Genomics and host specialization of honey bee and bumble bee gut symbionts

Abstract

Gilliamella apicola and Snodgrassella alvi are dominant members of the honey bee (Apis spp.) and bumble bee (Bombus spp.) gut microbiota. We generated complete genomes of the type strains G. apicola wkB1(T) and S. alvi wkB2(T) (isolated from Apis), as well as draft genomes for four other strains from Bombus. G. apicola and S. alvi were found to occupy very different metabolic niches: The former is a saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids. Together, they may form a syntrophic network for partitioning of metabolic resources. Both species possessed numerous genes [type 6 secretion systems, repeats in toxin (RTX) toxins, RHS proteins, adhesins, and type IV pili] that likely mediate cell-cell interactions and gut colonization. Variation in these genes could account for the host fidelity of strains observed in previous phylogenetic studies. Here, we also show the first experimental evidence, to our knowledge, for this specificity in vivo: Strains of S. alvi were able to colonize their native bee host but not bees of another genus. Consistent with specific, long-term host association, comparative genomic analysis revealed a deep divergence and little or no gene flow between Apis and Bombus gut symbionts. However, within a host type (Apis or Bombus), we detected signs of horizontal gene transfer between G. apicola and S. alvi, demonstrating the importance of the broader gut community in shaping the evolution of any one member. Our results show that host specificity is likely driven by multiple factors, including direct host-microbe interactions, microbe-microbe interactions, and social transmission.

Keywords: bacterial genomics; strain variation; symbiosis.

Fig. 1.

Schematics and statistics of sequenced G. apicola and S. alvi genomes. Protein-coding regions of wkB1^T and wkB2^T are plotted clockwise in dark red (+ strand) and light red (− strand). The locations of orthologous proteins in the Bombus-derived strains are shown in green and blue. G+C, guanine and cytosine.

Fig. 2.

(A) Numbers of shared orthologs and unique genes in G. apicola and S. alvi genomes. (B) Gene content as categorized by the Kyoto Encyclopedia of Genes and Genomes (KEGG) subsystem. Within genomes, ∼50% of genes were not assigned to a category and ∼28–38% of predicted genes were annotated as hypothetical or putative; these are not shown here. (C) Pairwise dS values of all orthologs, plotted against each other (e.g., the ∼1:1 relationship of red points shows that genes are equally divergent between the Apis symbiont and either of the Bombus symbionts). dS values extend from 0 to 4 on all axes.

Fig. 3.

(A) Location of the gut microbial community. A bee with its gut removed shows the ileum and rectum, where most bacteria reside. An ileum cross-section shows the position of S. alvi (blue hatching) adjacent to the gut wall and G. apicola (red) toward the lumen (illustration based on ref. 16). (B) Metabolic pathways and interactions predicted from G. apicola and S. alvi genomes. Missing pathways are dashed, whereas pathways inferred to be complete are solid. Green lines denote possible interspecies interactions. Strains vary in the presence or absence of certain features, as indicated by circular icons. cyt. bo, cytochrome bo complex; FDH, formate dehydrogenase; GlcNAc, N-acetylglucosamine; NDH-1, NADH dehydrogenase I; T1SS, type 1 secretion system; YadA, Yersinia adhesin. *Only in wkB2^T. ^†Not all may be synthesized. A more detailed analysis of symbiont metabolism is included in SI Results and Figs. S1–S3.

Fig. 4.

Host specificity of S. alvi strains, as shown by colonization efficiency. Gut bacterial load (CFU) was counted 5 d after oral inoculation. The sample size for each treatment is ≥12. Means, 95% confidence interval of means, and the results of Mann–Whitney U tests (*P < 0.0001) are shown. In competition treatments, strain wkB2^T was coinoculated with strain wkB12 or wkB29 (1:10 ratio in A. mellifera, 10:1 ratio in B. impatiens). Percentage indicates average wkB2^T prevalence in competitions.

Fig. 5.

HGT in the bee gut microbiota. (Left) Number of shared genes of high identity between G. apicola and S. alvi strains is shown. Strains within the same host share more genes. (Right) Among transferred genes, several classes are overrepresented, such as RHS and restriction modification (RM) genes.