生物多样性 ›› 2019, Vol. 27 ›› Issue (5): 557-566.DOI: 10.17520/biods.2019021
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,*(
)
收稿日期:
2019-01-25
接受日期:
2019-05-07
出版日期:
2019-05-20
发布日期:
2019-05-20
通讯作者:
牛庆生,郑浩
基金资助:
Zhang Xue1,Li Xing’an2,Su Qinzhi1,Cao Qina1,Li Chenyi1,Niu Qingsheng2,*(),Zheng Hao1,*(
)
Received:
2019-01-25
Accepted:
2019-05-07
Online:
2019-05-20
Published:
2019-05-20
Contact:
Niu Qingsheng,Zheng Hao
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。
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.
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 |
表1 蜜蜂肠道核心菌命名校正
Table 1 List of the nomenclature of the curated bacterial species from bee gut
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%。
Fig. 1 A maximum-likelihood tree of the Apibacter genus from A. cerana based on the near full-length 16S rRNA sequences (1,168 bp). Bootstrap values are indicated at the branching nodes (· > 95%, 〇 > 75%).
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
Fig. 2 Comparison of the behaviors of the BGM-Db, SILVA, and Ribosomal Database Project (RDP) databases when they are used in the classification of the gut microbiota of Apis cerana and Apis mellifera
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