用于蜜蜂和熊蜂肠道微生物分类的细菌16S rRNA数据库优化

doi:10.17520/biods.2019021

摘要/Abstract

摘要：

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

Abstract:

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

张雪, 李兴安, 苏秦之, 曹棋钠, 李晨伊, 牛庆生, 郑浩. 用于蜜蜂和熊蜂肠道微生物分类的细菌16S rRNA数据库优化[J]. 生物多样性, 2019, 27(5): 557-566.

Zhang Xue, Li Xing’an, Su Qinzhi, Cao Qina, Li Chenyi, Niu Qingsheng, Zheng Hao. A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota[J]. Biodiv Sci, 2019, 27(5): 557-566.

图/表 3

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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	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	Firm-4	Lactobacillus Firm-4	Olofsson et al, 2014; Moran, 2015
	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	/	Bifidobacterium coryneforme/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	/	Apibacter	Praet et al, 2016

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	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	Firm-4	Lactobacillus Firm-4	Olofsson et al, 2014; Moran, 2015
	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	/	Bifidobacterium coryneforme/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	/	Apibacter	Praet et al, 2016