Identification, characterization and phylogenetic analysis of gut microbiota of the honey bee, Apis mellifera L., from Saudi Arabia

The honey bee, Apis mellifera is regarded one of the most beneficial creatures on our planet. The impact of gut
microbiota on insect host is lasting beyond the symbiotic interaction. Therefore, the current work was designed to identify
and characterize the gut microbiota of A. mellifera collected from beekeeping farm at Sakaka city, Aljouf, Saudi Arabia.
Bees were sampled from five distinct colonies (20 bees/ colony), disinfected, the whole guts were homogenized under
sterile conditions. Homogenates were cultured on different media, incubated and morphologically differentiated. A single
colony of each morphotype was propagated and purified. Phenotypic and biochemical and molecular characterization of
all purified colonies were carried out on the bases of 16S rRNA and 18S rRNA genes. Sequence and phylogeny were
analyzed. Combining morphological, biochemical and molecular data, species composition of the gut microbiota was
determined. Out of 12 bacilli bacteria, 6 aerobic and 6 facultative anaerobic, 7 non-sporulating and 5 endospore-forming
bacteria were identified. One yeast-like facultative anaerobic, endospore-forming fungus was recognized. Biochemical
tests confirmed that the gut bacteria are capable of producing commercial enzymes and biologically active substances,
as well as they have ability to ferment carbohydrates and acidify the gut media. Some on these bacteria are revealed to
be waterborne or foodborne. We identified 12 bacterial species belonging to 8 genera. Out of the 8 genera, 6 genera
belong to the phylum Proteobacteria (75.0%), and 2 genera belong to the phylum Firmicutes (25.0%). In addition, one
fungal species belonging to the phylum Ascomycota and family Saccharomycetaceae. Eleven bacteria and one fungus
were, successfully, identified at species level. One bacteria was identified at its genus level. Four species were indicated
to be novel strains or subspecies. Phylogentic analyses revealed both overlap and divergence of genera. Identification of
the species was methodology-dependent. Species constituting gut microbiota community may function to generate bioproducts which ultimately enable the honey bees to tolerate climatic and infectious stresses. Our findings provide a basic
step for investigating the specific impacts of the gut microbiota on A. mellifera.