Microbial Ecology

, Volume 78, Issue 1, pp 195–205 | Cite as

Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives

  • Céline Ribière
  • Claire Hegarty
  • Hannah Stephenson
  • Padraig Whelan
  • Paul W. O’TooleEmail author
Invertebrate Microbiology


The recent worldwide decline of honey bee colonies is a major ecological problem which also threatens pollinated crop production. Several interacting stressors such as environmental pressures and pathogens are suspected. Recently, the gut microbiota has emerged as a critical factor affecting bee health and fitness. We profiled the bacterial communities associated with the gut and whole body of worker bees to assess whether non-thriving colonies could be separated from thriving hives based on their microbial signature. The microbiota of thriving colonies was characterised by higher diversity and higher relative abundance of bacterial taxa involved in sugar degradation that were previously associated with healthy bees (e.g. Commensalibacter sp. and Bartonella apis). In contrast, the microbiota of non-thriving bees was depleted in health-associated species (e.g. Lactobacillus apis), and bacterial taxa associated with disease states (e.g. Gilliamella apicola) and pollen degradation (e.g. G. apicola and Bifidobacterium asteroides) were present in higher abundance compared to thriving colonies. Gut and whole-body microbiota shared a similar dominant core but their comparison showed differences in composition and relative abundance. More differences in taxon relative abundance between gut and whole body were observed in non-thriving bees, suggesting that microbiota associated with other bee organs might also be different. Thus, microbiota profiling could be used as a diagnostic tool in beekeeping practices to predict hive health and guide hive management.


Honey bee Apis mellifera Microbiota 16S rRNA sequencing 



We thank the beekeeper for allowing us to collect honey bee workers and for his assistance in conducting this survey. Work in PWOT’s lab was supported in part by Science Foundation Ireland through a Centre award to the APC Microbiome Ireland (SFI/12/RC/2273).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2018_1287_MOESM1_ESM.pdf (1.3 mb)
ESM 1 (PDF 1335 kb)
248_2018_1287_MOESM2_ESM.xlsx (335 kb)
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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Céline Ribière
    • 1
  • Claire Hegarty
    • 1
  • Hannah Stephenson
    • 1
  • Padraig Whelan
    • 2
  • Paul W. O’Toole
    • 1
    Email author
  1. 1.School of Microbiology and APC Microbiome Ireland, Food Science BuildingUniversity College CorkCorkIreland
  2. 2.Apis Protect Limited, Environmental Research CentreCorkIreland

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