Comparative genomics of Elusimicrobiaceae (phylum Elusimicrobiota) and description of the isolates Elusimicrobium simillimum sp. nov., Elusimicrobium posterum sp. nov., and Parelusimicrobium proximum gen. nov. sp. nov.

Abstract

The tree of life comprises many deep-branching lineages with no or only very few cultured representatives. One such lineage is the phylum Elusimicrobiota, which contains only two described species and whose biology has been only poorly explored. We isolated three new species from this phylum from the intestinal tracts of cockroaches. Like their closest relative, Elusimicrobium minutum, the only member of the family Elusimicrobiaceae described to date, they are small, pleomorphic gram-negative rods characterized by a distinct cell cycle, and like all ultramicrobacteria, they pass through a 0.22-μm filter membrane. Physiological characterization of all isolates revealed that they are obligately anaerobic fermenters that lack catalase and cytochrome c oxidase activities but can remove oxygen from their environment in a non-respiratory manner. Their substrate range is limited to a few hexoses, such as d-glucose, d-galactose, and N-acetyl-d-glucosamine, which are fermented to lactate, acetate, ethanol, and hydrogen as major products. Comparative genome analysis, which included more than 100 MAGs of uncultured lineages of Elusimicrobiaceae, revealed the underlying metabolic pathways and outlined a new phylogenomic framework of the family. Based on phylogenomic, physiological, and morphological evidence, we describe the new isolates as Parelusimicrobium proximum gen. nov., sp. nov., Elusimicrobium posterum sp. nov., and Elusimicrobium simillimum sp. nov. under the rules of ICNP. Based on high-quality genomes of all uncultured representatives, we propose a comprehensive taxonomy of all lineages in the family under the rules of SeqCode, including the new genera Avelusimicrobium, Proelusimicrobium, and the candidate genus “Pseudelusimicrobium”.