Niche partitioning facilitates coexistence of closely related honey bee gut bacteria.

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.

Microbes colonize nearly every environment on Earth, from the ocean and soil to the inner and outer surfaces of animals, such as the gut or skin. They form communities that are usually made up of a diverse range of bacteria, often containing closely related species ­ a key factor for a successful community. But closely related bacteria can battle for the same resources, so it is unclear how they manage to live alongside each other without competing against one another. While diet is thought to play a key role in enabling closely related bacterial species to co-exist in the gut of an animal, experimental evidence is lacking, due to the difficulty in replicating these systems in the laboratory. One strategy for investigating microbial communities is using honeybees. A major dietary source for honeybees is pollen, which can also be applied in the laboratory to grow diverse types of bacteria found in the honeybee gut. In addition, scientists can generate bees that lack microbial communities in the gut, allowing them to add specific types of bacteria to study their impact. Brochet et al. used this approach with Western honeybees to assess whether diet enables closely related bacteria to live alongside one another in the gut. First, they colonized bees that lacked gut microbes with four closely related bacteria of the genus Lactobacillus, alone or together, and fed the bees either sugar water or sugar water and pollen. After five days, the gut bacteria were analysed. This revealed that bees fed on sugar water only had one dominant Lactobacillus species present in their gut, while bees fed with additional pollen harboured all four Lactobacillus species. Further analysis of these four bacterial species revealed that each of them activates distinct genes when grown on pollen, allowing the different species to consume specific nutrients from broken down pollen. These findings show that closely related bacteria can coexist in the gut by sharing the different nutrients provided in the diet of the host. Consequently, differences in dietary intake in honeybees and other animals may affect the diversity of gut bacteria, and potentially the health of an animal.

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.

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.

T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens.

Pseudomonas protegens are multi-talented plant-colonizing bacteria that suppress plant pathogens and stimulate plant defenses. In addition, they are capable of invading and killing agriculturally important plant pest insects that makes them promising candidates for biocontrol applications. Here we assessed the role of type VI secretion system (T6SS) components of type strain CHA0 during interaction with larvae of the cabbage pest Pieris brassicae. We show that the T6SS core apparatus and two VgrG modules, encompassing the respective T6SS spikes (VgrG1a and VgrG1b) and associated effectors (RhsA and Ghh1), contribute significantly to insect pathogenicity of P. protegens in oral infection assays but not when bacteria are injected directly into the hemolymph. Monitoring of the colonization levels of P. protegens in the gut, hemolymph, and excrements of the insect larvae revealed that the invader relies on T6SS and VgrG1a module function to promote hemocoel invasion. A 16S metagenomic analysis demonstrated that T6SS-supported invasion by P. protegens induces significant changes in the insect gut microbiome affecting notably Enterobacteriaceae, a dominant group of the commensal gut bacteria. Our study supports the concept that pathogens deploy T6SS-based strategies to disrupt the commensal microbiota in order to promote host colonization and pathogenesis.