Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius

Parasites & Vectors

Research

Bo-Young Jeon¹  Ju Yeong Kim²  Tai-Soon Yong²  Singeun Oh²  Myung-hee Yi²  Seogwon Lee²  Jun Ho Choi²  In-Yong Lee²  Soo Lim Kim²  Myungjun Kim² 

[1] Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, 26493, Wonju, Republic of Korea;Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, 03722, Seoul, Republic of Korea;

关键词: 18S rDNA;    16S rDNA;    Apodemus agrarius;    Parasite;    Microbiome;   

DOI  :  10.1186/s13071-022-05608-w

 received in 2022-08-05, accepted in 2022-12-03,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundThe striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis.MethodsWe conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified.ResultsAmong the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group.ConclusionsThis study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.Graphical Abstract

【 授权许可】

CC BY   
© The Author(s) 2022

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