Genomic features of a bumble bee symbiont reflect its host environment

Here, we report the genome of one gammaproteobacterial member of the gut microbiota, for which we propose the name "Candidatus Schmidhempelia bombi," that was inadvertently sequenced alongside the genome of its host, the bumble bee, Bombus impatiens. This symbiont is a member of the recently described bacterial order Orbales, which has been collected from the guts of diverse insect species; however, "Ca. Schmidhempelia" has been identified exclusively with bumble bees. Metabolic reconstruction reveals that "Ca. Schmidhempelia" lacks many genes for a functioning NADH dehydrogenase I, all genes for the highoxygen cytochrome o, and most genes in the tricarboxylic acid (TCA) cycle. "Ca. Schmidhempelia" has retained NADH dehydrogenase II, the low-oxygen specific cytochrome bd, anaerobic nitrate respiration, mixed-acid fermentation pathways, and citrate fermentation, which may be important for survival in low-oxygen or anaerobic environments found in the bee hindgut. Additionally, a type 6 secretion system, a Flp pilus, and many antibiotic/multidrug transporters suggest complex interactions with its host and other gut commensals or pathogens. This genome has signatures of reduction (2.0 megabase pairs) and rearrangement, as previously observed for genomes of host-associated bacteria. A survey of wild and laboratory B. impatiens revealed that "Ca. Schmidhempelia" is present in 90% of individuals and, therefore, may provide benefits to its host.