Characterization of the honey bee and stingless bee gut microbiota: A hidden diversity and host-specific microbiomes from sub-Saharan-African region

Abstract

Pollinators are significant contributors to world’s economy, nutrition, food security and biodiversity. Among all animal pollinators, the honey bee, Apis mellifera, is one of the most important and widely used managed pollinators worldwide, while stingless bees (Apidae: Meliponini) are becoming important alternative pollinators of horticulture crops, particularly with the recent honey bee colony losses worldwide. Recently, attention has been drawn to the microbiota communities associated with bee gut and their potential impact on the host physiology and health. However, no comprehensive study on this subject has been conducted in Africa, where important native diversity of the bees is found. Here, I characterized the gut microbiota of honey bee and stingless bee species/sub-species from sub-Saharan Africa using 16S rRNA amplicon sequence. In honey bees, I found all the core gut microbiota members reported elsewhere in the world, bees from the coastal regions of Kenya harbours a higher relative abundance and diversity of core members than bees from other regions. Additionally, I showed that Gilliamella, Snodgrassella and Frischella dominated in all locations, and that altitude and humidity affect Gilliamella abundance. In contrast, I found that Lactobacillus was less common compared to temperate regions of the world. In stingless bees, I found that Firmicutes, Actinobacteria and Proteobacteria were the dominant and conserved phyla across the eight studied species. Nevertheless, I found significant continent-specific and host intra-species diversity where each stingless bee species has a distinct gut composition, and African bacterial strains cluster together based on phylogeny. Furthermore, I established protocols in the laboratory for newly emerged microbe-deprived worker bee rearing, and bee mono-inoculation. Using these protocols, I showed that Commensalibacter sp. AMU001 effectively colonized and multiplied in the bee gut and it did not affect its survival. This study is a first comprehensive study of the gut microbiota of bees from sub-Saharan Africa. The data and protocols develop in this thesis represent an important step towards the development of state-of-the-art bee gut microbiota research in Africa. Additionally, results will guide future strategies to improve bee health in the continent, the development of potential probiotics to increase bee resistance against pest and pathogens, to improve bee nutrition, and increase resilience against climate change.