Culturing the Uncultured: New Strategies for Growing Human Microbiota in the Sequencing Era
Despite the dominance of culture-independent methods, this review highlights a renaissance in culture-based microbiome research using high-throughput anaerobic techniques, enriched media, and coculture systems. The authors describe how NGS and flow cytometry have been repurposed to guide isolation of previously uncultured bacteria, including Candidate Phyla Radiation organisms. The work also addresses MALDI-TOF MS identification of fungal isolates and the clinical potential of bacteriotherapy to correct dysbiosis.
The original study
State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.
- Authors
- Tidjani Alou M, Naud S, Khelaifia S, Bonnet M, Lagier JC, Raoult D
- Journal
- Clinical microbiology reviews
- Type
- Journal Article, Research Support, Non-U.S. Gov't, Review
- PMID
- 33115723
Original abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.