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Background  In previous studies, the gram-positive firmicute genus  Paenibacillus  was found with significant abundances in nests of wild solitary bees.  Paenibacillus larvae  is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either secondary invaders of European foulbrood or considered a threat to honey bees. We thus investigated whether  Paenibacillus  is a common bacterium associated with various wild bees and hence poses a latent threat to honey bees visiting the same flowers.    Results  We collected 202 samples from 82 individuals or nests of 13 bee species at the same location and screened each for  Paenibacillus  using high-throughput sequencing-based 16S metabarcoding. We then isolated the identified strain  Paenibacillus  MBD-MB06 from a solitary bee nest and sequenced its genome. We did find conserved toxin genes and such encoding for chitin-binding proteins, yet none specifically related to foulbrood virulence or chitinases. Phylogenomic analysis revealed a closer relationship to strains of root-associated  Paenibacillus  rather than strains causing foulbrood or other accompanying diseases. We found anti-microbial evidence within the genome, confirmed by experimental bioassays with strong growth inhibition of selected fungi as well as gram-positive and gram-negative bacteria.    Conclusions  The isolated wild bee associate  Paenibacillus  MBD-MB06 is a common, but irregularly occurring part of wild bee microbiomes, present on adult body surfaces and guts and within nests especially in megachilids. It was phylogenetically and functionally distinct from harmful members causing honey bee colony diseases, although it shared few conserved proteins putatively toxic to insects that might indicate ancestral predisposition for the evolution of insect pathogens within the group. By contrast, our strain showed anti-microbial capabilities and the genome further indicates abilities for chitin-binding and biofilm-forming, suggesting it is likely a useful associate to avoid fungal penetration of the bee cuticula and a beneficial inhabitant of nests to repress fungal threats in humid and nutrient-rich environments of wild bee nests.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0614-1) contains supplementary material, which is available to authorized users.

Wild bees and their nests host Paenibacillus bacteria with functional potential of avail