Conservation Genetics

, Volume 18, Issue 3, pp 701–711 | Cite as

Hunting for healthy microbiomes: determining the core microbiomes of Ceratina, Megalopta, and Apis bees and how they associate with microbes in bee collected pollen

  • Peter GraystockEmail author
  • Sandra M. Rehan
  • Quinn S. McFrederick
Research Article


Social corbiculate bees such as honey bees and bumble bees maintain a specific beneficial core microbiome which is absent in wild bees. It has been suggested that maintaining this microbiome can prevent disease and keep bees healthy. The main aim of our study was to identify if there are any core bacterial groups in the non-corbiculate bees Ceratina and Megalopta that have been previously overlooked. We additionally test for associations between the core bee microbes and pollen provisions to look for potential transmission between the two. We identify three enterotypes in Ceratina samples, with thirteen core bacterial phylotypes in Ceratina females: Rosenbergiella, Pseudomonas, Gilliamella, Lactobacillus, Caulobacter, Snodgrassella, Acinetobacter, Corynebacterium, Sphingomonas, Commensalibacter, Methylobacterium, Massilia, and Stenotrophomonas, plus 19 in pollen (6 of which are shared by bees). Unlike Apis bees, whose gut microbial community differs compared to their pollen, Ceratina adults and pollen largely share a similar microbial composition and enterotype difference was largely explained by pollen age. Megalopta displays a highly diverse composition of microbes throughout all adults, yet Lactobacillus and Saccharibacter were prevalent in 90% of adults as core bacteria. Only Lactobacillus was both a core bee and pollen provision microbe in all three species. The consequences of such diversity in core microbiota between bee genera and their associations with pollen are discussed in relation to identifying potentially beneficial microbial taxa in wild bees to aid the conservation of wild, understudied, non-model bee species.


Core microbiome Hymenoptera Pollen diet 16S Foraging ecology Bacterial diversity Enterotype Pollen provision 



We thank Sean Lombard and Nicholas Pizzi for assistance with nest collections, Krista Ciaccio and Wyatt Shell for nest processing, and Jason Rothman for DNA extractions and library preparation. Funding from the University of California Riverside to QSM, the New Hampshire Agricultural Experiment Station, Tuttle Research Foundation, and the University of New Hampshire to SMR supported this work. Media acknowledgements; Ceratina calcarata (in Fig. 4) photo by J.C. Lucier (CC BY-NC 2.0); Megalopta genalis (in Fig. 6) photo by Sam Droege (CC BY 2.0); Apis mellifera (in Fig. 8) photo by Gustavo Fotoopa (CC BY-NC-ND); Ceratina nest diagram (Fig. 5a) by Wyatt Shell.

Supplementary material

10592_2017_937_MOESM1_ESM.pdf (440 kb)
Supplementary material 1 (PDF 440 KB)
10592_2017_937_MOESM2_ESM.xlsx (64 kb)
Supplementary material 2 (XLSX 63 KB)


  1. Arumugam M, Raes J, Pelletier E et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180. doi: 10.1038/nature09944 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Becking JH (2006) The genus Beijerinckia. In: The Prokaryotes: Alphaproteobacteria and Betaproteobacteria, Springer, New York, pp 151–162CrossRefGoogle Scholar
  3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  4. Brysch-Herzberg M (2004) Ecology of yeasts in plant-bumblebee mutualism in Central Europe. FEMS Microbiol Ecol 50:87–100. doi: 10.1016/j.femsec.2004.06.003 CrossRefPubMedGoogle Scholar
  5. Caliński T, Harabasz J (1974) A dendrite method for cluster analysis. Commun Stat. Methods 3:1–27. doi: 10.1080/03610917408548446 Google Scholar
  6. Caporaso JG, Bittinger K, Bushman FD et al (2010a) PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267. doi: 10.1093/bioinformatics/btp636 CrossRefPubMedGoogle Scholar
  7. Caporaso JG, Kuczynski J, Stombaugh J et al (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi: 10.1038/nmeth.f.303 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cardinal S, Straka J, Danforth BN (2010) Comprehensive phylogeny of apid bees reveals the evolutionary origins and antiquity of cleptoparasitism. Proc Natl Acad Sci U S A 107:16207–16211. doi: 10.1073/pnas.1006299107 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270. doi: 10.1038/nrg3182 PubMedPubMedCentralGoogle Scholar
  10. Colman DR, Toolson EC, Takacs-Vesbach CD (2012) Do diet and taxonomy influence insect gut bacterial communities? Mol Ecol 21:5124–5137. doi: 10.1111/j.1365-294X.2012.05752.x CrossRefPubMedGoogle Scholar
  11. Corby-Harris V, Maes P, Anderson KE (2014a) The bacterial communities associated with honey bee (Apis mellifera) foragers. PLoS ONE. doi: 10.1371/journal.pone.0095056 PubMedPubMedCentralGoogle Scholar
  12. Corby-Harris V, Snyder L a, Schwan MR et al (2014b) Origin and effect of Acetobacteraceae Alpha 2.2 in honey bee larvae and description of Parasaccharibacter apium, gen. nov., sp. nov. Appl Environ Microbiol. doi: 10.1128/AEM.02043-14 PubMedPubMedCentralGoogle Scholar
  13. DeSantis TZ, Hugenholtz P, Larsen N et al (2006) Greengenes, a chimera-checked 16 S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. doi: 10.1128/AEM.03006-05 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Engel P, James RR, Koga R et al (2013) Standard methods for research on Apis mellifera gut symbionts. J Apic Res 52:1–24. doi: 10.3896/IBRA. CrossRefGoogle Scholar
  15. Engel P, Kwong WK, McFrederick QS, et al (2016) The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions. MBio 7:1–9. doi: 10.1128/mBio.02164-15 Google Scholar
  16. Gallai N, Salles JM, Settele J, Vaissiere BE (2009) Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol Econ 68:810–821. doi: 10.1016/j.ecolecon.2008.06.014 CrossRefGoogle Scholar
  17. Graystock P, Goulson D, Hughes WOH (2015) Parasites in bloom: flowers aid dispersal and transmission of pollinator parasites within and between bee species. Proc R Soc B Biol Sci 282:20151371. doi: 10.1098/rspb.2015.1371 CrossRefGoogle Scholar
  18. Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152CrossRefPubMedPubMedCentralGoogle Scholar
  19. Kaufman MG, Klug MJ (1991) The contribution of hindgut bacteria to dietary carbohydrate utilization by crickets (Orthoptera: Gryllidae). Comp Biochem Physiol—Part A Physiol 98:117–123. doi: 10.1016/0300-9629(91)90588-4 CrossRefGoogle Scholar
  20. Koch H, Schmid-Hempel P (2011a) Bacterial communities in central European bumblebees: low diversity and high specificity. Microb Ecol 62:121–133. doi: 10.1007/s00248-011-9854-3 CrossRefPubMedGoogle Scholar
  21. Koch H, Schmid-Hempel P (2011b) Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc Natl Acad Sci USA 108:19288–19292. doi: 10.1073/pnas.1110474108 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Koch H, Abrol DP, Li J, Schmid-Hempel P (2013) Diversity and evolutionary patterns of bacterial gut associates of corbiculate bees. Mol Ecol 22:2028–2044. doi: 10.1111/mec.12209 CrossRefPubMedGoogle Scholar
  23. Kong HH, Oh J, Deming C et al (2012) Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22:850–859. doi: 10.1101/gr.131029.111 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kwong WK, Moran NA (2016) Gut microbial communities of social bees. Nat Rev Microbiol 14:374–384. doi: 10.1038/nrmicro.2016.43 CrossRefPubMedGoogle Scholar
  25. Li J, Powell JE, Guo J et al (2015) Two gut community enterotypes recur in diverse bumblebee species. Curr Biol 25:R652–R653. doi: 10.1016/j.cub.2015.06.031 CrossRefPubMedGoogle Scholar
  26. Martins AC, Melo GAR, Renner SS (2014) The corbiculate bees arose from New World oil-collecting bees: implications for the origin of pollen baskets. Mol Phylogenet Evol 80:88–94. doi: 10.1016/j.ympev.2014.07.003 CrossRefPubMedGoogle Scholar
  27. Martinson VG, Danforth BN, Minckley RL et al (2011) A simple and distinctive microbiota associated with honey bees and bumble bees. Mol Ecol 20:619–628. doi: 10.1111/j.1365-294X.2010.04959.x CrossRefPubMedGoogle Scholar
  28. McFrederick QS, Rehan SM (2016) Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee. Mol Ecol 25:2302–2311. doi: 10.1111/mec.13608 CrossRefPubMedGoogle Scholar
  29. McFrederick QS, Wcislo WT, Taylor DR et al (2012) Environment or kin: whence do bees obtain acidophilic bacteria? Mol Ecol 21:1754–1768. doi: 10.1111/j.1365-294X.2012.05496.x CrossRefPubMedGoogle Scholar
  30. McFrederick QS, Wcislo WT, Hout MC, Mueller UG (2014) Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees. FEMS Microbiol Ecol 88:398–406. doi: 10.1111/1574-6941.12302 CrossRefPubMedGoogle Scholar
  31. McFrederick QS, Thomas JM, Neff JL et al (2016) Flowers and Wild Megachilid Bees Share Microbes. Microb Ecol. doi: 10.1007/s00248-016-0838-1 PubMedGoogle Scholar
  32. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Abstr In: SeqBio 25–26th Nov 2013 27. doi: 10.1002/ejoc.201200111
  33. Mesquite Project Team (2014) Mesquite: A modular system for evolutionary analysis. In: Available from
  34. Michener CD (2007) Bees of the World. Johns Hopkins University Press, BaltimoreGoogle Scholar
  35. Olofsson TC, Alsterfjord M, Nilson B et al (2014) Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. n. Int J Syst Evol Microbiol 64:3109–3119. doi: 10.1099/ijs.0.059600-0 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Powell JE, Martinson VG, Urban-Mead K, Moran N a (2014) Routes of acquisition of the gut microbiota of the honey bee Apis mellifera. Appl Environ Microbiol 80:7378–7387. doi: 10.1128/AEM.01861-14 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Price MN, Dehal PS, Arkin AP (2009) Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650. doi: 10.1093/molbev/msp077 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Rehan SM, Richards MH (2010) Nesting biology and subsociality in Ceratina calcarata (Hymenoptera: Apidae). Can Entomol 142:65–74. doi: 10.4039/n09-056 CrossRefGoogle Scholar
  39. Reynolds AP, Richards G, de la Iglesia B, Rayward-Smith VJ (2006) Clustering rules: a comparison of partitioning and hierarchical clustering algorithms. J Math Model Algorithms 5:475–504. doi: 10.1007/s10852-005-9022-1 CrossRefGoogle Scholar
  40. Rognes T, Flouri T, Nichols B, et al (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ Prepr 4:e2409v1. doi: 10.7287/peerj.preprints.2409v1 Google Scholar
  41. Rousseeuw PJ (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20:53–65. doi: 10.1016/0377-0427(87)90125-7 CrossRefGoogle Scholar
  42. Russell J a, Moreau CS, Goldman-Huertas B et al (2009) Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants. Proc Natl Acad Sci U S A 106:21236–21241. doi: 10.1073/pnas.0907926106 CrossRefPubMedPubMedCentralGoogle Scholar
  43. Shade A, Handelsman J (2012) Beyond the Venn diagram: The hunt for a core microbiome. Environ Microbiol 14:4–12. doi: 10.1111/j.1462-2920.2011.02585.x CrossRefPubMedGoogle Scholar
  44. Sharon G, Segal D, Ringo JM, et al (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci USA 107:20051–20056. doi: 10.1073/pnas.1009906107 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Starr MP, Chatterjee AK (1972) The genus Erwinia: enterobacteria pathogenic to plants and animals. Annu Rev Microbiol 26:389–426. doi: 10.1146/annurev.mi.26.100172.002133 CrossRefPubMedGoogle Scholar
  46. Turnbaugh PJ, Turnbaugh PJ, Ley RE et al (2007) The human microbiome project. Nature 449:804–810. doi: 10.1038/nature06244 CrossRefPubMedPubMedCentralGoogle Scholar
  47. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive bayesian classifier for rapid assignment of rRNA sequences into the New bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi: 10.1128/AEM.00062-07 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Woodard SH, Lozier JD, Goulson D et al (2015) Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system. Mol Ecol 24:2916–2936. doi: 10.1111/mec.13198 CrossRefPubMedGoogle Scholar
  49. Yun JH, Roh SW, Whon TW et al (2014) Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host. Appl Environ Microbiol 80:5254–5264. doi: 10.1128/AEM.01226-14 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.Department of EntomologyUniversity of California RiversideRiversideUSA
  2. 2.Department of Biological SciencesUniversity of New HampshireDurhamUSA

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