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 E-mail:1463199779@qq.com;hao.zheng@cau.edu.cn

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

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"

[1] Asama T, Arima TH, Gomi T, Keishi T, Tani H, Kimura Y, Tatefuji T, Hashimoto K ( 2015) Lactobacillus kunkeei YB38 from honeybee products enhances IgA production in healthy adults. Journal of Applied Microbiology, 119, 818-826.
doi: 10.1111/jam.12889
[2] Bottacini F, Milani C, Turroni F, Sánchez B, Foroni E, Duranti S, Serafini F, Viappiani A, Strati F, Ferrarini A, Delledonne M, Henrissat B, Coutinho P, Fitzgerald GF, Margolles A, van Sinderen D, Ventura M ( 2012) Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PLoS ONE, 7, e44229.
doi: 10.1371/journal.pone.0044229
[3] Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM ( 2014) Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Research, 42, D633-D642.
doi: 10.1093/nar/gkt1244
[4] Corby-Harris V, Snyder L, Meador CAD, Naldo R, Mott B, Anderson KE ( 2016) Parasaccharibacter apium, gen. nov., sp. nov., improves honey bee (Hymenoptera: Apidae) resistance to Nosema. Journal of Economic Entomology, 109, 537-543.
doi: 10.1093/jee/tow012
[5] Corby-Harris V, Snyder LA, Schwan MR, Maes P, McFrederick QS, Anderson KE ( 2014) Origin and effect of Alpha 2.2 Acetobacteraceae in honey bee larvae and description of Parasaccharibacter apium gen. nov., sp. nov. Applied and Environmental Microbiology, 80, 7460-7472.
doi: 10.1128/AEM.02043-14
[6] Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI ( 2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318, 283-287.
doi: 10.1126/science.1146498
[7] Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE, Vásquez A ( 2015) Extensive intra-phylotype diversity in Lactobacilli and Bifidobacteria from the honeybee gut. BMC Genomics, 16, 284.
doi: 10.1186/s12864-015-1476-6
[8] Engel P, Bartlett KD, Moran NA ( 2015) The bacterium Frischella perrara causes scab formation in the gut of its honeybee host. mBio, 6, e00193-15.
[9] Engel P, Kwong WK, Moran NA ( 2013) Frischella perrara gen. nov., sp. nov., a Gammaproteobacterium isolated from the gut of the honeybee, Apis mellifera. International Journal of Systematic and Evolutionary Microbiology, 63, 3646-3651.
[10] Engel P, Martinson VG, Moran NA ( 2012) Functional diversity within the simple gut microbiota of the honey bee. Proceedings of the National Academy of Sciences, USA, 109, 11002-11007.
doi: 10.1073/pnas.1202970109
[11] Engel P, Stepanauskas R, Moran NA ( 2014) Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genetics, 10, e1004596.
doi: 10.1371/journal.pgen.1004596
[12] Killer J, Kopečný J, Mrázek J, Havlík J, Koppová I, Benada O, Rada V, Kofroňová O ( 2010) Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Systematic and Applied Microbiology, 33, 359-366.
doi: 10.1016/j.syapm.2010.08.002
[13] Killer J, Kopecny J, Mrazek J, Koppova I, Havlik J, Benada O, Kott T ( 2011) Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. International Journal of Systematic and Evolutionary Microbiology, 61, 1315-1321.
doi: 10.1099/ijs.0.022525-0
[14] Killer J, Kopecny J, Mrazek J, Rada V, Benada O, Koppova I, Havlik J, Straka J ( 2009) Bifidobacterium bombi sp. nov., from the bumblebee digestive tract. International Journal of Systematic and Evolutionary Microbiology, 59, 2020-2024.
doi: 10.1099/ijs.0.002915-0
[15] Kim EK, Kim SH, Nam HJ, Choi MK, Lee KA, Choi SH, Seo YY, You H, Kim B, Lee WJ ( 2012) Draft genome sequence of Commensalibacter intestini A911T, a symbiotic bacterium isolated from Drosophila melanogaster intestine. Journal of Bacteriology, 194, 1246.
doi: 10.1128/JB.06669-11
[16] Klein AM, Vaissière BE, Cane JH, Steffan-Dewenter I, Cunningham SA, Kremen C, Tscharntke T ( 2007) Importance of pollinators in changing landscapes for world crops. Proceedings of the Royal Society B: Biological Sciences, 274, 303-313.
doi: 10.1098/rspb.2006.3721
[17] Kwong WK, Engel P, Koch H, Moran NA ( 2014 a) Genomics and host specialization of honey bee and bumble bee gut symbionts. Proceedings of the National Academy of Sciences, USA, 111, 11509-11514.
doi: 10.1073/pnas.1405838111
[18] Kwong WK, Mancenido AL, Moran NA ( 2014 b) Genome sequences of Lactobacillus sp. strains wkB8 and wkB10, members of the Firm-5 clade, from honey bee guts. Genome Announcements, 2, e01176-14.
[19] Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, Jaffé R, Moran NA ( 2017) Dynamic microbiome evolution in social bees. Science Advances, 3, 1-16.
[20] Kwong WK, Moran NA ( 2013) Cultivation and characterization of the gut symbionts of honey bees and bumble bees: Description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology, 63, 2008-2018.
doi: 10.1099/ijs.0.044875-0
[21] Kwong WK, Moran NA ( 2016) Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees. International Journal of Systematic and Evolutionary Microbiology, 66, 1323-1329.
doi: 10.1099/ijsem.0.000882
[22] Lane DJ ( 1991) 16S/23S rRNA Sequencing. In: Nucleic Acid Techniques in Bacterial Systematic (eds Stackebrandt E, Goodfellow M), pp. 115-175. John Wiley and Sons, New York
[23] Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme P ( 2015) Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop. International Journal of Systematic and Evolutionary Microbiology, 65, 267-273.
doi: 10.1099/ijs.0.068049-0
[24] Martinson VG, Danforth BN, Minckley RL, Rueppell O, Tingek S, Moran NA ( 2011) A simple and distinctive microbiota associated with honey bees and bumble bees. Molecular Ecology, 20, 619-628.
doi: 10.1111/mec.2011.20.issue-3
[25] Martinson VG, Mago T, Koch H, Salzberg SL, Moran NA ( 2014) Genomic features of a bumble bee symbiont reflect its host environment. Applied and Environmental Microbiology, 80, 3793-3803.
doi: 10.1128/AEM.00322-14
[26] Martinson VG, Moy J, Moran NA ( 2012) Establishment of characteristic gut bacteria during development of the honeybee worker. Applied and Environmental Microbiology, 78, 2830-2840.
doi: 10.1128/AEM.07810-11
[27] Mikaelyan A, Köhler T, Lampert N, Rohland J, Boga H, Meuser K, Brune A ( 2015) Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb). Systematic and Applied Microbiology, 38, 472-482.
doi: 10.1016/j.syapm.2015.07.004
[28] Moran NA ( 2015) Genomics of the honey bee microbiome. Current Opinion in Insect Science, 10, 22-28.
doi: 10.1016/j.cois.2015.04.003
[29] Newton IL, Roeselers G ( 2012) The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier. BMC Microbiology, 12, 221.
doi: 10.1186/1471-2180-12-221
[30] Olofsson TC, Alsterfjord M, Nilson B, Butler E, Vásquez A ( 2014) Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera. International Journal of Systematic and Evolutionary Microbiology, 64, 3109-3119.
doi: 10.1099/ijs.0.059600-0
[31] Praet J, Aerts M, Brandt ED, Meeus I, Smagghe G, Vandamme P ( 2016) Apibacter mensalis sp. nov.: A rare member of the bumblebee gut microbiota. International Journal of Systematic and Evolutionary Microbiology, 66, 1645-1651.
doi: 10.1099/ijsem.0.000921
[32] Praet J, Meeus I, Cnockaert M, Aerts M, Smagghe G, Vandamme P ( 2015) Bifidobacterium commune sp. nov. isolated from the bumble bee gut. Antonie van Leeuwenhoek, 107, 1307-1313.
doi: 10.1007/s10482-015-0425-3
[33] Praet J, Parmentier A, Schmid-Hempel R, Meeus I, Smagghe G, Vandamme P ( 2018) Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition. Environmental Microbiology, 20, 214-227.
doi: 10.1111/1462-2920.13973
[34] Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO ( 2007) SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 7188-7196.
doi: 10.1093/nar/gkm864
[35] Raymann K, Shaffer Z, Moran NA ( 2017) Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees. PLoS Biology, 15, e2001861.
doi: 10.1371/journal.pbio.2001861
[36] Segers FH, Kešnerová L, Kosoy M, Engel P ( 2017) Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. The ISME Journal, 11, 1232-1244.
doi: 10.1038/ismej.2016.201
[37] Steele MI, Kwong WK, Whiteley M, Moranb NA ( 2017) Diversification of type VI secretion system toxins reveals ancient antagonism among bee gut microbes. mBio, 8, e01630-17.
[38] Tarpy DR, Mattila HR, Newton ILG ( 2015) Development of the honey bee gut microbiome throughout the Queen- Rearing Process. Applied and Environmental Microbiology, 81, 3182-3191.
doi: 10.1128/AEM.00307-15
[39] vanEngelsdorp D, Evans JD, Saegerman C, Mullin C, Haubruge E, Nguyen BK, Frazier M, Frazier J, Cox-Foster D, Chen Y, Underwood R, Tarpy DR, Pettis JS ( 2009) Colony collapse disorder: A descriptive study. PLoS ONE, 4, e6481.
doi: 10.1371/journal.pone.0006481
[40] Wang Q, Garrity GM, Tiedje JM, Cole JR ( 2007) Naïve Bayesian Classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.
doi: 10.1128/AEM.00062-07
[41] Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO ( 2014) The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research, 42, D643-D648.
doi: 10.1093/nar/gkt1209
[42] Yun JH, Lee JY, Hyun DW, Jung MJ, Bae JW ( 2017) Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee. International Journal of Systematic and Evolutionary Microbiology, 67, 2184-2188.
doi: 10.1099/ijsem.0.001921
[43] Zheng H, Nishida A, Kwong WK, Koch H, Engel P, Steele MI, Moran NA ( 2016) Metabolism of toxic sugars by strains of the bee gut symbiont Gilliamella apicola. mBio, 7, e01326-16.
[44] Zheng H, Powell JE, Steele MI, Dietrich C, Moran NA ( 2017) Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proceedings of the National Academy of Sciences, USA, 114, 4775-4780.
doi: 10.1073/pnas.1701819114
[1] Ke Wang Mingjun Zhao Jinhe Su Liu Yang Hong Deng Yonghui Wang Haijun Wu Yi Li Hongmei Wu Xiaodan Wei Tiezheng Wei Lei Cai Yijian Yao. (2020) The Use of Checklist of Fungi in China Database in the Red List Assessment of Macrofungi in China . Biodiv Sci, 28(1): 0-0.
[2] Qi Lu, Qiang Hu, Xiaogang Shi, Senlong Jin, Sheng Li, Meng Yao. (2019) Metabarcoding diet analysis of snow leopards (Panthera uncia) in Wolong National Nature Reserve, Sichuan Province . Biodiv Sci, 27(9): 960-969.
[3] Jun Liu, Ning Wang, Daizong Cui, Lei Lu, Min Zhao. (2019) Diversity of bacterial resources in the Greater and Lesser Khinggan Mountains . Biodiv Sci, 27(8): 903-910.
[4] Xiao Yaqian,Liu Chuan,Xiao Liang. (2019) The role of model animals in the study of symbiotic microorganisms . Biodiv Sci, 27(5): 505-515.
[5] Chen Zhixiang, Yao Xueying, Stephen R. Downie, Wang Qizhi. (2019) Assembling and analysis of Sanicula orthacantha chloroplast genome . Biodiv Sci, 27(4): 366-372.
[6] Xiaojuan Deng, Jianli Liu, Xingfu Yan, Peigui Liu. (2018) Community composition of bacteria associated with ascocarps of Tuber indicum using traditional culture method and Roche 454 high-throughput sequencing . Biodiv Sci, 26(12): 1318-1324.
[7] Qiaoli Li, Na Yan, Qiong Song, Junzhan Guo. (2018) Complete Chloroplast Genome Sequence and Characteristics Analysis of Morus multicaulis . Chin Bull Bot, 53(1): 94-103.
[8] Hua Feng,Wenhao Cao,Xiaoyang Tian,Zhiqiang Cheng,Tao Yan. (2016) Design and development of a data management system for marine fouling organisms . Biodiv Sci, 24(7): 838-846.
[9] Cibin Ge,Rong Zheng,Bo Liu,Guohong Liu,Jianmei Che,Jianyang Tang. (2016) Diversity and distribution of cultivable Bacillus-like species in soils collected from Wuyishan Nature Reserve . Biodiv Sci, 24(10): 1164-1176.
[10] Guohong Liu,Bo Liu,Yujing Zhu,Jianmei Che,Cibin Ge,Mingxing Su,Jianyang Tang. (2016) Diversity of Bacillus-like species in Taiwan . Biodiv Sci, 24(10): 1154-1163.
[11] Aihua Zhao,Xiaojun Du,Jing Zang,Shouren Zhang,Zhihua Jiao. (2015) Soil bacterial diversity in the Baotianman deciduous broad-leaved forest . Biodiv Sci, 23(5): 649-657.
[12] Haitao Li,Baoxue Zhang,Yang Gao,Xiaojun Shi,Peng Zhou. (2015) DNA barcoding in species identification of seashells: a case study in the ecological monitoring zone of Daya Bay, Guangdong . Biodiv Sci, 23(3): 299-305.
[13] Zili Wu, Mengyao Yu, Lu Chen, Jing Wei, Xiaoqin Wang, Yong Hu, Yan Yan, Ping Wan. (2015) Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network . Chin Bull Bot, 50(2): 171-179.
[14] Panpan Wang, Yongxiu Wu, Tongtong Song, Chunling Ma, Wen Zhao, Ying Wang, Lei Sun. (2015) Genetic diversity of culturable endophytic bacteria in the roots of wild and greenhouse Cymbidium faberi . Biodiv Sci, 23(1): 61-67.
[15] Jingbo Kan,Lina Li,Dong Qu,Baoli Wang. (2014) Changes in bacterial abundance and community structure associated with flooding in paddy soil . Biodiv Sci, 22(4): 508-515.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed