Honey bees, bumble bees, and stingless bees have related gut microbial communities that are shaped by host evolutionary history.

Significance: Gut microbes are increasingly recognized as influential components of animal biology. Genomic, mechanistic, and evolutionary aspects of gut symbiont specialization remain understudied, however, largely due to the complexity of gut communities, especially in vertebrate systems. We show that the simple microbiota of eusocial bees exhibits host specificity and that coresident species in the bee gut possess complementary capabilities for energy metabolism, implying their occupancy in distinct ecological niches. In addition, coresidence in the gut of a host species results in horizontal exchange of genes between unrelated symbionts. Strains in different hosts have diverged, and honey bee symbionts are evolutionarily and functionally distinct from their bumble bee counterparts, indicating that gut symbionts may be critical elements in biological differences among bee species.

Gut microbial communities can greatly affect host health by modulating the host's immune system. For many important insects, however, the relationship between the gut microbiota and immune function remains poorly understood. Here, we test whether the gut microbial symbionts of the honey bee can induce expression of antimicrobial peptides (AMPs), a crucial component of insect innate immunity. We find that bees up-regulate gene expression of the AMPs apidaecin and hymenoptaecin in gut tissue when the microbiota is present. Using targeted proteomics, we detected apidaecin in both the gut lumen and the haemolymph; higher apidaecin concentrations were found in bees harbouring the normal gut microbiota than in bees lacking gut microbiota. In in vitro assays, cultured strains of the microbiota showed variable susceptibility to honey bee AMPs, although many seem to possess elevated resistance compared to Escherichia coli . In some trials, colonization by normal gut symbionts resulted in improved survivorship following injection with E. coli . Our results show that the native, non-pathogenic gut flora induces immune responses in the bee host. Such responses might be a host mechanism to regulate the microbiota, and could potentially benefit host health by priming the immune system against future pathogenic infections.

Gut-associated bacteria were isolated in axenic culture from the honey bee Apis mellifera and the bumble bees Bombus bimaculatus and B. vagans and are here placed in the novel genera and species Snodgrassella alvi gen. nov., sp. nov. and Gilliamella apicola gen. nov., sp. nov. Two strains from A. mellifera were characterized and are proposed as the type strains of Snodgrassella alvi (type strain wkB2^T = NCIMB 14803^T = ATCC BAA-2449^T = NRRL B-59751^T) and Gilliamella apicola (type strain wkB1^T = NCIMB 14804^T = ATCC BAA-2448^T), representing, respectively, phylotypes referred to as ‘Betaproteobacteria’ and ‘Gammaproteobacteria-1’/‘Gamma-1’ in earlier publications. These strains grew optimally under microaerophilic conditions, and did not grow readily under a normal atmosphere. The predominant fatty acids in both strains were palmitic acid (C_16 : 0) and cis-vaccenic acid (C_18 : 1ω7c and/or C_18 : 1ω6c), and both strains had ubiquinone-8 as their major respiratory quinone. The DNA G+C contents were 41.3 and 33.6 mol% for wkB2^T and wkB1^T, respectively. The Snodgrassella alvi strains from honey bees and bumble bees formed a novel clade within the family Neisseriaceae of the Betaproteobacteria , showing about 94 % 16S rRNA gene sequence identity to their closest relatives, species of Stenoxybacter , Alysiella and Kingella . The Gilliamella apicola strains showed the highest 16S rRNA gene sequence identity to Orbus hercynius CN3^T (93.9 %) and several sequences from uncultured insect-associated bacteria. Phylogenetic reconstruction using conserved, single-copy amino acid sequences showed Gilliamella apicola as sister to the order ‘Enterobacteriales’ of the Gammaproteobacteria . Given its large sequence divergence from and basal position to the well-established order ‘Enterobacteriales’, we propose to place the clade encompassing Gilliamella apicola and O. hercynius in a new family and order, Orbaceae fam. nov. and Orbales ord. nov.

The regulated expansion of membrane contact sites, which mediate the nonvesicular exchange of lipids between organelles, requires the recruitment of additional contact site proteins. Yeast Vps13 dynamically localizes to membrane contacts that connect the ER, mitochondria, endosomes, and vacuoles and is recruited to the prospore membrane in meiosis, but its targeting mechanism is unclear. In this study, we identify the sorting nexin Ypt35 as a novel adaptor that recruits Vps13 to endosomal and vacuolar membranes. We characterize an interaction motif in the Ypt35 N terminus and identify related motifs in the prospore membrane adaptor Spo71 and the mitochondrial membrane protein Mcp1. We find that Mcp1 is a mitochondrial adaptor for Vps13, and the Vps13–Mcp1 interaction, but not Ypt35, is required when ER-mitochondria contacts are lost. All three adaptors compete for binding to a conserved six-repeat region of Vps13 implicated in human disease. Our results support a competition-based model for regulating Vps13 localization at cellular membranes.