A Metagenomic Analysis with Oligotrophic Enrichment Approach for Detecting Specified Microorganisms.

Abstract

In pharmaceutical manufacturing, benefit is conferred in detection of specified microorganism (i.e., Burkholderia cepacia complex (BCC), E. coli, Pseudomonas aeruginosa, Salmonella enterica) not readily identified by culture-dependent methods. It's logical to test for the presence of "specified microorganism" using metagenomic analysis before culturing a "specified organism", especially when the organism isn't easy to culture. We developed a metagenomic analysis during enrichment to identify specified organisms. The enriched bacterial community consisted predominantly of Bacillus spp. and Stenotrophomonas spp., each contributing about 97-99% to total taxon abundance in TSB and 1/10× TSB. The specified microorganisms that were observed were Clostridium spp., Burkholderia spp., and Staphylococcus spp. (0.04 - 0.07%) in TSB, otherwise Burkholderia spp., Pseudomonas spp., Salmonella spp., Staphylococcus spp. and Escherichia spp. (0.01 - 1.73%) in 1/10× TSB. PreQ0 biosynthesis (PWY-6703) and guanosine ribonucleotides de novo biosynthesis (PWY-7221) were the most abundant pathways in 1/10× TSB-24 h. BCC chiefly contributed to the toluene degradation (PWY-5180 and PWY-5182) pathways. Initial results demonstrate the potential of the metagenomic approach during enrichment in water-based environments. These results indicate that a metagenomic enrichment approach to evaluating water samples can be useful to monitor specified organisms over time, including oligotrophs such as BCC in 1/10× TSB.