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

Author:

Schwarzerova Jana12,Zeman Michal3,Babak Vladimir3,Jureckova Katerina1,Nykrynova Marketa1,Varga Margaret4,Weckwerth Wolfram25,Dolejska Monika6789,Provaznik Valentine110,Rychlik Ivan3,Cejkova Darina1ORCID

Affiliation:

1. Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology , Brno, Czech Republic

2. Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna , Vienna, Austria

3. Veterinary Research Institute , Brno, Czech Republic

4. Department of Biology, University of Oxford , Oxford, United Kingdom

5. Vienna Metabolomics Center (VIME), University of Vienna , Vienna, Austria

6. Central European Institute of Technology, University of Veterinary Sciences Brno , Brno, Czech Republic

7. Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno , Brno, Czech Republic

8. Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno , Brno, Czech Republic

9. Biomedical Center, Faculty of Medicine, Charles University , Pilsen, Czech Republic

10. Department of Physiology, Faculty of Medicine, Masaryk University , Brno, Czech Republic

Abstract

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. IMPORTANCE Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.

Funder

Czech Science Foundation

Internal Grant Agency of the University of Veterinary Sciences Brno

Publisher

American Society for Microbiology

Subject

Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology

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