The dairy product quality and risk assessment team of Beijing Institute of Animal Science and Veterinary Medicine, Chinese Academy of Agricultural Sciences, reviewed a new method for the isolation and culture of metagenomics to guide the isolation and culture of uncultured microorganisms

Recently, the scientific and technological innovation team of dairy product quality and risk assessment of Beijing Institute of Animal Science and Veterinary Medicine, Chinese Academy of Agricultural Sciences was invited to write a review article, expounding the opportunities and challenges of metagenomics to guide the isolation and culture of uncultured microorganisms, and systematically summarizing the methods
of isolated and cultured uncultured microorganisms based on metagenomics.
The review article was published in Microbiome (IF=14.
652).

In recent years, with the rapid development of metagenomic sequencing technology, it has been recognized that there are a large number of diverse uncultured microbial communities in the environment, human body and animals, and play an important role
in the earth's ecosystem.
Although metagenomic data have deepened the understanding of the structure and function of uncultured microbial communities, the lack of isolation of uncultured microbial strains makes it impossible to directly assess the metabolic and physiological functions of uncultured microorganisms, nor can the interaction between microbial species be verified
.
Therefore, the isolation and cultivation of uncultured microorganisms is of great significance
to drive microbiome research into deep water areas and promote the development of biological and health industries.

The isolation of uncultured microorganisms must rely on new technologies and new ideas, and the current explosion of metagenomic data, especially the metagenomic assembled genome (MAG), provides the genome information of uncultured microorganisms, which brings new opportunities
to guide the isolation and culture of target uncultured microorganisms.
Through the analysis and extraction of a large number of literature materials, combined with his own research on uncultured microorganisms, the authors summarize and propose methods for isolating and cultivating uncultured microorganisms based on metagenomic data, mainly including the design of specific culture conditions, specific antibody capture and isolation, targeted functional gene isolation and other technologies
.

Design
of specific culture conditions.
Metagenomic data provides information on microbial metabolism, substrate utilization, oxygen demand, antibiotic resistance, etc.
, according to which media or growth conditions can be designed for target microorganisms, and target microorganisms can be isolated and cultured
by combining plate dilution culture, stable isotope labeling assisted cell sorting of Raman active microorganisms, etc.
Specific antibody capture isolation
.
Predict the membrane protein or antigen epitope encoded by the target microbial gene, synthesize the antigen protein and prepare specific antibodies and fluoresce label, bind the labeled antibody to the target microorganism, and use fluorescent cell sorting technology to separate the labeled target microorganism.

Targeted functional gene screening and isolation
.
Design specific primers or probes based on the target gene sequence, label or screen by PCR or fluorescence in situ hybridization, use cell sorting to obtain target cells, and also modify the functional genes or resistance genes of target microorganisms through genome editing, combined with corresponding antibiotics or substrate culture media, to achieve the isolation
of target microorganisms.

The research was supported
by the Agricultural Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences and the Modern Agricultural Industry Technology Research System.
The first author of the article is Liu Sijia, a graduate student of the Institute of Animal Husbandry and Medicine, and the corresponding authors are Associate Researcher Zhao Shengguo and Researcher
Wang Jiaqi.

Original link: https://doi.
org/10.
1186/s40168-022-01272-5