Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species

• Published in: Current biology Vol. 30; no. 13; pp. 2520 - 2531.e7
• Main Authors: Ellegaard, Kirsten M., Suenami, Shota, Miyazaki, Ryo, Engel, Philipp
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 06.07.2020; Cell Press
• Subjects: Apis cerana; Apis mellifera; gut microbiota; honey bee; host associated; metagenomics; pan-genome; species; strain-level diversity; Apis mellifera; honey bee; species; metagenomics; pan-genome; Apis cerana; gut microbiota; host associated; strain-level diversity
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2020.04.070

Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities. [Display omitted] •Metagenomics reveals differences in gut microbiota diversity beyond the 16S rRNA gene•Apis cerana and Apis mellifera harbor distinct species and strains in their gut•Diversity is much higher in A. mellifera per individual bee and within colonies•Major differences in functions are related to polysaccharide degradation Bacteria have highly flexible gene content; functions of bacterial communities therefore depend on their strain-level composition. Using metagenomics, Ellegaard et al. find major differences in composition and diversity in the gut microbiota of two related honey bees, raising new questions on function and evolution of host-associated bacteria.