content/early/2017/02/20/106856.abstract
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.