If you work in microbiology, you know the statistics: as many as 99% of bacterial species have yet to succumb to science’s best efforts to cultivate them. Even many of the bacteria we harbor within our bodies resist growing in culture, and if they can’t be grown in the laboratory we have limited opportunities to figure out what they do for us (or what they do to us). In mBio this week, a new approach to cultivating these reluctant microbes reads the metatranscriptome – the RNA a community of bacteria makes as a blueprint for making their proteins – for guidance on what those bacteria might eat.
Bomar et al. successfully used the metatranscriptome as a care and feeding guide for a Rikenella-like bacterium that dominates the gut of a medicinal leech, Hirudo verbana. The authors focused their analysis on highly expressed genes that encode hydrolytic enzymes, binding proteins, and transporters in an attempt to discern what the dominant players in the gut might enjoy as sustenance. The expression data revealed an important fact: surprisingly for a leech symbiont, their target bacterium’s favorite meal is not blood. It apparently forages on mucin, a food provided by the host that, unlike the seasonally available red stuff, is available regardless of whether the leech has eaten recently.
With this knowledge in hand, the authors created a designer medium for their target, rich with mucin. As confirmed by diagnostic PCR, they were able to isolate a few strains of the Rikenella-like bacterium in pure liquid culture and as colonies on plates. The authors say a tailored metatranscriptomics approach like the one they demonstrated can shed light on microbial metabolism in situ and provide critical clues that can direct the culturing of other uncultured microorganisms.