Diversity of Functional Genes in Deeply Branching Uncultures Microbes.
Published in American Geophysical Union, Fall Meeting 2019, 2019
The microbial world primarily consists of taxa that are distantly related to species that have been grown in culture. These taxa are a potential wellspring of undiscovered genomic function, but the quantity of novel functional genes in an organism does not necessarily track the phylogenetic divergence of that organism from cultured lineages. In order to test whether phylogenetically divergent microbes also contain more novel genetic material, we measured the sequence similarity between each gene in approximately 15,000 genomes of bacterial and archaeal isolates, metagenome-assembled genomes, and single-cell genomes, to the most similar gene in the SwissProt database of genes of well-known function. We compared these sequence similarities between predicted proteins to the phylogenetic distance between each organism and its closest cultured relative, allowing us to assess whether uncultured phyla contain more genetic novelty than cultured phyla. A similar analysis allowed us to measure the quantity of genetic novelty within ecosystems. Finally, we measured the typical distance between genes of unknown function within taxa and within environments in order to test whether some phyla or environments contain more, different kinds of genes than others. We will assess whether uncultured phyla contain greater genetic novelty than cultured phyla, in which case uncharacterized organisms may be a source for novel metabolic functions that influence geochemical cycles.