Metagenomic analysis reveals the microbiome and resistome in migratory birds

Jian Cao,Jing Li,Yongfei Hu,Yuhai Bi,Yanan Wang,Na Lv,Fei Liu,Baoli Zhu,George F Gao

doi:10.1186/s40168-019-0781-8

Abstract

BackgroundAntibiotic-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.ResultsHere, 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.ConclusionsOur 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.9vRT3BmK5LZQjoS1YmKYZoVideo abstract.

Highlights

The coevolution of vertebrates and their associated microbes can improve the adaptability of a host to new dietary niches [1, 2]
Distinct gut bacterial communities in different migratory bird population Bacterial units predominated in all bird species and contributed more phylogenetic diversity than archaea, eukaryotes, and viruses (Additional file 11: Table S3)
We found that bird species differed from each other in their resistomes, with species explaining the variation between samples (Fig. 4a), suggesting bird species contributed mostly to the antibiotic resistance genes (ARGs) composition dissimilarity

Summary

Introduction

The coevolution of vertebrates and their associated microbes can improve the adaptability of a host to new dietary niches [1, 2]. An increasing amount of data, from humans and mice to insects and fish, has provided the insight that microbial communities colonizing the gut play a critical role in affecting host physiology and health [3]. These communities are capable of extracting nutrients from ingested food and Approximately 700,000 people die annually due to resistant infections, and this number will increase to 10 million annual deaths by the year 2050 [4, 5]. The structure and function of the gut bacterial community, as well as the ARGs they carry in migratory birds remain unknown

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Discussion

Conclusion