生物多样性 ›› 2019, Vol. 27 ›› Issue (5): 557-566.doi: 10.17520/biods.2019021

• 研究报告 • 上一篇    下一篇

用于蜜蜂和熊蜂肠道微生物分类的细菌16S rRNA数据库优化

张雪1, 李兴安2, 苏秦之1, 曹棋钠1, 李晨伊1, 牛庆生2, *(), 郑浩1, *()   

  1. 1 北京市食品营养与人类健康高精尖创新中心, 中国农业大学食品科学与营养工程 学院, 北京 100083
    2 吉林省养蜂科学研究所蜜蜂遗传育种省重点实验室, 吉林省吉林市 132108
  • 收稿日期:2019-01-25 接受日期:2019-05-07 出版日期:2019-05-20
  • 通讯作者: 牛庆生,郑浩 E-mail:1463199779@qq.com;hao.zheng@cau.edu.cn
  • 基金项目:
    国家自然科学基金(31870472;31470123)

A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota

Zhang Xue1, Li Xing’an2, Su Qinzhi1, Cao Qina1, Li Chenyi1, Niu Qingsheng2, *(), Zheng Hao1, *()   

  1. 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083
    2 Provincial Key Laboratory of Bee Genetics and Breeding, Apiculture Science Institute of Jilin Province, Jilin City, Jilin Province 132108
  • Received:2019-01-25 Accepted:2019-05-07 Online:2019-05-20
  • Contact: Niu Qingsheng,Zheng Hao E-mail:1463199779@qq.com;hao.zheng@cau.edu.cn

蜜蜂和熊蜂是重要的传粉昆虫, 对农业生产及生态平衡的维持具有重要作用。近年来, 研究发现蜜蜂及熊蜂肠道内含有大量微生物, 其组成简单、特异。正常的肠道微生物群落对蜜蜂的生长、激素调节、致病菌抵抗等具有重要作用。随着高通量测序的发展, 研究者们也可快速获得传粉蜂肠道微生物组成, 这给生物多样性和物种保护及蜂类健康等的研究带来了便捷。但是由于蜜蜂和熊蜂肠道微生物群落均由特殊菌种组成, 目前的细菌16S rRNA数据库无法对其进行准确的分类, 并且部分东方蜜蜂(Apis cerana)特有的肠道微生物菌种缺乏16S rRNA序列信息。本文从来源于5个不同省份的东方蜜蜂肠道中分离得到在东方蜜蜂中普遍含有的Apibacter菌属纯菌, 获取其全长16S rRNA序列, 并对目前蜜蜂和熊蜂肠道的5个核心菌种的分类进行了综述, 对其分类和命名进行了修正。根据蜜蜂肠道微生物的明确分类, 在目前常用的SILVA细菌分类数据库基础之上对其进行了命名及分类优化, 并加入东方蜜蜂中普遍含有的Apibacter序列, 从而获得了优化数据库Bee Gut Microbiota-Database (BGM-Db)。通过1组东方蜜峰及1组西方蜜蜂(Apis mellifera)的肠道菌群高通量测序结果, 分析不同数据库的表现, 我们发现相比于SILVA和Ribosomal Database Project (RDP), BGM-Db对蜜蜂肠道16S rRNA高通量测序短序列实现了菌种级别的分类, 分辨率更高。

关键词: 蜜蜂, 肠道微生物, 高通量测序, 数据库, 16S rRNA

Honey and bumble bees are import pollinators, playing significant roles in the agricultural industry and maintaining the bio-ecosystem balance. Recently, it was found that the bees harbor a simple, yet specific gut microbiota. The normal bee gut microbiota makes essential contributions to host growth, endocrine signaling, and pathogen resistance. With the development of high through-put sequencing technology, researchers can now quickly identify the gut community structure for a low cost. This is helpful for biodiversity, conservation and bee health studies. However, the currently-used 16S rRNA databases are not specific enough to classify the bee gut microbiota properly. Many of the specific bacteria that enrich the gut of Apis cerana are in the genus Apibacter. Here, we isolated Apibacter species from A. cerana collected in five provinces of China, and added them to the current SILVA database. We also curated the nomenclature of some existing sequences and re-classified them in the updated database. Based on the analysis of the 16S rRNA sequencing data from one A. cerana and one Apis mellifera sample, our Bee Gut Microbiota-Database (BGM-Db) offers a more accurate classification of bee gut microbiota at a higher resolution than either the SILVA or Ribosomal Database Project (RDP) database.

Key words: honey bee, gut microbiota, high-throughput sequencing, database, 16S rRNA

表1

蜜蜂肠道核心菌命名校正"

属名 Genus 种名 Species 其他名
Other names
BGM-Db数据库聚类名
BGM-Db names
参考文献 References
Snodgrassella Snodgrassella alvi Beta Snodgrassella Martinson et al, 2012; Kwong & Moran, 2013
Gilliamella Gilliamella apicola Gamma-1 Gilliamella Martinson et al, 2012; Kwong & Moran, 2013
Frischella Frischella perrara Gamma-2 Frischella Engel et al, 2013
Schmidhempelia Candidatus Schmidhempelia bombi’ Schmidhempelia Martinson et al, 2014
Bartonella Bartonella apis Alpha-1 Bartonella apis Moran, 2015
Commensalibacter Commensalibacter intestini Alpha-2.1 Commensalibacter Alpha2.1 Kwong et al, 2014b
Bombella Bombella apis Alpha-2.2 Bombella Alpha2.2 Yun et al, 2017
Bombella intestini Yun et al, 2017
Parasaccharibacter Parasaccharibacter apium Moran, 2015
Lactobacillus Lactobacillus mellis Firm-4
Lactobacillus Firm-4 Olofsson et al, 2014; Moran, 2015
Lactobacillus mellifer
Lactobacillus apis Firm-5 Lactobacillus Firm-5 Kwong et al, 2014b
Lactobacillus helsingborgensis Olofsson et al, 2014; Moran, 2015
Lactobacillus melliventris
Lactobacillus kimbladii
Lactobacillus kullabergensis
Lactobacillus apinorum
Lactobacillus kunkeei / Lactobacillus kunkeei Moran, 2015
Bifidobacterium Bifidobacterium asteroides / Bifidobacterium asteroides Bottacini et al, 2012
Bifidobacterium coryneforme / Bifidobacterium coryneforme/indicum Ellegaard et al, 2015
Bifidobacterium indicum / Ellegaard et al, 2015
Bifidobacterium bombi / Bifidobacterium bombi/commune/bohemicum Killer et al, 2009
Bifidobacterium commune / Praet et al, 2015
Bifidobacterium bohemicum / Killer et al, 2011
Bombiscardovia Bombiscardovia coagulans / Bombiscardovia Killer et al, 2010
Apibacter Apibacter adventoris / Apibacter
Kwong & Moran, 2016
Apibacter mensalis / Praet et al, 2016

图1

基于接近全长16S rRNA序列(1,168 bp)的东方蜜蜂Apibacter菌属系统发育树。节点处白圈表示自展支持率大于75%, 黑圈表示大于95%。"

图2

利用BGM-Db、SILVA及Ribosomal Database Project (RDP)数据库对东方蜜蜂和西方蜜蜂16S rRNA测序结果分类比较"

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