Abstract
Isolating relevant microorganisms is still a substantial challenge that limits the use of bacteria in the maintenance of human health. To confirm which media and which bacterial colony densities can enrich certain kinds of bacteria, we selected eight common media and used them to enrich the gut microorganisms on agar plates. Then, we calculated the numbers of bacterial colonies and collected the bacterial culture mixtures from each kind of medium. Using the Illumina HiSeq platform, we analyzed the composition and diversity of the culture-enriched gut bacterial community. Our data suggested that medium supplemented with blood could increase the diversity of the bacterial community. In addition, beef powder and peptone could significantly change the culture-enriched bacterial community. A moderate density (100–150 colony-forming units per plate) was optimal for obtaining the highest diversity on the agar. Similarly, membrane transport was significantly enriched in the moderate-density group, which indicated a more active metabolism in this density range. Overall, these results reveal the optimal culture conditions, including the densities of colonies and nutritional components for various gut bacteria, that provide a novel strategy for isolating bacteria in a way that is targeted and avoids blinded and repetitive work.
Highlights
The important role of the gut microbiota in human health is becoming abundantly apparent
We investigated how the nutritional components and densities influence the composition and diversity of the bacterial community, which bacteria could be enriched and the conditions of nutritional composition or density that allowed enrichment, and what the interaction was among bacteria at various densities
These results indicated that the medium influenced the diversity of the gut bacterial community after the anaerobic cultivation (Fig. 1a–d)
Summary
The important role of the gut microbiota in human health is becoming abundantly apparent. It is difficult to elucidate the role of microorganisms in human health without the ability to culture some microorganism. Because of their importance of unculturable microorganisms, the methods that isolate them have received more attention. Microbial interactions are important for population viability, and microorganisms can cooperate with each other by releasing metabolites and signaling molecules Substances such as humic acid, signaling molecules, enzymes (for coping with reactive oxygen species), or inhibitors of undesired organisms (Alain and Querellou 2009; Leadbetter et al 1999; Stevenson et al 2004) were added to the medium, and more unculturable microorganisms were collected. Many microorganisms were isolated that had previously been considered unculturable (Lagier et al 2016)
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