Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F23%3APU149617" target="_blank" >RIV/00216305:26220/23:PU149617 - isvavai.cz</a>
Result on the web
<a href="https://journals.asm.org/journal/spectrum" target="_blank" >https://journals.asm.org/journal/spectrum</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1128/spectrum.01964-23" target="_blank" >10.1128/spectrum.01964-23</a>
Alternative languages
Result language
angličtina
Original language name
Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis
Original language description
The 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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/GA22-16786S" target="_blank" >GA22-16786S: Horizontal gene transfer network in chicken gut microbiome: detection and prediction of antibiotic resistome and mobilome</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Microbiology spectrum
ISSN
2165-0497
e-ISSN
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Volume of the periodical
12
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
23
Pages from-to
„“-„“
UT code for WoS article
001126360200003
EID of the result in the Scopus database
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