The use of metagenomic technologies in the study of potentially highly effective cellulolytic microorganisms as part of a complex microbial consortium.

The accumulation of plant residues in the modern agricultural industry and the need for their further processing require new approaches in the study, search and creation of highly effective drugs for the decomposition of cellulose-containing compounds.
The decomposition of cellulose and its derivatives is carried out by a group of glycosyl hydrolase enzymes, united into several hundred families, differing both in substrate specificity and principle of action. In addition, the genes responsible for the synthesis of these enzymes in the genomes of microorganisms are often combined into so–called clusters of pool - polysaccharide loci. The high diversity of genes and the complexity of their organization complicates the search for targeted microorganisms based on markers based on single genes. Thus, in the study of associative microbial consortia aimed at the decomposition of plant residues, it is necessary to use modern metagenomic approaches that allow analyzing the genomic structure of dozens and hundreds of components of such communities.
In an article by Kimeklis and co-authors in the journal Frontiers in Microbiology, published in January 2025, research on this topic was published, carried out within the framework of the Russian Science Foundation 23-16-00147 under the leadership of E.E. Andronov. As part of the experiment, it was shown that hundreds of microorganisms are mobilized from the microbiome of the soil of the Cherny taiga to decompose straw and leaf litter, potentially capable of decomposing cellulolytic residues.. Using an integrated approach to sequencing amplicon libraries of the 16C rRNA gene on the Miseq Illumina platform, USA, and complete metagenomes on the Oxford nanopor mignon platform at different stages of decomposition, it was revealed that only some of the participants in these consortia, specific to each substrate, have an increased content of bullets, which makes them potential targets for selection and use as part of complex biologics. The laboratory is currently developing approaches to this task.
The research was carried out on the basis of the Central Research Laboratory "Genomic Technologies, Proteomics and Cell Biology" of the Federal State Budgetary Budgetary Institution ARRIAM.
Kimeklis A.K., Gladkov G.V., Orlova O.V., Lisina K.T., Afonin A.M., Aksenova T.S., Kichko A.A., Lapidus A.L., Abakumov E.V. and Andronov E.E. (2025) A metagenomic view on the development of microbial communities of straw and leaf compost. Before. Microbiol. 15:1485353. doi: 10.3389/fmicb.2024.1485353