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Metagenomic analysis reveals the microbiome and resistome in migratory birds

BACKGROUND: Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated. However, the structure and function of the gut b...

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Autores principales: Cao, Jian, Hu, Yongfei, Liu, Fei, Wang, Yanan, Bi, Yuhai, Lv, Na, Li, Jing, Zhu, Baoli, Gao, George F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053137/
https://www.ncbi.nlm.nih.gov/pubmed/32122398
http://dx.doi.org/10.1186/s40168-019-0781-8
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author Cao, Jian
Hu, Yongfei
Liu, Fei
Wang, Yanan
Bi, Yuhai
Lv, Na
Li, Jing
Zhu, Baoli
Gao, George F.
author_facet Cao, Jian
Hu, Yongfei
Liu, Fei
Wang, Yanan
Bi, Yuhai
Lv, Na
Li, Jing
Zhu, Baoli
Gao, George F.
author_sort Cao, Jian
collection PubMed
description BACKGROUND: Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated. However, the structure and function of the gut bacterial community, as well as the ARGs they carry in migratory birds remain unknown. RESULTS: Here, we collected samples from migratory bird species and their associated environments and characterized their gut microbiomes and resistomes using shotgun metagenomic sequencing. We found that migratory birds vary greatly in gut bacterial composition but are similar in their microbiome metabolism and function. Birds from the same environment tend to harbor similar bacterial communities. In total, 1030 different ARGs (202 resistance types) conferring resistance to tetracycline, aminoglycoside, β-lactam, sulphonamide, chloramphenicol, macrolide-lincosamide-streptogramin (MLS), and quinolone are identified. Procrustes analysis indicated that microbial community structure is not correlated with the resistome in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate from Proteobacteria. Co-occurrence patterns revealed by network analysis showed that emrD, emrY, ANT(6)-Ia, and tetO, the hubs of ARG type network, are indicators of other co-occurring ARG types. Compared with the microbiomes and resistomes in the environment, migratory birds harbor a lower phylogenetic diversity but have more antibiotic resistance proteins. Interestingly, we found that the mcr-1 resistance gene is widespread among different birds, accounting for 50% of the total samples. Meanwhile, a large number of novel β-lactamase genes are also reconstructed from bird metagenomic assemblies based on fARGene software. CONCLUSIONS: Our study provides a comprehensive overview of the diversity and abundance of ARGs in migratory birds and highlights the possible role of migratory birds as ARG disseminators into the environment.
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spelling pubmed-70531372020-03-10 Metagenomic analysis reveals the microbiome and resistome in migratory birds Cao, Jian Hu, Yongfei Liu, Fei Wang, Yanan Bi, Yuhai Lv, Na Li, Jing Zhu, Baoli Gao, George F. Microbiome Research BACKGROUND: Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated. However, the structure and function of the gut bacterial community, as well as the ARGs they carry in migratory birds remain unknown. RESULTS: Here, we collected samples from migratory bird species and their associated environments and characterized their gut microbiomes and resistomes using shotgun metagenomic sequencing. We found that migratory birds vary greatly in gut bacterial composition but are similar in their microbiome metabolism and function. Birds from the same environment tend to harbor similar bacterial communities. In total, 1030 different ARGs (202 resistance types) conferring resistance to tetracycline, aminoglycoside, β-lactam, sulphonamide, chloramphenicol, macrolide-lincosamide-streptogramin (MLS), and quinolone are identified. Procrustes analysis indicated that microbial community structure is not correlated with the resistome in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate from Proteobacteria. Co-occurrence patterns revealed by network analysis showed that emrD, emrY, ANT(6)-Ia, and tetO, the hubs of ARG type network, are indicators of other co-occurring ARG types. Compared with the microbiomes and resistomes in the environment, migratory birds harbor a lower phylogenetic diversity but have more antibiotic resistance proteins. Interestingly, we found that the mcr-1 resistance gene is widespread among different birds, accounting for 50% of the total samples. Meanwhile, a large number of novel β-lactamase genes are also reconstructed from bird metagenomic assemblies based on fARGene software. CONCLUSIONS: Our study provides a comprehensive overview of the diversity and abundance of ARGs in migratory birds and highlights the possible role of migratory birds as ARG disseminators into the environment. BioMed Central 2020-03-02 /pmc/articles/PMC7053137/ /pubmed/32122398 http://dx.doi.org/10.1186/s40168-019-0781-8 Text en © The Author(s). 2020 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cao, Jian
Hu, Yongfei
Liu, Fei
Wang, Yanan
Bi, Yuhai
Lv, Na
Li, Jing
Zhu, Baoli
Gao, George F.
Metagenomic analysis reveals the microbiome and resistome in migratory birds
title Metagenomic analysis reveals the microbiome and resistome in migratory birds
title_full Metagenomic analysis reveals the microbiome and resistome in migratory birds
title_fullStr Metagenomic analysis reveals the microbiome and resistome in migratory birds
title_full_unstemmed Metagenomic analysis reveals the microbiome and resistome in migratory birds
title_short Metagenomic analysis reveals the microbiome and resistome in migratory birds
title_sort metagenomic analysis reveals the microbiome and resistome in migratory birds
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053137/
https://www.ncbi.nlm.nih.gov/pubmed/32122398
http://dx.doi.org/10.1186/s40168-019-0781-8
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