Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.

Autor: Sonets IV; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia. Electronic address: ignatsonets@gmail.com., Solovyev MA; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia., Ivanova VA; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia., Vasiluev PA; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Research Center for Medical Genetics, Moscow, Russia., Kachalkin AV; Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia., Ochkalova SD; Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, 197101, Russia; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia., Korobeynikov AI; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, 199004, Russia., Razin SV; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia., Ulianov SV; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia., Tyakht AV; Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.
Jazyk: angličtina
Zdroj: Food microbiology [Food Microbiol] 2024 Aug; Vol. 121, pp. 104520. Date of Electronic Publication: 2024 Mar 26.
DOI: 10.1016/j.fm.2024.104520
Abstrakt: Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.
Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Alexander V. Tyakht was an employee of Knomics LLC and Atlas Biomed Group companies at the time of the study. Other authors declare no conflict of interest.
(Copyright © 2024 Elsevier Ltd. All rights reserved.)
Databáze: MEDLINE
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