Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis

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dc.contributor.authorSchwarzerová, Janacs
dc.contributor.authorZeman, Michalcs
dc.contributor.authorBabák, Vladimírcs
dc.contributor.authorJurečková, Kateřinacs
dc.contributor.authorNykrýnová, Markétacs
dc.contributor.authorVarga, Margaretcs
dc.contributor.authorWeckwerth, Wolframcs
dc.contributor.authorDolejská, Monikacs
dc.contributor.authorProvazník, Valentinecs
dc.contributor.authorRychlík, Ivancs
dc.contributor.authorČejková, Darinacs
dc.coverage.issue1cs
dc.coverage.volume12cs
dc.date.accessioned2024-02-22T10:45:21Z
dc.date.available2024-02-22T10:45:21Z
dc.date.issued2023-11-30cs
dc.description.abstractThe study presents an innovative pipeline for detecting horizontal gene transfer (HGT) among a collection of sequenced genomes from gut microbiota. Herein, chicken and porcine gut microbiota were analyzed. Based on statistical analysis, we propose that nearly identical genes co-shared between distinct genera can be evidence for a previous event of mobilization of that gene from genome to genome via HGT. Data mining, computational analysis, and network analysis were used to investigate genomes of 452 isolates of chicken or porcine origin to detect genes involved in HGT. The proposed pipeline is user-friendly and includes network visualization. The study highlights that different species and strains of the same genera typically carry different cargo of mobilized genes. The pipeline is capable of identifying not yet characterized genes, as well as genes that are usually co-transferred with genes involved in resistance, virulence, and/or mobilization. Among the analyzed genome collection, the main reservoirs of the HGT genes were found in Phocaeicola spp. (Bacteroidaceae) and UBA9475 spp. (early Pseudoflavonifractor, Oscillospiraceae). Altogether, over 6,000 genes suspected of HGT were identified. Genes associated with intracellular trafficking and secretion and DNA repair were enriched, while genes of unknown and general functions were dominant but not enriched. Only 15 genes were co-shared between Gram-positive and Gram-negative bacteria, mostly genes directly associated with mobilome or antibiotic resistance. However, most HGTs were identified among different genera of the same phylum. Therefore, we suggest that a significant selection pressure exists on gene variants at the phylum level.en
dc.formattextcs
dc.format.extent23cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationMicrobiology spectrum. 2023, vol. 12, issue 1, 23 p.en
dc.identifier.doi10.1128/spectrum.01964-23cs
dc.identifier.issn2165-0497cs
dc.identifier.orcid0000-0003-2918-9313cs
dc.identifier.orcid0000-0001-5143-9521cs
dc.identifier.orcid0000-0002-0205-6935cs
dc.identifier.orcid0000-0002-3422-7938cs
dc.identifier.orcid0000-0002-6989-6330cs
dc.identifier.other185434cs
dc.identifier.researcheridAAC-2736-2019cs
dc.identifier.researcheridR-3181-2018cs
dc.identifier.researcheridF-4121-2012cs
dc.identifier.scopus57205673155cs
dc.identifier.scopus57202469794cs
dc.identifier.scopus6701729526cs
dc.identifier.scopus23099215700cs
dc.identifier.urihttps://hdl.handle.net/11012/245170
dc.language.isoencs
dc.publisherAmerican Society for Microbiologycs
dc.relation.ispartofMicrobiology spectrumcs
dc.relation.urihttps://journals.asm.org/journal/spectrumcs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2165-0497/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectanimal microbiomeen
dc.subjectgenome evolutionen
dc.subjectmobile genetic elementsen
dc.subjectmobilomeen
dc.subjectresistance genesen
dc.subjecthorizontal gene transferen
dc.subjectgut microbiotaen
dc.titleDetecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysisen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-185434en
sync.item.dbtypeVAVen
sync.item.insts2024.02.22 11:45:21en
sync.item.modts2024.02.22 11:13:29en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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