Detecting horizontal gene transfer among microbiota
- Author(s)
- Jana Schwarzerova, Michal Zeman, Vladimir Babak, Katerina Jureckova, Marketa Nykrynova, Margaret Varga, Wolfram Weckwerth, Monika Dolejska, Valentine Provaznik, Ivan Rychlik, Darina Cejkova
- 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.
- Organisation(s)
- Functional and Evolutionary Ecology, Research Platform Vienna Metabolomics Center
- External organisation(s)
- Brno University of Technology, Veterinary Research Institute, University of Oxford, University of Veterinary Sciences Brno, Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno , Brno, Czech Republic., Charles University Prague, Masaryk University
- Journal
- Microbiology Spectrum
- Volume
- 12
- No. of pages
- 23
- ISSN
- 2165-0497
- DOI
- https://doi.org/10.1128/spectrum.01964-23
- Publication date
- 01-2024
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106023 Molecular biology, 106014 Genomics
- Keywords
- ASJC Scopus subject areas
- Microbiology (medical), Infectious Diseases, Genetics, Immunology and Microbiology(all), Physiology, Cell Biology, Ecology
- Sustainable Development Goals
- SDG 3 - Good Health and Well-being
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/detecting-horizontal-gene-transfer-among-microbiota(1e517e4a-5ddd-438f-8f91-2320cac169d5).html