Fig. 2: Bacterial and fungal microbiota of the gut compartments in honeybees.

a Schematic representation of honeybee gut compartments (the crop, midgut, ileum, and rectum). Red circles and black rods indicate the relative distribution of total fungi and bacteria, respectively. b The abundance of the bacterial (black bars) and fungal (red bars) members in the honeybee gut compartments are indicated as ln-transformed number of bacterial cells (number of 16S rRNA gene copies measured are normalized for the number of 16S rRNA genes in a bacterial community, n = 4.7) and fungal cells (number of measured internal transcribed spacer [ITS] copies are normalized for the number of ITSs in a fungal community, n = 75.5). Significant differences among the bacterial and fungal cell abundance along gut tracts are indicated with capital and lower-case letters, respectively (Tukey’s multiple comparison test, p < 0.05), whereas the comparison among bacteria and fungi in each trait is indicated by an asterisk (*; t-test, p < 0.05). Abundance (ln-transformed) of Snodgrassella, Lactobacillus Firm-5, and Gilliamella in the different gut compartments are represented by shades of green and are expressed as the number of bacterial cells (number of 16S rRNA gene copies measured are normalized for the number of 16S rRNA gene in these phylotypes, n = 4). Significant differences among the above-mentioned bacterial species for each gut tract are indicated by an asterisk (*; ANOVA, p < 0.05). All the results are expressed per organ. Principal coordinates analysis (PCoA) showing the (c) bacterial and (g) fungal communities per each gut compartment, respectively. f Beta-diversity analysis of the other potential environmental bacteria portion. Samples were distributed following a “horseshoe shape” ordination (indicated by the arrow) in the space of the canonical analysis of principal coordinates (CAP). d, e Taxonomic affiliation of total (DNA) and active (cDNA) bacterial communities inhabiting the honeybee gut, respectively, along with (h) one for fungal communities (DNA). Abundance of bacterial taxa obtained from DNA are expressed as the number of reads normalized for the mean number of bacterial 16S rRNA genes and fungal ITSs available for each genus/class, respectively (for details, see “Material and methods”). b–d, f–h are referred to the gut compartments’ pools (each pool, n = 10) originating from Italian A. mellifera ligustica forager bees, whereas e is referred to the entire gut of Saudi Arabian A. mellifera jemenitica (n = 6). Compartmentalization of bacterial and fungal communities associated with Saudi Arabian forager bees is reported in Supplementary Fig. S5.