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

J 2024

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

SCHWARZEROVA, Jana, Michal ZEMAN, Vladimir BABAK, Katerina JURECKOVA, Marketa NYKRYNOVA et. al.

Základní údaje

Originální název

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

Autoři

SCHWARZEROVA, Jana (203 Česká republika), Michal ZEMAN (203 Česká republika), Vladimir BABAK (203 Česká republika), Katerina JURECKOVA (203 Česká republika), Marketa NYKRYNOVA (203 Česká republika), Margaret VARGA (203 Česká republika), Wolfram WECKWERTH (203 Česká republika), Monika DOLEJSKA (203 Česká republika), Valentine PROVAZNÍK (203 Česká republika, domácí), Ivan RYCHLIK (203 Česká republika) a Darina CEJKOVA (203 Česká republika, garant)

Vydání

Microbiology spectrum, WASHINGTON, AMER SOC MICROBIOLOGY, 2024, 2165-0497

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.700 v roce 2022

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1128/spectrum.01964-23

UT WoS

001126360200003

Klíčová slova anglicky

animal microbiome; genome evolution; mobile genetic elements; mobilome; resistance genes; horizontal gene transfer; gut microbiota

Štítky

14110515, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 12. 7. 2024 12:57, Mgr. Tereza Miškechová

Anotace

V originále

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.IMPORTANCEHorizontal 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.

Citovat

SCHWARZEROVA, Jana, Michal ZEMAN, Vladimir BABAK, Katerina JURECKOVA, Marketa NYKRYNOVA, Margaret VARGA, Wolfram WECKWERTH, Monika DOLEJSKA, Valentine PROVAZNÍK, Ivan RYCHLIK a Darina CEJKOVA. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Microbiology spectrum. WASHINGTON: AMER SOC MICROBIOLOGY, 2024, roč. 12, č. 1, s. 1-23. ISSN 2165-0497. Dostupné z: https://dx.doi.org/10.1128/spectrum.01964-23.

@article{2368677,
   author = {Schwarzerova, Jana and Zeman, Michal and Babak, Vladimir and Jureckova, Katerina and Nykrynova, Marketa and Varga, Margaret and Weckwerth, Wolfram and Dolejska, Monika and Provazník, Valentine and Rychlik, Ivan and Cejkova, Darina},
   article_location = {WASHINGTON},
   article_number = {1},
   doi = {http://dx.doi.org/10.1128/spectrum.01964-23},
   keywords = {animal microbiome; genome evolution; mobile genetic elements; mobilome; resistance genes; horizontal gene transfer; gut microbiota},
   language = {eng},
   issn = {2165-0497},
   journal = {Microbiology spectrum},
   title = {Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis},
   url = {https://journals.asm.org/doi/10.1128/spectrum.01964-23},
   volume = {12},
   year = {2024}
}

TY  - JOUR
ID  - 2368677
AU  - Schwarzerova, Jana - Zeman, Michal - Babak, Vladimir - Jureckova, Katerina - Nykrynova, Marketa - Varga, Margaret - Weckwerth, Wolfram - Dolejska, Monika - Provazník, Valentine - Rychlik, Ivan - Cejkova, Darina
PY  - 2024
TI  - Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis
JF  - Microbiology spectrum
VL  - 12
IS  - 1
SP  - 1-23
EP  - 1-23
PB  - AMER SOC MICROBIOLOGY
SN  - 21650497
KW  - animal microbiome
KW  - genome evolution
KW  - mobile genetic elements
KW  - mobilome
KW  - resistance genes
KW  - horizontal gene transfer
KW  - gut microbiota
UR  - https://journals.asm.org/doi/10.1128/spectrum.01964-23
N2  - 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.IMPORTANCEHorizontal 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.
ER  -

SCHWARZEROVA, Jana, Michal ZEMAN, Vladimir BABAK, Katerina JURECKOVA, Marketa NYKRYNOVA, Margaret VARGA, Wolfram WECKWERTH, Monika DOLEJSKA, Valentine PROVAZNÍK, Ivan RYCHLIK a Darina CEJKOVA. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. \textit{Microbiology spectrum}. WASHINGTON: AMER SOC MICROBIOLOGY, 2024, roč.~12, č.~1, s.~1-23. ISSN~2165-0497. Dostupné z: https://dx.doi.org/10.1128/spectrum.01964-23.

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