T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plantbeneficial Pseudomonas protegens
Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.
Bacteria that engage in long-standing associations with particular hosts are expected to evolve host-specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep-branching host-specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate-related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate-related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.
23Bacteria that engage in longstanding associations with particular hosts are expected 24 to evolve host-specific adaptations that limit their capacity to thrive in other 25 environments. Consistent with this, many gut symbionts seem to have a limited host 26 range, based on community profiling and phylogenomics. However, few studies have 27 experimentally investigated host specialization of gut symbionts and underlying 28 mechanisms have largely remained elusive. Here, we studied host specialization of a 29 dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 30 strains isolated from honey bees and bumble bees separate into deep-branching host-31 specific phylogenetic lineages. Despite their divergent evolution, colonization 32 experiments show that bumble bee strains are capable of colonizing the honey bee 33 gut. However, they were less successful than honey bee strains, and competition with 34 honey bee strains completely abolished their colonization. In contrast honey bee 35 strains of divergent phylogenetic lineages were able to coexist within individual bees. 36This suggests that both host selection and interbacterial competition play important 37 roles for host specialization. Using comparative genomics of 27 Firm5 isolates, we 38 found that the genomes of honey bee strains harbor more carbohydrate-related 39 functions than bumble bee strains, possibly providing a competitive advantage in the 40 honey bee gut. Remarkably, most of the genes encoding carbohydrate-related 41 functions were not conserved among the honey bee strains, which suggests that 42 honey bees can support a metabolically more diverse community of Firm5 strains 43 than bumble bees. These findings advance our understanding of genomic changes 44 underlying host specialization. 45
Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, but not in simple sugars independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding symbiotic associations, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.
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