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Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region. Full article

The honey bee Apis mellifera is exposed to a variety of biotic and abiotic stressors, such as the highly prevalent microsporidian parasite Nosema (Vairimorpha) ceranae and neonicotinoid insecticides. Both can affect honey bee physiology and microbial gut communities, eventually reducing its lifespan. They can also have a combined effect on the insect’s survival. The use of bacterial probiotics has been proposed to improve honey bee health, but their beneficial effect remains an open question. In the present study, western honey bees were experimentally infected with N. ceranae spores, chronically exposed to the neonicotinoid thiamethoxam, and/or supplied daily with the homofermentative bacterium Pediococcus acidilactici MA18/5M thought to improve the honey bees’ tolerance to the parasite. Deep shotgun metagenomic sequencing allowed the response of the gut microbiota to be investigated with a taxonomic resolution at the species level. All treatments induced significant changes in honey bee gut bacterial communities. Nosema ceranae infection increased the abundance of Proteus mirabilis, Frischella perrara, and Gilliamella apicola and reduced the abundance of Bifidobacterium asteroides, Fructobacillus fructosus, and Lactobacillus spp. Supplementation with P. acidilactici overturned some of these alterations, bringing back the abundance of some altered species close to the relative abundance found in the controls. Surprisingly, the exposure to thiamethoxam also restored the relative abundance of some species modulated by N. ceranae. This study shows that stressors and probiotics may have an antagonistic impact on honey bee gut bacterial communities and that P. acidilactici may have a protective effect against the dysbiosis induced by an infection with N. ceranae. Full article

Gut microbiota plays important roles in many physiological processes of the host including digestion, protection, detoxification, and development of immune responses. The honey bee (Apis mellifera) has emerged as model for gut-microbiota host interaction studies due to its gut microbiota being highly conserved and having a simple composition. A key gap in this model is understanding how the microbiome differs regionally, including sampling from the tropics and in particular from Africa. The African region is important from the perspective of the native diversity of the bees, and differences in landscape and bee management. Here, we characterized the honey bee gut microbiota in sub-Saharan Africa using 16S rRNA amplicon sequencing. We confirm the presence of the core gut microbiota members and highlight different compositions of these communities across regions. We found that bees from the coastal regions harbor a higher relative abundance and diversity on core members. Additionally, we showed that Gilliamella, Snodgrassella, and Frischella dominate in all locations, and that altitude and humidity affect Gilliamella abundance. In contrast, we found that Lactobacillus was less common compared temperate regions of the world. This study is a first comprehensive characterization of the gut microbiota of honey bees from sub-Saharan Africa and underscores the need to study microbiome diversity in other indigenous bee species and regions. Full article