A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota
Zhang Xue, Li Xing’an, Su Qinzhi, Cao Qina, Li Chenyi, Niu Qingsheng, Zheng Hao
Biodiv Sci
2019, 27 ( 5):
557-566.
DOI: 10.17520/biods.2019021
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.
| 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 |
Table 1
List of the nomenclature of the curated bacterial species from bee gut
Extracts from the Article
由于目前对于蜜蜂肠道细菌的分类比较模糊, 命名也比较繁杂、多样, 因此首先对蜜蜂肠道核心菌的发现历史进行简要总结, 进而对其分类及命名进行规范。2010年Martinson等(2011)通过16S rRNA克隆建库的方法对西方蜜蜂、大蜜蜂、黑小蜜蜂(Apis andreniformis)和熊蜂肠道共生菌进行了系统的研究, 发现社会性蜜蜂核心肠道共生菌8种, 将相应的分类类群命名为Alpha-1, Alpha-2.1, Alpha-2.2, Beta, Firm-4, Firm-5, Gamma-1, Gamma-2 (表1)。但是当时并没有得到这几种核心菌的纯菌, 因此没有具体的菌种命名。在接下来的研究当中, 陆续分离得到了相应纯菌, 逐步构建了蜜蜂肠道菌的命名体系。
(2) g-变形菌Gilliamella, Frischella, ‘Candidatus Schmidhempelia bombi’。蜜蜂中的g-变形菌主要来自Orbaceae科, 包括Gamma-1和Gamma-2两个不同菌属(Martinson et al, 2011)。16S rRNA分析表明Gamma-1广泛存在于各种社会性蜜蜂肠道中, 且丰度较高, 为15%-40% (Kwong et al, 2017)。Gamma-1与Pasteurellaceae和Enterobacteriaceae相近, 但是形成不同的聚类, 其差异超过10%, 该菌属被命名为Gilliamella (Martinson et al, 2012), 主要定殖于回肠部位, 占比约为47%。Kwong和Moran (2013)从西方蜜蜂和熊蜂中分离到3株Gilliamella纯菌, 并将菌种命名为Gilliamella apicola。宏基因组分析发现Gamma-1基因组中富集碳水化合物代谢途径, 并且含有能够降解花粉主要成分果胶的裂解酶(Engel et al, 2012)。花粉降解产物中部分单糖对蜜蜂具有毒性, 如甘露糖。Zheng等(2016)对42株Gilliamella基因组测序发现, 部分Gilliamella菌株编码甘露糖降解酶, 并通过体外实验验证了其功能, 说明其在蜜蜂解毒中发挥作用。
(5)双歧杆菌。Bifidobacterium是另一蜜蜂核心肠道菌, 具有丰富的属内多样性, 主要分布在蜜蜂的直肠, 丰度较高, 在Apis属的蜜蜂肠道中丰度范围在10%-30%, 在不同熊蜂种群中丰度差异较大(Kwong et al, 2017)。目前从蜜蜂中分离到的Bifidobacterium可分为多个菌种(表1), 其中Bifidobacterium asteroides被分离到的概率最高, 说明其分布广、丰度高。1株从西方蜜蜂后肠分离到的该菌种单菌PRL2011于2012年被Bottacini等(2012)测序, 证实其富集碳水化合物代谢相关基因, 在呼吸代谢上发挥重要的作用。Bifidobacterium coryneforme和Bifidobacterium indicum由于物种相似度较高, 与Bifidobacterium asteroides进化距离较近, 但系统发育形成一个单独聚类, 在本文建立的BGM-Db中被命名为Bifidobacterium coryneforme/ indicum组。而从熊蜂中分离到的Bombiscardovia coagulans, 其16S rRNA序列与这2种菌的相似度较高, 在92%左右, 但分类到Bifidobacteriaceae目的另一菌属(Killer et al, 2010)。与以上菌种进化距离较远的Bifidobacterium bombi、Bifidobacterium commune和Bifidobacterium bohemicum均从熊蜂中分离得到(Killer et al, 2009, 2011; Praet et al, 2015), 3个菌种通过200多个核糖体基因被聚为一类, 在本文建立的BGM-Db中命名为Bifidobacterium bombi/commune/bohemicum。
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