Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees

Abstract

Social bees harbor conserved gut microbiota that may have been acquired in a common ancestor of social bees and subsequently co-diversified with their hosts. However, most of this knowledge is based on studies on the gut microbiota of honey bees and bumble bees. Much less is known about the gut microbiota of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiota presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumble bee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host indicating that the evolution of the social bee gut microbiota was not driven by strict co-diversification, but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumble bee microbiota, we find substantial genomic divergence among strains of stingless bee gut bacteria suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota, and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota.

Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota

“…The accessory system including relaxases (MOBs)(44) were more variable across genomes with 5 MOB families (MOB B , MOB C , MOB Q , MOB T , MOB V ) detected (Figure S5). Hence, we classified these as conjugation system proteins (CONJ)(28).…”

“…The mixture was incubated for 30 min at 37°C with gentle agitation. After this, the volume was brought up to 500 μl with Gram-positive lysis buffer and the mixture was transferred to screw cap tubes in tubes containing 200 mg of 0.1-mm acid-washed zirconia beads and homogenized using a FastPrep-25 5G instrument (2 rounds of 30 s with the power set to 6), as previously described(28). This was followed by centrifugation at maximum speed for 5 minutes at room temperature.…”

“…Next, we predicted metabolic functions and macromolecular machineries using a custom rule-based based pipeline that included the GapMind, dbCAN and MacSysFinder tools (28)(29)(30)(31)(32) to comprehensively investigate the common catabolic and biosynthetic pathways, secretion systems, bacterial competence and carbohydrate-active enzymes (CAZymes)(33)(Figure 3, Table S6). The most prevalent mechanism for carbon catabolism in all streptococci including the lung isolates was the Embden-Meyerhof-Parnas (EMP) pathway.…”

“…Predictions of key metabolic pathways and macromolecular structures were performed by using a custom genome profiler as previously described (28). A set of rules were applied to conclude the presence and completeness of predicted pathways.…”

Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees

“…A comparison of the 16S rRNA sequence of strain LMG 33000 T with the GenBank NCBI database (December 2023) revealed a 99.65 % identity with the 16S rRNA sequence of strain GYUN-606 [accession number OL310493.1 (no isolation source was provided), unpublished data]. Additionally, 98.92-99.21 % identity was observed with sixteen 16S rRNA sequences of uncultivated bacteria detected in Diadasia opuntiae bees (accession numbers: HM112739.1, HM112665.1, HM112506.1, HM112762.1, HM112586.1, HM112779.1, HM112647.1, HM112535.1, HM112533.1, HM112743.1, HM112566.1, HM112758.1, HM112770.1, HM112680.1, HM112667.1 and HM112556.1) [38] and 96.71 % identity was observed with the 16S rRNA gene sequence of strain ESL0723 isolated from a Melipona fuliginosa stingless bee (accession number: CP113928.1) [39].…”