Publication detail

Comprehensive analysis of mobile genetic elements in chicken gut microbiome using a novel in-silico approach

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

Original Title

Comprehensive analysis of mobile genetic elements in chicken gut microbiome using a novel in-silico approach

Type

abstract

Language

English

Original Abstract

Antibiotic use in farming for decades led also 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 phages. We have established a bacterial culture collection originated from healthy chicken ceca with respect to gather novel commensal bacteria. Extracted DNA from each isolate was sequenced on Illumina platform and assembled by SPAdes. Draft genome sequences were annotated by the RAST tool and de-replicated by dRep tool. To identify traits of horizontal gene transfer, almost identical genes (> 99 % id over 100 % length) present in different bacterial species were extracted by BLAST; extracted protein-coding sequences were functionally annotated by the eggNOG-mapper, CD-Batch tool and CCD search. Genomes of 279 bacterial isolates from healthy chicken ceca were analyzed in this study; the isolates belonged to 7 different phyla. Within the analysis pipeline we identified 1,418 different genes co-shared by at least two different bacterial families. In total, 634 genes are prevalent among Gram positive bacteria, 785 genes are prevalent among Gram negative bacteria and 8 genes were found in both. The further analysis of identified genes with assigned function and associated with mobilome. Interestingly, we identified novel putative aminoglycoside resistance proteins, uridine phosphorylase (protein may be involved in drug metabolism) and protein with ATPase domain. On summary, we identified 1,418 genes envisaged to drive horizontal gene transfer between individual chicken gut microbiota members, not only across different genera and families but also between more distant bacterial taxa. Based on our comprehensive analysis we suppose many hypothetical genes represent important yet an unknown section of resistome or mobilome.

Keywords

Horizontal Gene Transfer, Antibiotic Resistance Genes, Mobilome, Resistome

Authors

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

Released

7. 11. 2022

Location

Hradec Kralove

ISBN

978-80-906723-2-1

Book

14th Host Pathogen Interaction Forum 2022

Pages count

1

BibTex

@misc{BUT180019,
  author="Jana {Schwarzerová} and Michal {Zeman} and Wolfram {Weckwerth} and Valentine {Provazník} and Ivan {Rychlík} and Darina {Čejková}",
  title="Comprehensive analysis of mobile genetic elements in chicken gut microbiome using a novel in-silico approach",
  booktitle="14th Host Pathogen Interaction Forum 2022",
  year="2022",
  pages="1",
  address="Hradec Kralove",
  isbn="978-80-906723-2-1",
  note="abstract"
}