Novel Genomes of Sphingomonadales Strains Isolated from Diverse Environments

Glycosphingolipids are amphiphilic compounds that feature sugar or glycan moieties installed onto a ceramide lipid. The synthesis of glycosphingolipids by members of the human gut microbiome, and their known immune stimulating activity, have made them of interest for potential pharmaceutical roles. However, the known diversity of glycosphingolipid glycans in bacteria remains limited, highlighting the need to isolate novel glycosphingolipid-producing organisms as a source of these compounds. The order Sphingomonadales, one of the major clades of sphingolipid producing bacteria, conserves a serine palmitoyltransferase (SPT) enzyme needed for the initial biosynthetic step in sphingolipid production which can be targeted as part of isolation efforts. With these bacteria known to live in diverse environments such as soil microbiomes, soap scum biofilms, and cyanobacterial microbiomes, there are many environments to target for the isolation of these bacteria. In this work, we designed a set of polymerase chain reaction (PCR) primers for the isolation of diverse Sphingomonadales strains by targeting the SPT gene (spt), which we used to isolate strains from the genera Sphingomonas and Novosphingobium in soil, soap scum biofilms, and xenic cyanobacterial cultures. In these efforts, streptomycin improved the encounter rate, as represented by the SPT assay true-positive rate. Our isolates represent novel genomic space: with genomes from both genera that have low similarity to known genomes, suggestive of novel species, while several novel plasmids were also missing known marker sequences.