Publication detail

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

SCHWARZEROVÁ, J. ZEMAN, M. BABÁK, V. JUREČKOVÁ, K. NYKRÝNOVÁ, M. VARGA, M. WECKWERTH, W. DOLEJSKÁ, M. PROVAZNÍK, V. RYCHLÍK, I. ČEJKOVÁ, D.

Original Title

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

Type

journal article in Web of Science

Language

English

Original Abstract

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.

Keywords

animal microbiome, genome evolution, mobile genetic elements, mobilome, resistance genes, horizontal gene transfer, gut microbiota

Authors

SCHWARZEROVÁ, J.; ZEMAN, M.; BABÁK, V.; JUREČKOVÁ, K.; NYKRÝNOVÁ, M.; VARGA, M.; WECKWERTH, W.; DOLEJSKÁ, M.; PROVAZNÍK, V.; RYCHLÍK, I.; ČEJKOVÁ, D.

Released

30. 11. 2023

Publisher

American Society for Microbiology

Location

USA

ISBN

2165-0497

Periodical

Microbiology spectrum

Year of study

12

Number

1

State

United States of America

Pages count

23

URL

https://journals.asm.org/journal/spectrum

Full text in the Digital Library

http://hdl.handle.net/11012/245170

BibTex

@article{BUT185434,
  author="Jana {Schwarzerová} and Michal {Zeman} and Vladimír {Babák} and Kateřina {Šabatová} and Markéta {Jakubíčková} and Margaret {Varga} and Wolfram {Weckwerth} and Monika {Dolejská} and Valentine {Provazník} and Ivan {Rychlík} and Darina {Čejková}",
  title="Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis",
  journal="Microbiology spectrum",
  year="2023",
  volume="12",
  number="1",
  pages="23",
  doi="10.1128/spectrum.01964-23",
  issn="2165-0497",
  url="https://journals.asm.org/journal/spectrum"
}