Detail publikace

Systems biology approach for analysis of mobile genetic elements in chicken gut microbiome

SCHWARZEROVÁ, J. ZEMAN, M. RYCHLÍK, I. WECKWERTH, W. PROVAZNÍK, I. DOLEJSKÁ, M. ČEJKOVÁ, D.

Originální název

Systems biology approach for analysis of mobile genetic elements in chicken gut microbiome

Anglický název

Systems biology approach for analysis of mobile genetic elements in chicken gut microbiome

Jazyk

en

Originální abstrakt

Antibiotic use in farming for decades has led to the selection pressure on chicken commensal bacteria which adapted to those changes by the acquisition of antibiotic resistance genes via horizontal gene transfer. Extensive gene transfer between gut bacteria is mediated by mobile genetic elements such as plasmids, integrative conjugative elements and temperate phages. Therefore, chicken gut commensal bacteria are considered reservoirs of antibiotic resistance genes. Recently, we initiated a systemic cultivation of chicken gut anaerobes followed by subsequent whole genome sequencing and analysis. In this study, we implemented a novel in silico approach using systems biology methods to detect horizontal gene traits and mobile genetic elements associated with it in the genomes of chicken gut commensals. In total, we identified 1,427 genes envisaged to drive horizontal gene transfer between individual chicken gut microbiota members across different families. Except for genes known to be vertically transferred, we also revealed hypothetical genes which may represent important, yet unknown section of mobilome

Anglický abstrakt

Antibiotic use in farming for decades has led to the selection pressure on chicken commensal bacteria which adapted to those changes by the acquisition of antibiotic resistance genes via horizontal gene transfer. Extensive gene transfer between gut bacteria is mediated by mobile genetic elements such as plasmids, integrative conjugative elements and temperate phages. Therefore, chicken gut commensal bacteria are considered reservoirs of antibiotic resistance genes. Recently, we initiated a systemic cultivation of chicken gut anaerobes followed by subsequent whole genome sequencing and analysis. In this study, we implemented a novel in silico approach using systems biology methods to detect horizontal gene traits and mobile genetic elements associated with it in the genomes of chicken gut commensals. In total, we identified 1,427 genes envisaged to drive horizontal gene transfer between individual chicken gut microbiota members across different families. Except for genes known to be vertically transferred, we also revealed hypothetical genes which may represent important, yet unknown section of mobilome

Dokumenty

BibTex 


@inproceedings{BUT180013,
  author="Jana {Schwarzerová} and Michal {Zeman} and Ivan {Rychlík} and Wolfram {Weckwerth} and Valentine {Provazník} and Monika {Dolejská} and Darina {Čejková}",
  title="Systems biology approach for analysis of mobile genetic elements in chicken gut microbiome",
  annote="Antibiotic use in farming for decades has led to the selection pressure on chicken commensal bacteria which adapted to those changes by the acquisition of antibiotic resistance genes via horizontal gene transfer. Extensive gene transfer between gut bacteria is mediated by mobile genetic elements such as plasmids, integrative conjugative elements and temperate phages. Therefore, chicken gut commensal bacteria are considered reservoirs of antibiotic resistance genes. Recently, we initiated a systemic cultivation of chicken gut anaerobes followed by subsequent whole genome sequencing and analysis. In this study, we implemented a novel in silico approach using systems biology methods to detect horizontal gene traits and mobile genetic elements associated with it in the genomes of chicken gut commensals. In total, we identified 1,427 genes envisaged to drive horizontal gene transfer between individual chicken gut microbiota members across different families. Except for genes known to be vertically transferred, we also revealed hypothetical genes which may represent important, yet unknown section of mobilome",
  address="IEEE Computer Society",
  booktitle="2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)",
  chapter="180013",
  doi="10.1109/BIBM55620.2022.9995414",
  howpublished="online",
  institution="IEEE Computer Society",
  year="2022",
  month="december",
  pages="2865--2870",
  publisher="IEEE Computer Society",
  type="conference paper"
}