Publication detail

Exploring Mobile Genetic Elements: A Novel In-Silico Approach to Analyzing the Microbiome

SCHWARZEROVÁ, J. VARGA, M. NEJEZCHLEBOVÁ, J. WECKWERTH, W. RYCHLÍK, I. ČEJKOVÁ, D.

Original Title

Exploring Mobile Genetic Elements: A Novel In-Silico Approach to Analyzing the Microbiome

Type

abstract

Language

English

Original Abstract

This research introduces a pioneering methodology for identifying horizontal gene transfer (HGT) within a dataset of sequenced gut microbiota genomes. Through rigorous statistical analysis, the study proposes that closely related genes shared across distinct genera may be transferred between genomes via HGT mechanisms [1,2]. Utilizing data mining, computational techniques, and network analyses, the study delved into 452 isolates sourced from chicken or porcine origins to pinpoint genes implicated in HGT [1,3]. The methodology is user-friendly, intuitive, and incorporates network visualization tools. We also developed a novel analysis tool, implemented as an R package, tailored for detecting HGT events in bacterial lineages (https://github.com/JanaSchwarzerova/HorGeneVis). The tool combines a heat-map matrix integration with advanced phylogenetic analysis visualization techniques to enhance detection accuracy and efficiency. Furthermore, the study underscores that various species and strains within the same genera often harbor different assortments of transferred genes. Notably, the pipeline [1] can uncover previously uncharacterized genes and those frequently co-transferred with genes linked to resistance, virulence, or mobilome activity. Drawing from the statistical insights, the study proposes an innovative pipeline for identifying closely related genes shared across diverse genera. Among the genomes scrutinized, primary reservoirs of HGT genes were identified in Phocaeicola spp. (Bacteroidaceae) and UBA9475 spp. (early Pseudoflavonifractor, Oscillospiraceae), yielding over 6000 suspected HGT genes. Enriched gene categories included those associated with intracellular trafficking, secretion, DNA repair, and a prevalence of genes with unknown functions. Limited cross-sharing of genes was observed between Gram-positive and Gram-negative bacteria, primarily linked to mobilome components or antibiotic resistance. However, the predominant mobilome activity was detected among different genera within the same phylum, implying significant selection pressures at the phylum-level gene variant level.

Keywords

Horizontal Gene Transfer (HGT), Gut Microbiota, Phylogenetic Analysis , Data Mining

Authors

SCHWARZEROVÁ, J.; VARGA, M.; NEJEZCHLEBOVÁ, J.; WECKWERTH, W.; RYCHLÍK, I.; ČEJKOVÁ, D.

Released

30. 9. 2024

Location

Germany

Pages count

1

URL

https://dechema.converia.de/frontend/index.php?page_id=16489&v=List&do=0&day=1994

BibTex

@misc{BUT193449,
  author="Jana {Schwarzerová} and Margaret {Varga} and Julie {Nejezchlebová} and Wolfram {Weckwerth} and Ivan {Rychlík} and Darina {Čejková}",
  title="Exploring Mobile Genetic Elements: A Novel In-Silico Approach to Analyzing the Microbiome",
  year="2024",
  pages="1",
  address="Germany",
  url="https://dechema.converia.de/frontend/index.php?page_id=16489&v=List&do=0&day=1994",
  note="abstract"
}