The honeybee microbiota and its impact on health and disease

Fecal transplant allows transmission of the gut microbiota in honey bees

The study of the fecal microbiota is crucial for unraveling the pathways through which gut symbionts are acquired and transmitted. While stable gut microbial communities are essential for honey bee health, their modes of acquisition and transmission are yet to be confirmed. The gut of honey bees is colonized by symbiotic bacteria within 5 days after emergence from their wax cells as adults. Few studies have suggested that bees could be colonized in part via contact with fecal matter in the hive. However, the composition of the fecal microbiota is still unknown. It is particularly unclear whether all bacterial species can be found viable in the feces and can therefore be transmitted to newborn nestmates. Using 16S rRNA gene amplicon sequencing, we revealed that the composition of the honey bee fecal microbiota is strikingly similar to the microbiota of entire guts. We found that fecal transplantation resulted in gut microbial communities similar to those obtained from feeding gut homogenates. Our study shows that fecal sampling and transplantation are viable tools for the non-invasive analysis of bacterial community composition and host-microbe interactions. It also implies that contact of young bees with fecal matter in the hive is a plausible route for gut microbiota acquisition.

IMPORTANCE

Honey bees are crucial pollinators for many crops and wildflowers. They are also powerful models for studying microbiome-host interactions. However, current methods rely on gut tissue disruption to analyze microbiota composition and use gut homogenates to inoculate microbiota-deprived bees. Here, we provide two new and non-invasive approaches that will open doors to longitudinal studies: fecal sampling and transplantation. Furthermore, our findings provide insights into gut microbiota transmission in social insects by showing that ingestion of fecal matter can result in gut microbiota acquisition.

Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera)

Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.

One-step genome engineering in bee gut bacterial symbionts

Mechanistic understanding of interactions in many host-microbe systems, including the honey bee microbiome, is limited by a lack of easy-to-use genome engineering approaches. To this end, we demonstrate a one-step genome engineering approach for making gene deletions and insertions in the chromosomes of honey bee gut bacterial symbionts. Electroporation of linear or non-replicating plasmid DNA containing an antibiotic resistance cassette flanked by regions with homology to a symbiont genome reliably results in chromosomal integration. This lightweight approach does not require expressing any exogenous recombination machinery. The high concentrations of large DNAs with long homology regions needed to make the process efficient can be readily produced using modern DNA synthesis and assembly methods. We use this approach to knock out genes, including genes involved in biofilm formation, and insert fluorescent protein genes into the chromosome of the betaproteobacterial bee gut symbiont Snodgrassella alvi. We are also able to engineer the genomes of multiple strains of S. alvi and another species, Snodgrassella communis, which is found in the bumble bee gut microbiome. Finally, we use the same method to engineer the chromosome of another bee symbiont, Bartonella apis, which is an alphaproteobacterium. As expected, gene knockout in S. alvi using this approach is recA-dependent, suggesting that this straightforward procedure can be applied to other microbes that lack convenient genome engineering methods.

IMPORTANCE

Honey bees are ecologically and economically important crop pollinators with bacterial gut symbionts that influence their health. Microbiome-based strategies for studying or improving bee health have utilized wild-type or plasmid-engineered bacteria. We demonstrate that a straightforward, single-step method can be used to insert cassettes and replace genes in the chromosomes of multiple bee gut bacteria. This method can be used for investigating the mechanisms of host-microbe interactions in the bee gut community and stably engineering symbionts that benefit pollinator health.

Gut microbiota influences onset of foraging-related behavior but not physiological hallmarks of division of labor in honeybees

Gut microbes can impact cognition and behavior, but whether they regulate the division of labor in animal societies is unknown. We addressed this question using honeybees since they exhibit division of labor between nurses and foragers and because their gut microbiota can be manipulated. Using automated behavioral tracking and controlling for co-housing effects, we show that gut microbes influence the age at which bees start expressing foraging-like behaviors in the laboratory but have no effects on the time spent in a foraging arena and number of foraging trips. Moreover, the gut microbiota did not influence hallmarks of behavioral maturation such as body weight, cuticular hydrocarbon profile, hypopharyngeal gland size, gene expression, and the proportion of bees maturing into foragers. Overall, this study shows that the honeybee gut microbiota plays a role in controlling the onset of foraging-related behavior without permanent consequences on colony-level division of labor and several physiological hallmarks of behavioral maturation.

IMPORTANCE

The honeybee is emerging as a model system for studying gut microbiota-host interactions. Previous studies reported gut microbiota effects on multiple worker bee phenotypes, all of which change during behavioral maturation-the transition from nursing to foraging. We tested whether the documented effects may stem from an effect of the microbiota on behavioral maturation. The gut microbiota only subtly affected maturation: it accelerated the onset of foraging without affecting the overall proportion of foragers or their average output. We also found no effect of the microbiota on host weight, cuticular hydrocarbon (CHC) profile, hypopharyngeal gland size, and the expression of behavioral maturation-related genes. These results are inconsistent with previous studies reporting effects of the gut microbiota on bee weight and CHC profile. Our experiments revealed that co-housed bees tend to converge in behavior and physiology, suggesting that spurious associations may emerge when rearing environments are not replicated sufficiently or accounted for analytically.

Symbiont-mediated antisense RNA delivery controls Nosema ceranae infections in Apis mellifera

Nosema ceranae is a main parasite for honeybees (Apis mellifera) which causes colony collapse in spring. Effective management of N. ceranae infections in bees is imperative for beekeepers. RNA interference (RNAi) has been proven a promising method to control bee pathogens, including IAPV, Varroa destructor, and Nosema. Most studies in this field focused on oral inoculation of double-stranded RNA (dsRNA). We developed an easier method with long-term RNAi effects by engineering the bee symbiont, Bacillus subtilis, to deliver single-stranded antisense RNA (asRNA) in the bee guts, targeting N. ceranae genes. We interfered with the expression of a spore wall protein (SWP12) and a polar tube protein (PTP3) of N. ceranae, resulting in a 60.5% increase in bee lifespan and a 72.7% decrease in Nosema spore load. Our research introduced a novel approach to bee parasite control: B. subtilis-mediated asRNA delivery. Our strategy simplifies the procedure of RNAi, presenting a more efficient mechanism with both prophylactic and therapeutic effects on N. ceranae-infected bees.

Targeted viromes and total metagenomes capture distinct components of bee gut phage communities

BACKGROUND

Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.

RESULTS

We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.

CONCLUSIONS

Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.

Changes in bumblebee queen gut microbiotas during and after overwintering diapause

Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post-diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees.

Genomic investigations of diverse corbiculate bee gut-associated Gilliamella reveal conserved pathways for energy metabolism, with diverse and variable energy sources

Gilliamella is a genus of bacteria commonly found as symbionts of corbiculate bees. Research into energy metabolism by this genus has predominantly been done through in vivo and in vitro experiments focused on the type species Gilliamella apicola. This study examined 95 publicly available genomes representing at least 18 Gilliamella species isolated predominantly from the hindgut of corbiculate bees. Energy metabolism pathways were found to be highly conserved across not only the Gilliamella but also other members of the family Orbaceae. Evidence suggests Gilliamella are capable of fermentation of both fumarate and pyruvate. Fermentation of the former produces succinate. Fermentation of the latter can produce acetate, ethanol, formate, and both isoforms of lactate for all Gilliamella and acetoin for some G. apicola strains. According to genomic evidence examined, all Gilliamella are only capable of respiration under microoxic conditions, while higher oxygen conditions likely inhibits respiration. Evidence suggests that the glycolysis and pentose phosphate pathways are essential mechanisms for the metabolism of energy sources, with the TCA cycle playing little to no role in energy metabolism for all Gilliamella species. Uptake of energy sources, i.e. sugars and derivatives, likely relies predominantly on the phosphoenol-pyruvate-dependent phosphotransferase system. Differences in the utilized energy sources may confer fitness advantages associated with specific host species.

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome

BACKGROUND

In this study, a probiotic mixture (Honeybeeotic) consisting of seven bacterial strains isolated from a unique population of honeybees (Apis mellifera ligustica) was used. That honeybee population was located in the Roti Abbey locality of the Marche Region in Italy, an area isolated from human activities, and genetic contamination from other honeybee populations. The aim was to investigate the effects of this probiotic mixture on the innate immunity and intestinal microbiome of healthy common honeybees in two hives of the same apiary. Hive A received a diet of 50% glucose syrup, while hive B received the same syrup supplemented with the probiotics, both administered daily for 1 month. To determine whether the probiotic altered the immune response, phenoloxidase activity and hemolymph cellular subtype count were investigated. Additionally, metagenomic approaches were used to analyze the effects on gut microbiota composition and function, considering the critical role the gut microbiota plays in modulating host physiology.

RESULTS

The results revealed differences in hemocyte populations between the two hives, as hive A exhibited higher counts of oenocytoids and granulocytes. These findings indicated that the dietary supplementation with the probiotic mixture was safe and well-tolerated. Furthermore, phenoloxidase activity significantly decreased in hive B (1.75 ± 0.19 U/mg) compared to hive A (3.62 ± 0.44 U/mg, p < 0.005), suggesting an improved state of well-being in the honeybees, as they did not require activation of immune defense mechanisms. Regarding the microbiome composition, the probiotic modulated the gut microbiota in hive B compared to the control, retaining core microbiota components while causing both positive and negative variations. Notably, several genes, particularly KEGG genes involved in amino acid metabolism, carbohydrate metabolism, and branched-chain amino acid (BCAA) transport, were more abundant in the probiotic-fed group, suggesting an effective nutritional supplement for the host.

CONCLUSIONS

This study advocated that feeding with this probiotic mixture induces beneficial immunological effects and promoted a balanced gut microbiota with enhanced metabolic activities related to digestion. The use of highly selected probiotics was shown to contribute to the overall well-being of the honeybees, improving their immune response and gut health.

Engineered fungus containing a caterpillar gene kills insects rapidly by disrupting their ecto- and endo-microbiomes

Similar to the physiological importance of gut microbiomes, recent works have shown that insect ectomicrobiotas can mediate defensive colonization resistance against fungal parasites that infect via cuticle penetration. Here we show that engineering the entomopathogenic fungus Metarhizium robertsii with a potent antibacterial moricin gene from silkworms substantially enhances the ability of the fungus to kill mosquitos, locusts, and two Drosophila species. Further use of Drosophila melanogaster as an infection model, quantitative microbiome analysis reveals that engineered strains designed to suppress insect cuticular bacteria additionally disrupt gut microbiomes. An overgrowth of harmful bacteria such as the opportunistic pathogens of Providencia species is detected that can accelerate insect death. In support, quantitative analysis of antimicrobial genes in fly fat bodies and guts indicates that topical fungal infections result in the compromise of intestinal immune responses. In addition to providing an innovative strategy for improving the potency of mycoinsecticides, our data solidify the importance of both the ecto- and endo-microbiomes in maintaining insect wellbeing.

Temporal microbiome changes in axolotl limb regeneration: Stage-specific restructuring of bacterial and fungal communities with a Flavobacterium bloom during blastema proliferation

The intricate relationship between regeneration and microbiota has recently gained attention, spanning diverse model organisms. Axolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite its significance, a noticeable gap exists in understanding the interplay between axolotl regeneration and its microbiome. Here, we analyse in depth bacterial 16S rRNA amplicon dataset that we reported before as data resource and profile fungal community by sequencing ITS amplicons at the critical stages of limb regeneration (0-1-4-7-30-60 days post amputation, 'dpa'). Results reveal a decline in richness and evenness in the course of limb regeneration, with bacterial community richness recovering beyond 30 dpa unlike fungi community. Beta diversity analysis reveals precise restructuring of the bacterial community along the three phases of limb regeneration, contrasting with less congruent changes in the fungal community. Temporal dynamics of the bacterial community highlight prevalent anaerobic bacteria in initiation phase and Flavobacterium bloom in the early phase correlating with limb blastema proliferation. Predicted functional analysis mirrors these shifts, emphasising a transition from amino acid metabolism to lipid metabolism control. Fungal communities shift from Blastomycota to Ascomycota dominance in the late regeneration stage. Our findings provide ecologically relevant insights into stage specific role of microbiome contributions to axolotl limb regeneration.

Early-Life Sublethal Exposure to Thiacloprid Alters Adult Honeybee Gut Microbiota

Thiacloprid, a neonicotinoid pesticide, is known to affect the gut microbiome of honeybees, yet studies often focus on immediate alternations during exposure, overlooking long-term microbiological impacts post-exposure. This study investigates the influences of sublethal thiacloprid administered during the larval developmental stage of honeybees on physiological changes and gut microbiota of adult honeybees. We found that thiacloprid exposure increased mortality and sugar intake in emerged honeybees. Using 16S rDNA sequencing, we analyzed intestinal microbial diversity of honeybees at one and six days post-emergence. Our findings reveal a significant but transient disruption in gut microbiota on day 1, with recovery from dysbiosis by day 6. This study emphasizes the importance of evaluating chronic sublethal exposure risks of thiacloprid to protect honeybee health.

Temporospatial dynamics and host specificity of honeybee gut bacteria

Honeybees are important pollinators worldwide, with their gut microbiota playing a crucial role in maintaining their health. The gut bacteria of honeybees consist of primarily five core lineages that are spread through social interactions. Previous studies have provided a basic understanding of the composition and function of the honeybee gut microbiota, with recent advancements focusing on analyzing diversity at the strain level and changes in bacterial functional genes. Research on honeybee gut microbiota across different regions globally has provided insights into microbial ecology. Additionally, recent findings have shed light on the mechanisms of host specificity of honeybee gut bacteria. This review explores the temporospatial dynamics in honeybee gut microbiota, discussing the reasons and mechanisms behind these fluctuations. This synopsis provides insights into host-microbe interactions and is invaluable for honeybee health.

Microbiomes, diet flexibility, and the spread of a beetle parasite of honey bees

Invasive pests may disturb and destructively reformat the local ecosystem. The small hive beetle (SHB), Aethina tumida, originated in Africa and has expanded to America, Australia, Europe, and Asia. A key factor facilitating its fast global expansion is its ability to subsist on diverse food inside and outside honey bee colonies. SHBs feed on various plant fruits and exudates in the environment while searching for bee hives. After sneaking into a bee hive, they switch their diet to honey, pollen, and bee larvae. How SHBs survive on such a broad range of food remains unclear. In this study, we simulated the outside and within hive stages by providing banana and hive resources and quantified the SHB associated microbes adjusted by the diet. We found that SHBs fed on bananas were colonized by microbes coding more carbohydrate-active enzymes and a higher alpha diversity than communities from SHBs feeding on hive products or those collected directly from bee hives. SHBs fed on bananas and those collected from the hive showed high symbiont variance, indicated by the beta diversity. Surprisingly, we found the honey bee core symbiont Snodgrassella alvi in the guts of SHBs collected in bee hives. To determine the role of S. alvi in SHB biology, we inoculated SHBs with a genetically tagged culture of S. alvi, showing that this symbiont is a likely transient of SHBs. In contrast, the fungus Kodamaea ohmeri is the primary commensal of SHBs. Diet-based microbiome shifts are likely to play a key role in the spread and success of SHBs.

Pathogen- and host-directed pharmacologic strategies for control of Vairimorpha (Nosema) spp. infection in honey bees

Microsporidia are obligate intracellular parasites of the Fungal Kingdom that cause widespread infections in nature, with important effects on invertebrates involved in food production systems. The two microsporidian species Vairimorpha (Nosema) ceranae (and the less common Vairimorpha (Nosema) apis) can cause individual disease in honey bees and contribute to colony collapse. The efficacy, safety, and availability of fumagillin, the only drug currently approved to treat microsporidia infection in bees, is uncertain. In this review, we will discuss some of the most promising alternative strategies for the mitigation of Vairimorpha spp. with an emphasis on infection by V. ceranae, now the dominant species infecting bees. We will focus on pharmacologic interventions where the mechanism of action is known and examine both pathogen-directed and host-directed approaches. As limiting toxicity to host cells has been especially emphasized in treating bees that are already facing numerous stressors, strategies that disrupt pathogen-specific targets may be especially advantageous. Therefore, efforts to increase the knowledge and tools for facilitating the discovery of such targets and pharmacologic agents directed against them should be prioritized.

Enhancing knowledge of chemical exposures and fate in honey bee hives: Insights from colony structure and interactions

Honey bees are unintentionally exposed to a wide range of chemicals through various routes in their natural environment, yet research on the cumulative effects of multi-chemical and sublethal exposures on important caste members, including the queen bee and brood, is still in its infancy. The hive's social structure and food-sharing (trophallaxis) practices are important aspects to consider when identifying primary and secondary exposure pathways for residential hive members and possible chemical reservoirs within the colony. Secondary exposures may also occur through chemical transfer (maternal offloading) to the brood and by contact through possible chemical diffusion from wax cells to all hive members. The lack of research on peer-to-peer exposures to contaminants and their metabolites may be in part due to the limitations in sensitive analytical techniques for monitoring chemical fate and dispersion. Combined application of automated honey bee monitoring and modern chemical trace analysis techniques could offer rapid progress in quantifying chemical transfer and accumulation within the hive environment and developing effective mitigation strategies for toxic chemical co-exposures. To enhance the understanding of chemical fate and toxicity within the entire colony, it is crucial to consider both the intricate interactions among hive members and the potential synergistic effects arising from combinations of chemical and their metabolites.