Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective

Abstract

Ever-more-powerful 'omics'-based technologies are allowing us to pry deeper and more clearly into the workings of the human gut microbiota. Culture of the component microbes has fallen somewhat behind these efforts for a number of reasons, not least of which being the perceived difficulty in growing microbial species that have previously eluded all efforts to tame them. However, recent advances in the field are beginning to bring success in this area, allowing holistic study of microbes and microbial communities in defined systems. Innovative approaches to the culture and study of the human microbiota will ultimately guide medical practice, as the importance of a robust gut microbial ecosystem in the maintenance of health is increasingly realized.

Figure 1

Schematic outlining the general approaches to culturing microbial diversity. In the empirical approach, media components are used based on laboratory observations; in this case the diversity yield is low because the enormous range of microbial growth rates and conditions that unknown targets may use makes the approach time-consuming and inefficient. In the bioinformatic approach, the molecular signatures of a microbial target are studied before culture is attempted to infer culture conditions. Diversity yield is intentionally low, and target is efficiently recovered. In the culturomics approach, basic knowledge about ecosystem targets is known, and high throughput techniques such as flow cytometry and robotic media preparation allow multiple conditions to be tested for growth support simultaneously. As a result, the diversity yield is very high.