ИСТИНА

High-throughput metagenomic sequencing allows to assess taxonomic and functional composition of the microbiome. Disentangling the genomic content of individual species provides insight into ecological interactions in the community. However, metagenome-assembled genomes (MAGs) are typically fragmentary, essentially unordered sets of contigs. Beverages produced based on spontaneous fermentation are known to host non-trivial microbial communities. Investigations of their structure and functions are particularly interesting due to their major contribution to the organoleptic qualities of the products, as well as to the effects on consumers’ health. Here we show how augmentation with the data of chromosome conformation capture (Hi-C) sequencing significantly improves the genome reconstruction from the “shotgun” metagenomes of spontaneously fermented beer and cider. For a collection of beverages, we reconstructed multiple MAGs belonging to lactic acid and acetic acid bacteria, Enterobacteriaceae and other microbes from conventional metagenomes. The MAGs had high levels of completeness and low levels of contamination. We established a robust protocol for preparing Hi-C libraries from beer and cider samples. Using the obtained Hi-C contact maps as a complementary signal, by re-ordering the contigs we obtained chromosome-wide scaffolds for these MAGs - a significant improvement towards a complete genome. The approach highlighted the associations between specific microbes and their plasmids. These findings will elucidate the adaptation mechanisms of various bacterial taxa to survival in specific environments of the investigated beverages. Additionally, the microbial contact maps were used to identify the chromosome-interaction domains (CIDs) as well as to reconstruct the whole-chromosome 3D genome forms. The approach can be applied to an arbitrary microbiome type to improve the assembly of microbial genomes and explore bacterial chromosome spatial organization.