Biodiversity Science ›› 2019, Vol. 27 ›› Issue (5): 557-566.doi: 10.17520/biods.2019021

• Original Papers • Previous Article     Next Article

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
  • Niu Qingsheng,Zheng Hao;

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

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 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

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%)."

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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