The role of the gut microbiome in health and disease of adult honey bee workers

High abundance of lactobacilli in the gut microbiome of honey bees during winter

Honey bee gut microbiota play specific roles in promoting host growth and physiology by regulating the immune system, behavior, metabolism, and neurological processes. While the gut microbiota of honey bee queens, workers, and larvae has been extensively studied, less is known about the composition of gut microbiota in the winter worker bees. This study investigates the dynamics of the gut microbiota in overwintering adult worker bees, focusing on two commercial bee strains: Bolton™ bees and Mann Lake™ bees. These Apis mellifera strains were investigated under different storage conditions (indoor storage at 6 °C and outdoor storage in natural conditions) during the winter months (October, November, and December). Utilizing 16S rRNA gene amplicon sequencing, we characterized the microbial composition of the whole gut. We observed the Lactobacilli dominated in all the overwintering honey bee guts with a significantly higher abundance of unclassified Lactobacillus species in November, while Lactobacillus apis showed significantly higher abundance in October. Bolton bees exhibited significantly higher abundance levels of Bartonella (denoted as uncultured) and Bifidobacterium, along with an unexpected presence of Wolbachia. In contrast, Mann Lake bees demonstrated an increased abundance of Commensalibacter. Our results suggest that Shannon diversity is influenced by the month rather than by the bee strain or storage conditions. We also found significant differences in Bray Curtis diversity index by month. Overall, taxonomical abundance was not affected by whether the hives were stored outside or in constant temperature indoor storage. However, various bacterial species showed differences in abundance across different months, with slight variations observed between bee strains. Given the potential benefits of the honey bee gut microbiome for health and nutrition, our data suggests that the genus Lactobacillus may play a significant role in bee health during winter and overwintering storage.

The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure

Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.

Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes

The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.

A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database

Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.

Discovery of reproductive tissue-associated bacteria and the modes of microbiota acquisition in male honey bees (drones)

Honey bees are the third most economically important agricultural animal in the world due to their role as pollinators. Honey bee pollination services and all hive duties are performed by female workers, while the male drones have one job to mate and share their genetics with a virgin queen from another colony. Thus, drone fitness is directly tied to queen success and colony survival, yet they have been severely understudied compared to their female counterparts. In other insects, microbes discovered in the gut and reproductive organs have been shown to be important for reproductive success and/or overall host health. To our knowledge, the existence of microbes in drone reproductive tissues has never been investigated. Moreover, our understanding of the gut microbiota of drones is severely limited, especially when compared to honey bee workers. Here, we sampled conventional drones from healthy colonies and used 16S amplicon sequencing to identify and characterize bacteria in the reproductive organs of immature and mature drones. After identifying bacteria in drone reproductive tissues, we performed a controlled experiment in which newly emerged drones were exposed to different rearing conditions in order to determine when and how they acquire their reproductive and gut microbiota. Overall, we discovered a set of core bacteria in the reproductive and gut tissues of conventionally reared drones and revealed that social interactions are important for the proper development of the drone microbiota. Determining if these bacteria play a role in drone fecundity and health should be a goal of future research efforts.

IMPORTANCE

Over the last decade, annual honey bee colony loss has increased, resulting in a critical need to determine what factors contribute to honey bee and colony health. Gut microbes have been shown to play important roles in the health of the nonreproductive female honey bee workers, which make up 90% or more of a honey bee colony. However, we currently know very little about the impact of microbes on the health of male honey bees (drones), who only make up a small portion of the colony population but play a very key role in the success of future colonies by mating with virgin queens. Here, we discovered microbes within the reproductive organs of drones and illustrated that social interactions with worker bees are necessary for the proper development of the gut and reproductive tissue microbial communities in drones. Further studies are needed to determine if microbes play an important role in honey bee reproductive health and fitness.

Gut Microbiome Diversity in European Honeybees (Apis mellifera L.) from La Union, Northern Luzon, Philippines

Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.

Utilizing a novel fecal sampling method to examine resistance of the honey bee (Apis mellifera) gut microbiome to a low dose of tetracycline

Disruption of host-associated microbial communities can have detrimental impacts on host health. However, the capacity of individual host-associated microbial communities to resist disturbance has not been well defined. Using a novel fecal sampling method for honey bees (Apis mellifera), we examined the resistance of the honey bee gut microbiome to disruption from a low dose of the antibiotic, tetracycline (4.5 μg). Prior to the experiment, bacterial communities from fecal samples were compared to communities from dissected whole guts of the same individuals to ensure fecal samples accurately represented the gut microbiome. Fecal samples were collected from lab-caged honey bees prior to, and five days after, tetracycline exposure to assess how antibiotic disturbance affected the communities of individuals. We used metrics of alpha and beta diversity calculated from 16S rRNA gene amplicon sequences to compare gut community structure. Low dose tetracycline exposure did not consistently change honey bee gut microbiome structure, but there was individual variation in response to exposure and specific taxa (one ASV assigned to Lactobacillus kunkeei and one ASV in the genus Bombella) were differentially abundant following tetracycline treatment. To assess whether individual variation could be influenced by the presence of tetracycline resistance genes, we quantified the abundance of tet(B) and tet(M) with qPCR. The abundance of tet(M) prior to tetracycline treatment was negatively correlated with change in community membership, assessed by difference in Jaccard dissimilarity over the five-day experiment. Our results suggest that the honey bee gut microbiome has some ability to resist or recover from antibiotic-induced change, specific taxa may vary in their susceptibility to tetracycline exposure, and antibiotic resistance genes may contribute to gut microbiome resistance.

Phylogenetic characterization of Bifidobacterium kimbladii sp. nov., a novel species from the honey stomach of the honeybee Apis mellifera

Six novel Bifidobacterium strains H1HS16NT, Bin2N, Hma3N, H6bp22N, H1HS10N, and H6bp9N, were isolated from the honey stomach of Apis mellifera. Cells are Gram-positive, non-motile, non-sporulating, facultatively anaerobic, and fructose 6-phosphate phosphoketolase-positive. Optimal growth conditions occur at 37 °C in anaerobiosis in MRS medium added with 2 % fructose and 0.1 % L-cysteine. The 16S rRNA gene sequences analysis revealed clustering with Bifidobacterium species found in honeybees. Strains Hma3N, H6bp22N, and H1HS16NT showed significant similarity to Bifidobacterium polysaccharolyticum JCM 34588T, with an average similarity of 99.63 %. In contrast, strains Bin2N, H1HS10N, and H6bp9N were closely related to Bifidobacterium apousia JCM 34587T, with an average similarity of 99.22 %. Moreover, strains Hma3N and H6bp22N exhibited ANI values of 96.65 % and 96.53 % when compared to Bifidobacterium polysaccharolyticum JCM 34588T, while strains H1HS16NT, Bin2N, H6bp9N, and H1HS10N revealed ANI values of 94.18 %, 94.33 %, 94.22 %, and 95.50 % respectively when compared to B. apousia JCM 34587T. dDDH analysis confirmed that strains Hma3N and H6bp22N belong to B. polysaccharolyticum, whereas strains H1HS16NT, Bin2N, H6bp9N, and H1HS10N represent a novel species. The peptidoglycan of the novel species is of the A4α type (L-Lys-D-Asp). The main cellular fatty acids of the type strain H1HS16NT are C16:0, C14:0, C19:0 cyclo ω9c, and C18:1 ω9c. The DNA G + C content of the type strain is 60.8 mol%. Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, probiotic features, and ecological distribution patterns. Phenotypic and genotypic characterization show that strain H1HS16NT is distinct from the type strains of other recognized Bifidobacterium species. Thus, Bifidobacterium kimbladii sp. nov. (H1HS16NT = DSM 115187T = CCUG 76695T) is proposed as a novel Bifidobacterium species.

Honeybee defense mechanisms: Role of honeybee gut microbiota and antimicrobial peptides in maintaining colony health and preventing diseases

Honeybees play a vital role in pollination and the maintenance of ecosystem biodiversity, making their health and well-being crucial for agriculture and environmental sustainability. Bee health is modulated by symbiotic microorganisms colonizing the gut in balanced proportions. Studies have demonstrated that these beneficial bacteria have the capacity to enhance the immune system of honey bees, having substantial impact on regulating their immunological responses and hence aiding in defending against pathogenic illnesses. Another important aspect of honeybee health is their innate immune system that is related to their ability to synthesize antimicrobial peptides (AMP). AMPs, the small, cationic peptides are the humoral effector molecules that are synthesized in the hemolymph of the insects after being exposed to microbial infectious agents. A number of honeybee's gut microbiota especially Lactic Acid Bacteria (LAB), are known to regulate the production of several AMPs and hence are able to provide protection to these insects against a number of disease agents by modulating their innate immune response via induction of the AMPs genes. These AMPs mainly produced by adult workers are an important and integral part of an insect's immune response. Several AMPs namely apidaecins, abaecins, hymenoptaecins and defensins produced in the adult honeybee, hold the ability to control or prevent a number of diseases in these pollinator insects.

Consequences of "zombie-making" and generalist fungal pathogens on carpenter ant microbiota

The bacterial microbiome of the ant Camponotus floridanus has been well characterized across body regions and maturation levels. However, potential effects of entomopathogens on the gut microbiome, and the fungal communities therein, are yet to be assessed. Additionally, the mycobiome remains often overlooked despite playing a vital role in gut ecology with potential implications for health and infection outcomes. We characterized the effects of two entomopathogens with different infection strategies on the gut micro- and mycobiota of C. floridanus over time; Ophiocordyceps camponoti-floridani and Beauveria bassiana. Specialist, 'zombie-making' O. camponoti-floridani fungi hijack the behavior of C. floridanus ants over three weeks, leading them to find an elevated position and fix themselves in place with their mandibles. This summiting behavior is adaptive to Ophiocordyceps as the ant transports the fungus to conditions that favor fruiting body development, spore production, dispersal, and transmission. In contrast, the generalist entomopathogen B. bassiana infects and kills the ant within a few days, without the induction of obvious fungus-adaptive behaviors. By comparing healthy ants with Beauveria- and Ophiocordyceps-infected ants we aimed to 1) describe the dynamics of the micro- and mycobiome of C. floridanus during infection, and 2) determine if the effects on gut microbiota are distinctive between fungi that have different infection strategies. While Beauveria did not measurably affect the ant host micro-and mycobiome, Ophiocordyceps did, especially for the mycobiome. Moreover, ants that were sampled during Ophiocordyceps-adaptive summiting behavior had a significantly different micro- and mycobiome composition compared to healthy controls and those sampled before and after manipulation took place. This suggests that the host microbiome might have a role to play in the manipulation strategy of Ophiocordyceps.

Acetamiprid Exposure Disrupts Gut Microbiota in Adult and Larval Worker Honeybees (Apis mellifera L.)

Acetamiprid is a third-generation neonicotinoid insecticide that is now widely employed for the protection of crops grown in outdoor environments. This is because it is considerably less toxic to pollinating insects than other neonicotinoids. Previous studies have shown that acetamiprid has direct physiological effects on adult and larval bees. However, its effects on the potentially healthy gut microbiota of honeybees have not been fully elucidated. To further investigate the effects, adult and larval worker honeybees were exposed to sucrose solutions containing acetamiprid at concentrations of 0, 5, and 25 mg/L for a period of 7 days (adults) and 4 days (larvae). The results showed that acetamiprid exposure significantly disrupted the honeybees' intestinal microbiota. In adults, acetamiprid exposure led to a significant increase in the relative abundance of Commensalibacter, while the Bifidobacterium and Gilliamella levels decreased. In larvae, we observed significant changes in the microbial composition, notably a marked reduction in Bombella. Further analysis demonstrated that alterations in the gut microbiota of honeybee larvae were associated with disturbances in metabolic pathways that regulate energy metabolism and neurometabolism. These results suggest that acetamiprid affects bee health not only through direct physiological effects, but also through changes in the gut microbiota, which in turn affect the metabolic and immune function of bees. This study underscores the need to evaluate pesticides' risks from a microbiological standpoint and offers crucial insights into how acetamiprid impacts bee health by modifying the gut microbiota. These insights support the more comprehensive assessment of acetamiprid and similar pesticides regarding bee health.

Comparison of the Physicochemical Properties, Microbial Communities, and Hydrocarbon Composition of Honeys Produced by Different Apis Species

The chemical composition and quality of honey are influenced by its botanical, geographic, and entomological origins, as well as climatic conditions. In this study, the physicochemical characteristics, microbial communities, and hydrocarbon compounds of honey produced by Apis mellifera, Apis cerana, Apis laboriosa, Apis dorsata, and Apis florea were elucidated. The physicochemical profile of the honey exhibited significant differences across species, including moisture content (18.27-23.66%), fructose (33.79-38.70%), maltose (1.10-1.93%), electrical conductivity (0.37-0.74 mS/cm), pH (3.36-3.72), diastase activity (4.50-29.97 diastase number), and color (37.90-102.47 mm). Microbial analysis revealed a significant abundance of lactic acid bacteria, particularly the Apilactobacillus genus in A. laboriosa honey and the Lactobacillus in A. florea honey, indicating significant probiotic potential. Chemometric methods, principal component analysis, hierarchical cluster analysis, and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to classify the honey samples based on the 12 beeswax-derived hydrocarbons. The OPLS-DA model demonstrated 100% accuracy in predicting the entomological origin of honey, indicating that specific hydrocarbons are reliable markers for honey classification.

Deeper insight into the storage time of food waste on black soldier fly larvae growth and nutritive value: Interactions of substrate and gut microorganisms

Biological treatment of food waste (FW) by black soldier fly larvae (BSFL) is considered as an effective management strategy. The composition and concentrations of nutrients in FW change during its storage and transport period, which potentially affect the FW conversion and BSFL growth. The present study systematically investigated the effect of different storage times (i.e., 0-15 d) on FW characteristics and its substantial influence on the BSFL growth. Results showed that the highest larvae weight of 282 mg and the shortest growth time of 14 days were achieved at the group of FW stored for 15 days, but shorter storage time (i.e., 2-7 d) had adverse effect on BSFL growth. Short storage time (i.e., 2-4 d) improved protein content of BSFL biomass and prolonged storage time (i.e., 7-10 d) led to the accumulation of fat content. The changes of substrate characteristics and indigenous microorganisms via FW storage time were the main reasons for BSFL growth difference. Lactic acid (LA) accumulation (i.e., 19.84 g/L) in FW storage for 7 days significantly limited the BSFL growth, leading to lowest larvae weight. Both the substrate and BSFL gut contained same bacterial communities (e.g., Klebsiella and Proteus), which exhibited similar change trend with the prolonged storage time. The transfer of Clostridioides from substrate to BSFL gut promoted nutrients digestion and intestinal flora balance with the FW stored for 15 days. Pathogens (e.g., Acinetobacter) in BSFL gut feeding with FW storage time of 7 days led to the decreased digestive function, consistent with the lowest larvae weight. Overall, shorter storage time (i.e., 2-7 d) inhibited the BSFL digestive function and growth performance, while the balance of the substrate nutrients and intestinal flora promoted the BSFL growth when using the FW stored for 15 days.

The effect of lambda-cyhalothrin nanocapsules on the gut microbial communities and immune response of the bee elucidates the potential environmental impact of emerging nanopesticides

Emerging nanopesticides are gradually gaining widespread application in agriculture due to their excellent properties, but their potential risks to pollinating insects are not fully understood. In this study, lambda-cyhalothrin nanocapsules (LC-NCs) were constructed by electrostatic self-assembly method with iron mineralization optimization, and their effects on bee gut microbial communities and host immune-related factors were investigated. Microbiome sequencing revealed that LC-NCs increase the diversity of gut microbial communities and reduce the complexity of network features, disrupting the overall structure of the microbial communities. In addition, LC-NCs also had systemic effects on the immune response of bees, including increased activity of SOD and CAT enzymes and expression of their genes, as well as downregulation of Defensin1. Furthermore, we noticed that the immune system of the host was activated simultaneously with a rise in the abundance of beneficial bacteria in the gut. Our research emphasizes the importance of both the host and gut microbiota of holobiont in revealing the potential risks of LC-NCs to environmental indicators of honey bees, and provides references for exploring the interactions between host-microbiota systems under exogenous stress. At the same time, we hope that more research can focus on the potential impacts of nanopesticides on the ecological environment.

Diet affects reproductive development and microbiota composition in honey bees

BACKGROUND

Gut microbes are important to the health and fitness of many animals. Many factors have been shown to affect gut microbial communities including diet, lifestyle, and age. Most animals have very complex physiologies, lifestyles, and microbiomes, making it virtually impossible to disentangle what factors have the largest impact on microbiota composition. Honeybees are an excellent model to study host-microbe interactions due to their relatively simple gut microbiota, experimental tractability, and eusociality. Worker honey bees have distinct gut microbiota from their queen mothers despite being close genetic relatives and living in the same environment. Queens and workers differ in numerous ways including development, physiology, pheromone production, diet, and behavior. In the prolonged absence of a queen or Queen Mandibular Pheromones (QMP), some but not all workers will develop ovaries and become "queen-like". Using this inducible developmental change, we aimed to determine if diet and/or reproductive development impacts the gut microbiota of honey bee workers.

RESULTS

Microbiota-depleted newly emerged workers were inoculated with a mixture of queen and worker gut homogenates and reared under four conditions varying in diet and pheromone exposure. Three weeks post-emergence, workers were evaluated for ovary development and their gut microbiota communities were characterized. The proportion of workers with developed ovaries was increased in the absence of QMP but also when fed a queen diet (royal jelly). Overall, we found that diet, rather than reproductive development or pheromone exposure, led to more "queen-like" microbiota in workers. However, we revealed that diet alone cannot explain the microbiota composition of workers.

CONCLUSION

The hypothesis that reproductive development explains microbiota differences between queens and workers was rejected. We found evidence that diet is one of the main drivers of differences between the gut microbial community compositions of queens and workers but cannot fully explain the distinct microbiota of queens. Thus, we predict that behavioral and other physiological differences dictate microbiota composition in workers and queens. Our findings not only contribute to our understanding of the factors affecting the honey bee microbiota, which is important for bee health, but also illustrate the versatility and benefits of utilizing honeybees as a model system to study host-microbe interactions.

Honey microbiota, methods for determining the microbiological composition and the antimicrobial effect of honey - A review

Honey is a natural product used since ancient times due to its taste, aroma, and therapeutic properties (antibacterial, antiviral, anti-inflammatory, and antioxidant activity). The purpose of this review is to present the species of microorganisms that can survive in honey and the effect they can have on bees and consumers. The techniques for identifying the microorganisms present in honey are also described in this study. Honey contains bacteria, yeasts, molds, and viruses, and some of them may present beneficial properties for humans. The antimicrobial effect of honey is due to its acidity and high viscosity, high sugar concentration, low water content, the presence of hydrogen peroxide and non-peroxidase components, particularly methylglyoxal (MGO), phenolic acids, flavonoids, proteins, peptides, and non-peroxidase glycopeptides. Honey has antibacterial action (it has effectiveness against bacteria, e.g. Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter, etc.), antifungal (effectiveness against Candida spp., Aspergillus spp., Fusarium spp., Rhizopus spp., and Penicillium spp.), antiviral (effectiveness against SARS-CoV-2, Herpes simplex virus type 1, Influenza virus A and B, Varicella zoster virus), and antiparasitic action (effectiveness against Plasmodium berghei, Giardia and Trichomonas, Toxoplasma gondii) demonstrated by numerous studies that are comprised and discussed in this review.

Is it me or is it you? Physiological effects of the honey bee microbiota may instead be due to host maturation

Microbiota-mediated impacts on host physiology and behavior have been widely reported in honey bees (Apis mellifera). However, most of these studies are conducted in artificial lab settings and fail to take into account, or make incorrect assumptions about, the complex physical and social structures inherent to natural hive conditions. A new study by Liberti et al. (J. Liberti, E. T. Frank, T. Kay, L. Kesner, et al., mBio 15:e01034-24, 2024, https://doi.org/10.1128/mbio.01034-24) identifies one such overlooked aspect-the behavioral maturation from nurses to foragers-that can be a serious confounding factor in bee microbiota experiments. Using cuticular hydrocarbon profiling to discern between the two maturation states, they find that multiple physiological and behavioral differences between age-matched lab bees could potentially be explained by their maturation state instead of the intended treatment conditions, such as microbial inoculation. This study serves as a stark wake-up call on the necessity of careful replication and cross-disciplinary knowledge transfer (e.g., between animal specialists and microbiologists) in order to truly understand complex host-microbe systems.

Virulence-linked adhesin drives mutualist colonization of the bee gut via biofilm formation

Bacterial biofilms are stable multicellular structures that can enable long term host association. Yet, the role of biofilms in supporting gut mutualism is still not fully understood. Here, we investigate Snodgrassella alvi, a beneficial bacterial symbiont of honey bees, and find that biofilm formation is required for its colonization of the bee gut. We constructed fifteen S. alvi mutants containing knockouts of genes known to promote colonization with putative roles in biofilm formation. Genes required for colonization included staA and staB, encoding trimeric autotransporter adhesins (TAAs) and mltA, encoding a lytic transglycosylase. Intriguingly, TAAs are considered virulence factors in pathogens but support mutualism by the symbiont S. alvi. In vitro, biofilm formation was reduced in ΔstaB cells and abolished in the other two mutants. Loss of staA also reduced auto-aggregation and cell-cell connections. Based on structural predictions, StaA/B are massive (>300 nm) TAAs with many repeats in their stalk regions. Further, we find that StaA/B are conserved across Snodgrassella species, suggesting that StaA/B-dependent colonization is characteristic of this symbiont lineage. Finally, staA deletion increases sensitivity to bactericidal antimicrobials, suggesting that the biofilm indirectly buffers against antibiotic stress. In all, the inability of two biofilm-deficient strains (ΔstaA and ΔmltA) to effectively mono-colonize bees indicates that S. alvi biofilm formation is required for colonization of the bee gut. We envision the bee gut system as a genetically tractable model for studying the physical basis of biofilm-mutualist-gut interactions.

Modeling seasonal immune dynamics of honey bee (Apis mellifera L.) response to injection of heat-killed Serratia marcescens

The honey bee, Apis mellifera L., is one of the main pollinators worldwide. In a temperate climate, seasonality affects the life span, behavior, physiology, and immunity of honey bees. In consequence, it impacts their interaction with pathogens and parasites. In this study, we used Bayesian statistics and modeling to examine the immune response dynamics of summer and winter honey bee workers after injection with the heat-killed bacteria Serratia marcescens, an opportunistic honey bee pathogen. We investigated the humoral and cellular immune response at the transcriptional and functional levels using qPCR of selected immune genes, antimicrobial activity assay, and flow cytometric analysis of hemocyte concentration. Our data demonstrate increased antimicrobial activity at transcriptional and functional levels in summer and winter workers after injection, with a stronger immune response in winter bees. On the other hand, an increase in hemocyte concentration was observed only in the summer bee population. Our results indicate that the summer population mounts a cellular response when challenged with heat-killed S. marcescens, while winter honey bees predominantly rely on humoral immune reactions. We created a model describing the honey bee immune response dynamics to bacteria-derived components by applying Bayesian statistics to our data. This model can be employed in further research and facilitate the investigating of the honey bee immune system and its response to pathogens.

Honeybee gut bacterial strain improved survival and gut microbiota homeostasis in Apis mellifera exposed in vivo to clothianidin

Pesticides are causing honeybee mortality worldwide. Research carried out on honeybees indicates that application of pesticides has a significant impact on the core gut community, which ultimately leads to an increase in the growth of harmful pathogens. Disturbances caused by pesticides also affect the way bacterial members interact, which results in gut microbial dysbiosis. Administration of beneficial microbes has been previously demonstrated to be effective in treating or preventing disease in honeybees. The objective of this study was to measure under in vivo conditions the ability of two bacterial strains (the Enterobacter sp. and Pantoea sp.) isolated from honeybee gut to improve survival and mitigate gut microbiota dysbiosis in honeybees exposed to a sublethal clothianidin dose (0.1 ppb). Both gut bacterial strains were selected for their ability to degrade clothianidin in vitro regardless of their host-microbe interaction characteristics (e.g., beneficial, neutral, or harmful). To this end, we conducted cage trials on 4- to 6-day-old newly emerging honeybees. During microbial administration, we jointly monitored the taxonomic distribution and activity level of bacterial symbionts quantifying 16S rRNA transcripts. First, curative administration of the Pantoea sp. strain significantly improved the survival of clothianidin-exposed honeybees compared to sugar control bees (i.e., supplemented with sugar [1:1]). Second, curative administration of the Enterobacter sp. strain significantly mitigated the clothianidin-induced dysbiosis observed in the midgut structural network, but without improving survival.

IMPORTANCE

The present work suggests that administration of bacterial strains isolated from honeybee gut may promote recovery of gut microbiota homeostasis after prolonged clothianidin exposure, while improving survival. This study highlights that gut bacterial strains hold promise for developing efficient microbial formulations to mitigate environmental pesticide exposure in honeybee colonies.

Synergistic effects between microplastics and glyphosate on honey bee larvae

Microplastic (MPs) pollution has emerged as a global ecological concern, however, the impact of MPs exposure, particularly in conjunction with other pollutants such as glyphosate (GLY) on honey bee remains unknown. This study investigated the effects of exposure to different concentrations of MPs and their combination with GLY on honey bee larvae development, or during the larvae period, regulation of major detoxification, antioxidant and immune genes, and oxidative stress biomarkers. Results revealed that combined exposure to MPs and GLY decreased larvae survivorship and weight, while exposure to MPs alone showed no significant differences. Both MPs and GLY alone downregulated the defensin-1 gene, but only combined exposure with GLY downregulated the hymenoptaecin gene and increased catalase enzyme activity. The data suggest a synergistic effect of MPs and GLY, leading to immunosuppression and reduced larvae survival and weight. These findings highlight potential risks of two prevalent environmental pollutants on honey bee health.

The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus

South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.

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.

Host Species Affects Gut Microbial Community and Offspring Developmental Performances in the Pupal Parasitoid Chouioia cunea Yang (Hymenoptera: Eulophidae)

Chouioia cunea are known to exploit in varying degrees a wide range of lepidopteran species and its offspring development may vary with host species. This study examined its preimaginal development and larval gut microbiota in parasitizing five folivorous lepidopteran hosts including Hyphantria cunea (referred to thereafter as CcHc), Antherea pernyi (CcAp), Helicoverpa armigera (CcHa), Spodoptera exigua (CcSe), and Spodoptera frugiperda (CcSf). Though rates of parasitism and offspring eclosion did not change with host species, the development period and number of offspring eclosed varied with hosts, with the shortest period in CcSf and the highest number from CcAp. For offspring larval gut microbiota, though phylum Proteobacteria was dominant for attacking CcAp, Firmicutes was so for the other hosts. All microbial genera except Enterococcus were less abundant for CcSf than the other hosts. The database-based predictions indicate a significant positive correlation between Cutibacterium and Aureimonas with the relative number of wasp emergence, while Blastomonas exhibits a strong positive association with the developmental period. Our results imply the potential relevance of the gut microbial community in offspring larvae to host species attacked by C. cunea.

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata

Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remains less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on nonhost-specific environmental bacteria may not impact fitness of M. rotundata.IMPORTANCEThis study investigates the impact of environmentally acquired gut microbes of solitary bee fitness with insights into the microbial ecology of bee and their health. While the symbiotic microbiome is well-studied in social bees, the role of environmental acquired microbiota in solitary bees remains unclear. Assessing this relationship in a solitary pollinator, the leaf-cutting bee, Megachile rotundata, we discovered that this bee species does not depend on the diverse environmental bacteria found in pollen for either its larval growth or survival. Surprisingly, high concentrations of the most abundant pollen bacteria, Apilactobacillus micheneri did not consistently benefit bee fitness, but caused larval mortality. Our findings also suggest an interaction between Apilactobacillus and the Sodalis and perhaps their role in bee nutrition. Hence, this study provides significant insights that contribute to understanding the fitness, conservation, and pollination ecology of other solitary bee species in the future.

Gut fungal diversity across different life stages of the onion fly Delia antiqua

A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.

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.

Lactobacillus Firm-5-derived succinate prevents honeybees from having diabetes-like symptoms

The gut microbiome plays an important role in honeybee hormonal regulation and growth, but the underlying mechanisms are poorly understood. Here, we showed that the depletion of gut bacteria resulted in reduced expression of insulin-like peptide gene (ilp) in the head, accompanied by metabolic syndromes resembling those of Type 1 diabetes in humans: hyperglycemia, impaired lipid storage, and decreased metabolism. These symptoms were alleviated by gut bacterial inoculation. Gut metabolite profiling revealed that succinate, produced by Lactobacillus Firm-5, played deterministic roles in activating ilp gene expression and in regulating metabolism in honeybees. Notably, we demonstrated that succinate modulates host ilp gene expression through stimulating gut gluconeogenesis, a mechanism resembling that of humans. This study presents evidence for the role of gut metabolite in modulating host metabolism and contributes to the understanding of the interactions between gut microbiome and bee hosts.

Neuroactive metabolites modulated by the gut microbiota in honey bees

Honey bees have emerged as a new model to study the gut-brain axis, as they exhibit complex social behaviors and cognitive abilities, while experiments with gnotobiotic bees have revealed that their gut microbiota alters both brain and behavioral phenotypes. Furthermore, while honey bee brain functions supporting a broad range of behaviors have been intensively studied for over 50 years, the gut microbiota of bees has been experimentally characterized only recently. Here, we combined six published datasets from metabolomic analyses to provide an overview of the neuroactive metabolites whose abundance in the gut, hemolymph and brain varies in presence of the gut microbiota. Such metabolites may either be produced by gut bacteria, released from the pollen grains during their decomposition by bacteria, or produced by other organs in response to different bacterial products. We describe the current state of knowledge regarding the impact of such metabolites on brain function and behavior and provide further hypotheses to explore in this emerging field of research.

Infection by Crithidia bombi increases relative abundance of Lactobacillus spp. in the gut of Bombus terrestris

Gut microbial communities confer protection against natural pathogens in important pollinators from the genera Bombus and Apis. In commercial species B. terrestris and B. impatiens, the microbiota increases their resistance to the common and virulent trypanosomatid parasite Crithidia bombi. However, the mechanisms by which gut microorganisms protect the host are still unknown. Here, we test two hypotheses: microbiota protect the host (1) through stimulation of its immune response or protection of the gut epithelium and (2) by competing for resources with the parasite inside the gut. To test them, we reduced the microbiota of workers and then rescued the microbial community by feeding them with microbiota supplements. We then exposed them to an infectious dose of C. bombi and characterised gene expression and gut microbiota composition. We examined the expression of three antimicrobial peptide genes and Mucin-5AC, a gene with a putative role in gut epithelium protection, using qPCR. Although a protective effect against C. bombi was observed in bumblebees with supplemented microbiota, we did not observe an effect of the microbiota on gene expression that could explain alone the protective effect observed. On the other hand, we found an increased relative abundance of Lactobacillus bacteria within the gut of infected workers and a negative correlation of this genus with Gilliamella and Snodgrassella genera. Therefore, our results point to a displacement of bumblebee endosymbionts by C. bombi that might be caused by competition for space and nutrients between the parasite and the microbiota within the gut.

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome

Managed colonies of the European honey bee, Apis mellifera, have faced considerable losses in recent years. A widespread contributing factor is a microsporidian pathogen, Nosema ceranae, which occurs worldwide, is increasingly resistant to antibiotic treatment, and can alter the host's immune response and nutritional uptake. These obligate gut pathogens share their environment with a natural honey bee microbiome whose composition can affect pathogen resistance. We tested the effect of N. ceranae infection on this microbiome by feeding 5 day-old adult bees that had natural, fully developed microbiomes with live N. ceranae spores (40,000 per bee) or a sham inoculation, sterile 2.0 M sucrose solution. We caged and reared these bees in a controlled lab environment and tracked their mortality over 12 d, after which we dissected them, measured their infection levels (gut spore counts), and analyzed their microbiomes. Bees fed live spores had two-fold higher mortality by 12 d and 36.5-fold more spores per bee than controls. There were also strong colony effects on infection levels, and 9% of spore-inoculated bees had no spore counts at all (defined as fed-spores-but-not-infected). Nosema ceranae infection had significant but subtle effects on the gut microbiomes of experimentally infected bees, bees with different infection levels, and fed-spores-but-not-infected vs. bees with gut spores. Specific bacteria, including Gilliamella ASVs, were positively associated with infection, indicating that multiple strains of core gut microbes either facilitate or resist N. ceranae infection. Future studies on the interactions between bacterial, pathogen, and host genotypes would be illuminating.

Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet

Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects.

IMPORTANCE

Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.

Gut Bacterial Communities in the Ground Beetle Carabus convexus

Biological interactions, including symbiotic ones, have vital roles in ecological and evolutionary processes. Microbial symbionts in the intestinal tracts, known as the gut microbiome, are especially important because they can fundamentally influence the life history, fitness, and competitiveness of their hosts. Studies on the gut-resident microorganisms of wild animals focus mainly on vertebrates, and studies on species-rich invertebrate taxa, such as ground beetles, are sparse. In fact, even among the species-rich genus Carabus, only the gut microbiome of two Asian species was studied, while results on European species are completely missing. Here, we investigated the gut bacterial microbiome of a widespread European Carabus species, targeting the V3 and V4 regions of the 16S ribosomal RNA genes by next-generation high-throughput sequencing. We identified 1138 different operational taxonomic units assigned to 21 bacterial phyla, 90 families, and 197 genera. Members of the carbohydrate-degrading Prevotellaceae family, previously not detected in ground beetles, were the most abundant in the gut microbiome of the carnivorous C. convexus. Presumably, individuals from the studied wild populations also consume plant materials, especially fruits, and these carbohydrate-degrading bacterial symbionts can facilitate both the consumption and the digestion of these supplementary foods.

Integrating host and microbiome biology using holo-omics

Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.

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.

The Improving Effects of Probiotic-Added Pollen Substitute Diets on the Gut Microbiota and Individual Health of Honey Bee (Apis mellifera L.)

Honey bee (Apis mellifera L.) health is crucial for honey bee products and effective pollination, and it is closely associated with gut bacteria. Various factors such as reduced habitat, temperature, disease, and diet affect the health of honey bees by disturbing the homeostasis of the gut microbiota. In this study, high-throughput 16S rRNA gene sequencing was used to analyze the gut microbiota of honey bees subjected to seven diets over 5 days. Lactobacillus dominated the microbiota in all diets. Cage experiments (consumption, head protein content, and vitellogenin gene expression level) were conducted to verify the effect of the diet. Through a heatmap, the Diet2 (probiotic-supplemented) group was clustered together with the Beebread and honey group, showing high consumption (177.50 ± 26.16 mg/bee), moderately higher survival duration (29.00 ± 2.83 days), protein content in the head (312.62 ± 28.71 µg/mL), and diet digestibility (48.41 ± 1.90%). Additionally, we analyzed the correlation between gut microbiota and health-related indicators in honey bees fed each diet. Based on the overall results, we identified that probiotic-supplemented diets increased gut microbiota diversity and positively affected the overall health of individual honey bees.

Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers

Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.

Gut microbiome diversity and biogeography for Chinese bumblebee Bombus pyrosoma

Gut microbiota of the bumblebee is critical as it modulates the health and fitness of the host. However, the mechanisms underlying the formation and maintenance of the diversity of bumblebee gut bacteria over a long period of evolution have yet to be elucidated. In particular, the gut bacterial diversity and community assembly processes of Bombus pyrosoma across the Chinese border remain unclear. In this study, we systematically carried out unprecedented sampling of 513 workers of the species Bombus pyrosoma across the Chinese landscape and used full-length 16S rRNA gene sequencing to examine their gut microbiota diversity and biogeography. The gut microbiota composition and community structure of Bombus pyrosoma from different geographical locations were diverse. On the whole, the gut bacteria Gilliamella and Snodgrassella are dominant in bumblebees, but opportunistic pathogens Serratia and Pseudomonas are dominant in some sampling sites such as Hb15, Gs1, Gs45, Qhs15, and Ssx35. All or part of environmental factors such as latitude, annual mean temperature, elevation, human footprint, population density, and annual precipitation can affect the alpha diversity and community structure of gut bacteria. Further analysis showed that the assembly and shift of bumblebee gut bacterial communities under geographical variation were mainly driven by the stochastic drift of the neutral process rather than by variable selection of niche differentiation. In conclusion, our unprecedented sampling uncovers bumblebee gut microbiome diversity and shifts over evolutionary time.

IMPORTANCE

The microbiotas associated with organisms facilitates host health and fitness, and the homeostasis status of gut microbiota also reflects the habitat security faced by the host. In addition, managing gut microbiota is important to improve bumblebee health by understanding the ecological process of the gut microbiome. Thus, we first carried out an runprecedented sampling of 513 workers of the species Bombus pyrosoma across the Chinese landscape and used full-length 16S rRNA gene sequencing to uncover their gut microbiota diversity and biogeography. Our study provides new insights into the understanding of gut microbiome diversity and shifts for Chinese Bumblebee over evolutionary time.

Cytotoxic and genotoxic effects of a pendimethalin-based herbicide in Apis mellifera

Public concern about the effects of pesticides on non-target organisms has increased in the recent years. Nevertheless, there is a limited number of studies that address the actual toxic effects of herbicides on insects. This study investigated the side effects of herbicides on non-target organisms inhabiting agroecosystems and performing essential ecological and economic functions such as crop pollination. We analysed morphological alterations in the gut, Malpighian tubules and circulating haemocytes of Apis mellifera workers as markers of exposure effects. A commercial formulation of a pendimethalin-based herbicide (PND) was administered orally under laboratory conditions at a realistic concentration admitted in the field (330gL-1 of active ingredient., 4 L ha-1 for cereal and vegetable crops). The worker bees were exposed to a single application of PND for a period of one week, to simulate the exposure that can occur when foraging bees accidentally drink drops of contaminated water upon treatments. Histopathological analyses of the midgut, ileum and Malpighian tubules showed alterations over time (from 24 to 72 h after the beginning of exposure) such as loss of epithelial organisation, cellular vacuolisation and altered pyknotic nuclei as well as disruption of the peritrophic membrane over time. Semiquantitative analyses of the midgut showed a significant increase in the organ injury index 24 and 72 h after the initial exposure in PND-exposed bees compared to control bees. In addition, a change in positivity to Gram staining was observed in the midgut histological sections. A recovery of cytotoxic effects was observed one week after the initial exposure, which was favoured by the periodic renewal of the intestinal epithelium and the herbicide dissipation time. Cytochemical staining with Giemsa of haemocytes from PND-treated workers over 24 and 72 h showed significant nuclear alterations such as lobed or polymorphic nuclei and micronuclei compared to bees in the control group. These results show that the dose of PND used to protect crops from weeds can lead to significant cytotoxic and genotoxic effects in non-target organisms such as honey bees. In croplands, the sublethal effects on cell morphology can impair vital physiological processes such as nutrition, osmoregulation, and resistance to pathogens, contributing to the decline in biodiversity and abundance of species that play a prominent ecological role, such as pollinators.

Uncovering hidden dangers: The combined toxicity of abamectin and lambda-cyhalothrin on honey bees

Studying the toxic effects of pesticides on bees has consistently been a prominent area of interest for researchers. Nonetheless, existing research has predominantly concentrated on individual toxicity assessments, leaving a gap in our understanding of mixed toxicity. This study delves into the individual and combined toxic effects of abamectin (ABA) and lambda-cyhalothrin (LCY) on honey bees (Apis mellifera) in laboratory settings. We discovered that ABA (96 h-LC50 value of 0.079 mg/L) exhibited greater acute toxicity to honey bees compared to LCY (96 h-LC50 value of 9.177 mg/L). Moreover, the mixture of ABA and LCY presented an acute antagonistic effect on honey bees. Additionally, our results indicated that exposure to LCY, at medium concentration, led to a reduction in the abundance of gut core bacterium Snodgrassella. However, an increase in the abundance of Bifidobacterium was noted when exposed to a medium concentration of LCY and its mixture with ABA. Transcriptomic analysis revealed significant regulation of certain genes in the medium concentration of all three treatments compared to the control group, primarily enriching in metabolism and immune-related pathways. Following chronic exposure to field-relevant concentrations of ABA, LCY, and their mixture, there were significant alterations in the activities of immunity-related enzyme polyphenol oxidase (PPO) and detoxification enzymes glutathione S-transferase (GST) and carboxylesterase (CarE). Additionally, the expression of four genes (abaecin, cyp9e2, cyp302a1, and GstD1) associated with immune and detoxification metabolism was significantly altered. These findings suggest a potential health risk posed by the insecticides ABA and LCY to honey bees. Despite exhibiting acute antagonistic effect, mixed exposure still induced damage to bees at all levels. This study advances our knowledge of the potential adverse effects of individual or combined exposure to these two pesticides on non-target pollinators and offers crucial guidance for the use of insecticides in agricultural production.

Improving bee feed recipes to safeguard honeybee colonies during times of food scarcity

In beekeeping, when natural nectar or pollen sources become limited, it is crucial to provide supplemental bee feed to maintain the viability of the bee colony. This study was conducted during the autumn food shortage season, during which bees were fed with different proportions of modified bee feed. We identified an optimal bee diet by evaluating honeybee longevity, food consumption, body weight, and gut microbe distribution, with natural pollen serving as a control diet. The results indicated that bees preferred a mixture of 65% defatted soy flour, 20% corn protein powder, 13% wheat germ flour, 2% yeast powder, and a 50% sucrose solution. This bee food recipe significantly increased the longevity, feed consumption, and body weight of bees. The group fed the natural pollen diet exhibited a greater abundance of essential intestinal bacteria. The bee diets used in this study contained higher protein levels and lower concentrations of unsaturated fatty acids and vitamins than did the diets stored within the colonies. Therefore, we propose that incorporating both bee feed and natural pollen in beekeeping practices will achieve more balanced nutritional intake.

Exploring the risk of microplastics to pollinators: focusing on honey bees

The rapid increase in global plastic production and usage has led to global environmental contamination, with microplastics (MPs) emerging as a significant concern. Pollinators provide a crucial ecological service, while bee populations have been declining in recent years, and MPs have been recognized as a new risk factor contributing to their losses. Despite the pervasive distribution and persistence of MPs, understanding their risks to honey bees remains a critical knowledge gap. This review summarizes recent studies that investigate the toxicity of MPs on honey bee health from different perspectives. The findings revealed diverse and material-/size-/dosage-dependent outcomes, emphasizing the need for comprehensive assessments in the follow-up studies. MPs have been detected in honey and in bees' organs (e.g., gut and brain), posing potential threats to bee fitness, including altered behavior, cognitive abilities, compromised immunity, and dysfunction of the gut microbiota. It should be noticed that despite several laboratory studies suggesting the aforementioned adverse effects of MPs, field/semi-field experiments are still warranted. The synergistic toxicity of MPs with other environmental contaminants (pesticides, antibiotics, fungicides, heavy metals, etc.) still requires further investigation. Our review highlights the critical need to understand the relationships between MPs, pollinators, and the ecosystem to mitigate potential risks and ensure the sustainability of vital services provided by honey bees.

Melipona stingless bees and honey microbiota reveal the diversity, composition, and modes of symbionts transmission

The Melipona gut microbiota differs from other social bees, being characterized by the absence of crucial corbiculate core gut symbionts and a high occurrence of environmental strains. We studied the microbial diversity and composition of three Melipona species and their honey to understand which strains are obtained by horizontal transmission (HT) from the pollination environment, represent symbionts with HT from the hive/food stores or social transmission (ST) between nestmates. Bees harbored higher microbial alpha diversity and a different and more species-specific bacterial composition than honey. The fungal communities of bee and honey samples are also different but less dissimilar. As expected, the eusocial corbiculate core symbionts Snodgrassella and Gilliamella were absent in bees that had a prevalence of Lactobacillaceae - including Lactobacillus (formerly known as Firm-5), Bifidobacteriaceae, Acetobacteraceae, and Streptococcaceae - mainly strains close to Floricoccus, a putative novel symbiont acquired from flowers. They might have co-evolved with these bees via ST, and along with environmental Lactobacillaceae and Pectinatus (Veillonellaceae) strains obtained by HT, and Metschnikowia and Saccharomycetales yeasts acquired by HT from honey or the pollination environment, including plants/flowers, possibly compose the Melipona core microbiota. This work contributes to the understanding of Melipona symbionts and their modes of transmission.

Managing Microbiota Activity of Apis mellifera with Probiotic (Bactocell®) and Antimicrobial (Fumidil B®) Treatments: Effects on Spring Colony Strength

Against a backdrop of declining bee colony health, this study aims to gain a better understanding of the impact of an antimicrobial (Fumidil B®, Can-Vet Animal Health Supplies Ltd., Guelph, ON, Canada) and a probiotic (Bactocell®, Lallemand Inc., Montreal, QC, Canada) on bees' microbiota and the health of their colonies after wintering. Therefore, colonies were orally exposed to these products and their combination before wintering in an environmental room. The results show that the probiotic significantly improved the strength of the colonies in spring by increasing the total number of bees and the number of capped brood cells. This improvement translated into a more resilient structure of the gut microbiota, highlighted by a more connected network of interactions between bacteria. Contrastingly, the antimicrobial treatment led to a breakdown in this network and a significant increase in negative interactions, both being hallmarks of microbiota dysbiosis. Although this treatment did not translate into a measurable colony strength reduction, it may impact the health of individual bees. The combination of these products restored the microbiota close to control, but with mixed results for colony performance. More tests will be needed to validate these results, but the probiotic Bactocell® could be administrated as a food supplement before wintering to improve colony recovery in spring.

Toxic effects of acaricide fenazaquin on development, hemolymph metabolome, and gut microbiome of honeybee (Apis mellifera) larvae

Fenazaquin, a potent insecticide widely used to control phytophagous mites, has recently emerged as a potential solution for managing Varroa destructor mites in honeybees. However, the comprehensive impact of fenazaquin on honeybee health remains insufficiently understood. Our current study investigated the acute and chronic toxicity of fenazaquin to honeybee larvae, along with its influence on larval hemolymph metabolism and gut microbiota. Results showed that the acute median lethal dose (LD50) of fenazaquin for honeybee larvae was 1.786 μg/larva, and the chronic LD50 was 1.213 μg/larva. Although chronic exposure to low doses of fenazaquin exhibited no significant effect on larval development, increasing doses of fenazaquin resulted in significant increases in larval mortality, developmental time, and deformity rates. At the metabolic level, high doses of fenazaquin inhibited nucleotide, purine, and lipid metabolism pathways in the larval hemolymph, leading to energy metabolism disorders and physiological dysfunction. Furthermore, high doses of fenazaquin reduced gut microbial diversity and abundance, characterized by decreased relative abundance of functional gut bacterium Lactobacillus kunkeei and increased pathogenic bacterium Melissococcus plutonius. The disrupted gut microbiota, combined with the observed gut tissue damage, could potentially impair food digestion and nutrient absorption in the larvae. Our results provide valuable insights into the complex and diverse effects of fenazaquin on honeybee larvae, establishing an important theoretical basis for applying fenazaquin in beekeeping.

Engineering Gut Symbionts: A Way to Promote Bee Growth?

Bees play a crucial role as pollinators, contributing significantly to ecosystems. However, the honeybee population faces challenges such as global warming, pesticide use, and pathogenic microorganisms. Promoting bee growth using several approaches is therefore crucial for maintaining their roles. To this end, the bacterial microbiota is well-known for its native role in supporting bee growth in several respects. Maximizing the capabilities of these microorganisms holds the theoretical potential to promote the growth of bees. Recent advancements have made it feasible to achieve this enhancement through the application of genetic engineering. In this review, we present the roles of gut symbionts in promoting bee growth and collectively summarize the engineering approaches that would be needed for future applications. Particularly, as the engineering of bee gut symbionts has not been advanced, the dominant gut symbiotic bacteria Snodgrassella alvi and Gilliamella apicola are the main focus of the paper, along with other dominant species. Moreover, we propose engineering strategies that will allow for the improvement in bee growth with listed gene targets for modification to further encourage the use of engineered gut symbionts to promote bee growth.

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA)

For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome's role in winter survival is warranted.

Vairimorpha (Nosema) ceranae can promote Serratia development in honeybee gut: an underrated threat for bees?

The genus Serratia harbors opportunistic pathogenic species, among which Serratia marcescens is pathogenic for honeybees although little studied. Recently, virulent strains of S. marcescens colonizing the Varroa destructor mite's mouth were found vectored into the honeybee body, leading to septicemia and death. Serratia also occurs as an opportunistic pathogen in the honeybee's gut with a low absolute abundance. The Serratia population seems controlled by the host immune system, but its presence may represent a hidden threat, ready to arise when honeybees are weakened by biotic and abiotic stressors. To shed light on the Serratia pathogen, this research aims at studying Serratia's development dynamics in the honeybee body and its interactions with the co-occurring fungal pathogen Vairimorpha ceranae. Firstly, the degree of pathogenicity and the ability to permeate the gut epithelial barrier of three Serratia strains, isolated from honeybees and belonging to different species (S. marcescens, Serratia liquefaciens, and Serratia nematodiphila), were assessed by artificial inoculation of newborn honeybees with different Serratia doses (104, 106, and 108 cells/mL). The absolute abundance of Serratia in the gut and in the hemocoel was assessed in qPCR with primers targeting the luxS gene. Moreover, the absolute abundance of Serratia was assessed in the gut of honeybees infected with V. ceranae at different development stages and supplied with beneficial microorganisms and fumagillin. Our results showed that all tested Serratia strains could pass through the gut epithelial barrier and proliferate in the hemocoel, with S. marcescens being the most pathogenic. Moreover, under cage conditions, Serratia better proliferates when a V. ceranae infection is co-occurring, with a positive and significant correlation. Finally, fumagillin and some of the tested beneficial microorganisms could control both Serratia and Vairimorpha development. Our findings suggest a correlation between the two pathogens under laboratory conditions, a co-occurring infection that should be taken into consideration by researches when testing antimicrobial compounds active against V. ceranae, and the related honeybees survival rate. Moreover, our findings suggest a positive control of Serratia by the environmental microorganism Apilactobacillus kunkeei in a in vivo model, confirming the potential of this specie as beneficial bacteria for honeybees.

The buzz about honey-based biosurveys

Approximately 1.8 million metric tonnes of honey are produced globally every year. The key source behind this output, the honey bee (Apis mellifera), works tirelessly to create the delicious condiment that is consumed worldwide. The honey that finds its way into jars on store shelves contains a myriad of information about its biogeographical origins, such as the bees that produced it, the botanical constituents, and traces of other organisms or pathogens that have come in contact with the product or its producer. With the ongoing threat of honey bee decline and overall global biodiversity loss, access to ecological information has become an key factor in preventing the loss of species. This review delves into the various molecular techniques developed to characterize the collective DNA harnessed within honey samples, and how it can be used to elucidate the ecological interactions between honey bees and the environment. We also explore how these DNA-based methods can be used for large-scale biogeographical studies through the environmental DNA collected by foraging honey bees. Further development of these techniques can assist in the conservation of biodiversity by detecting ecosystem perturbations, with the potential to be expanded towards other critical flying pollinators.