Ethanol pretreatment and bile acid germinants help recover significant number of spore forming gut bacteria previously unculturable

Culture of microbes is an essential step towards understanding the behavior and function of the microbe in the ecosystem it was drawn from. This rings true despite the increasing prevalence of various culture independent methods that help lend a lens to the microbial dark matter, a pool of microorganisms whose identities have emanated from metagenomic sequencing but which could not be cultured in the lab; thereby, preventing their physiology and interactions with other microbes to be gleaned beyond their genetic repertoire. Known by various names such as the “Great Plate Count Anomaly” or “viable but not culturable”, the inability to culture most of the microorganisms in the environment have prevented understanding of how microbes contribute to ecosystem health holistically and microscopically. But, what are the tools microbiologists have which can circumvent or solve the problem? One approach utilizes the provision of needed cofactors and nutrients to allow the cultivation of fastidious microorganisms that require specific cofactors to grow. This could be achieved by direct supplementation of needed growth factors or bringing microbes able to secrete such cofactors into close proximity with the target microbe one seek to culture. On the other hand, a non culturable problem could manifest where fast growing microbes outcompetes slow growing ones and thereby present itself as a case of unculturability. But this could be ameliorated through a combination of manipulating the growth conditions such that non target microbes could not grow, as well as providing stimulants for inducing the growth of the target species. Using the above method, a recent manuscript describes the efforts of Lawley and coworkers, “Culturing of “unculturable” human microbiota reveals novel taxa and extensive sporulation” in culturing spore forming bacteria that reside in the gut microbiota through the exertion of two sequential selection pressures: ethanol pretreatment and provision of bile acid germinants. Isolation of the spore forming bacteria illustrates the utility of preventing the growth of most Proteobacteria in allowing more recalcitrant bacteria (that could play important roles in disease) to be profiled biochemically, which would add to our understanding of how spore formers aid normal gut function as well as abet pathogenic colonization of the intestines. With a means to culture, and profile, spore forming bacteria in the gut microbiota, their importance to healthy gut homeostasis as well as their roles in the gut microbiome community structure could be better understood holistically; thereby, helping answer questions on why a significant fraction of gut microorganisms comprise slow growing anaerobes or dormant spores, which, on ecological terms, could have been driven to extinction by fast growing species.