Gut microbial communities of social bees

Single-step genome engineering in the bee gut symbiont Snodgrassella alvi

Honey bees are economically relevant pollinators experiencing population declines due to a number of threats. As in humans, the health of bees is influenced by their microbiome. The bacterium Snodgrassella alvi is a key member of the bee gut microbiome and has a role in excluding pathogens. Despite this importance, there are not currently any easy-to-use methods for modifying the S. alvi chromosome to study its genetics. To solve this problem, we developed a one-step procedure that uses electroporation and homologous recombination, which we term SnODIFY (Snodgrassella-specific One-step gene Deletion or Insertion to alter FunctionalitY). We used SnODIFY to create seven single-gene knockout mutants and recovered mutants for all constructs tested. Nearly all transformants had the designed genome modifications, indicating that SnODIFY is highly accurate. Mutant phenotypes were validated through knockout of Type 4 pilus genes, which led to reduced biofilm formation. We also used SnODIFY to insert heterologous sequences into the genome by integrating fluorescent protein-coding genes. Finally, we confirmed that genome modification is dependent on S. alvi's endogenous RecA protein. Because it does not require expression of exogenous recombination machinery, SnODIFY is a straightforward, accurate, and lightweight method for genome editing in S. alvi. This workflow can be used to study the functions of S. alvi genes and to engineer this symbiont for applications including protection of honey bee health.

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.

Delivery mechanism can enhance probiotic activity against honey bee pathogens

Managed honey bee (Apis mellifera) populations play a crucial role in supporting pollination of food crops but are facing unsustainable colony losses, largely due to rampant disease spread within agricultural environments. While mounting evidence suggests that select lactobacilli strains (some being natural symbionts of honey bees) can protect against multiple infections, there has been limited validation at the field-level and few methods exist for applying viable microorganisms to the hive. Here, we compare how two different delivery systems-standard pollen patty infusion and a novel spray-based formulation-affect supplementation of a three-strain lactobacilli consortium (LX3). Hives in a pathogen-dense region of California are supplemented for 4 weeks and then monitored over a 20-week period for health outcomes. Results show both delivery methods facilitate viable uptake of LX3 in adult bees, although the strains do not colonize long-term. Despite this, LX3 treatments induce transcriptional immune responses leading to sustained decreases in many opportunistic bacterial and fungal pathogens, as well as selective enrichment of core symbionts including Bombilactobacillus, Bifidobacterium, Lactobacillus, and Bartonella spp. These changes are ultimately associated with greater brood production and colony growth relative to vehicle controls, and with no apparent trade-offs in ectoparasitic Varroa mite burdens. Furthermore, spray-LX3 exerts potent activities against Ascosphaera apis (a deadly brood pathogen) likely stemming from in-hive dispersal differences, whereas patty-LX3 promotes synergistic brood development via unique nutritional benefits. These findings provide a foundational basis for spray-based probiotic application in apiculture and collectively highlight the importance of considering delivery method in disease management strategies.

Escherichia coli O157:H7 strains in bovine carcasses and the impact on the animal production chain

Foodborne diseases are characterized by conditions that can induce symptomatic illnesses in their carriers, and therefore represent a serious problem. They are important conditions from a clinical and epidemiological point of view, and are associated with the occurrence of serious public health problems, with a strong impact on morbidity and mortality. The Escherichia coli (E. coli) is an enterobacterium associated with enteric conditions of variable intensity and which are accompanied by blood. The transmission routes are mainly based on the consumption of contaminated food and water sources. Shiga toxin-producing E. coli (STEC) are considered a serogroup of E. coli, are capable of producing Shiga-type toxins (Stx 1 and Stx 2) and the O157:H7 strain is one of the best-known serotypes. The early detection of this pathogen is very important, especially due to the capacity of contamination of carcasses destined for food consumption and supply of productive markets. Sanitary protocols must be developed and constantly reviewed in order to prevent/control the presence of the pathogen.

Divergence and convergence of gut microbiomes of wild insect pollinators

Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.

Interactions with alloparents are associated with the diversity of infant skin and fecal bacterial communities in Chicago, United States

INTRODUCTION

Social interactions shape the infant microbiome by providing opportunities for caregivers to spread bacteria through physical contact. With most research focused on the impact of maternal-infant contact on the infant gut microbiome, it is unclear how alloparents (i.e., caregivers other than the parents) influence the bacterial communities of infant body sites that are frequently contacted during bouts of caregiving, including the skin.

METHODS

To begin to understand how allocare may influence the diversity of the infant microbiome, detailed questionnaire data on infant-alloparent relationships and specific allocare behaviors were coupled with skin and fecal microbiome samples (four body sites) from 48 infants living in Chicago, United States.

RESULTS

Data from 16S rRNA gene amplicon sequencing indicated that infant skin and fecal bacterial diversity showed strong associations (positive and negative) to having female adult alloparents. Alloparental feeding and co-sleeping displayed stronger associations to infant bacterial diversity compared to playing or holding. The associations with allocare behaviors differed in magnitude and direction across infant body sites. Bacterial relative abundances varied by infant-alloparent relationship and breastfeeding status.

CONCLUSION

This study provides some of the first evidence of an association between allocare and infant skin and fecal bacterial diversity. The results suggest that infants' exposure to bacteria from the social environment may vary based on infant-alloparent relationships and allocare behaviors. Since the microbiome influences immune system development, variation in allocare that impacts the diversity of infant bacterial communities may be an underexplored dimension of the social determinants of health in early life.

Symbiosis of Carpenter Bees with Uncharacterized Lactic Acid Bacteria Showing NAD Auxotrophy

Eusocial bees (such as honey bees and bumble bees) harbor core gut microbiomes that are transmitted through social interaction between nestmates. Carpenter bees are not eusocial; however, recent microbiome analyses found that Xylocopa species harbor distinctive core gut microbiomes. In this study, we analyzed the gut microbiomes of three Xylocopa species in Japan between 2016 and 2021 by V1 to V2 region-based 16S rDNA amplicon sequencing, and 14 candidate novel species were detected based on the full-length 16S rRNA gene sequences. All Xylocopa species harbor core gut microbiomes consisting of primarily lactic acid bacteria (LAB) that were phylogenetically distant from known species. Although they were difficult to cultivate, two LAB species from two different Xylocopa species were isolated by supplementing bacterial culture supernatants. Both genomes exhibited an average LAB genome size with a large set of genes for carbohydrate utilization but lacked genes to synthesize an essential coenzyme NAD, which is unique among known insect symbionts. Our findings of phylogenetically distinct core LAB of NAD auxotrophy reflected the evolution of Xylocopa-restricted bacteria retention and maintenance through vertical transmission of microbes during solitary life. We propose five candidate novel species belonging to the families Lactobacillaceae and Bifidobacteriaceae, including a novel genus, and their potential functions in carbohydrate utilization. IMPORTANCE Recent investigations found unique microbiomes in carpenter bees, but the description of individual microbes, including isolation and genomics, remains largely unknown. Here, we found that the Japanese Xylocopa species also harbor core gut microbiomes. Although most of them were difficult to isolate a pure colony, we successfully isolated several strains. We performed whole-genome sequencing of the isolated candidate novel species and found that the two Lactobacillaceae strains belonging to the Xylocopa-specific novel LAB clade lack the genes for synthesizing NAD, a coenzyme central to metabolism in all living organisms. Here, we propose a novel genus for the two LAB species based on very low 16S rRNA gene sequence similarities and genotypic characters.

Reactive oxygen species are regulated by immune deficiency and Toll pathways in determining the host specificity of honeybee gut bacteria

Host specificity is observed in gut symbionts of diverse animal lineages. But how hosts maintain symbionts while rejecting their close relatives remains elusive. We use eusocial bees and their codiversified gut bacteria to understand host regulation driving symbiotic specificity. The cross-inoculation of bumblebee Gilliamella induced higher prostaglandin in the honeybee gut, promoting a pronounced host response through immune deficiency (IMD) and Toll pathways. Gene silencing and vitamin C treatments indicate that reactive oxygen species (ROS), not antimicrobial peptides, acts as the effector in inhibiting the non-native strain. Quantitative PCR and RNAi further reveal a regulatory function of the IMD and Toll pathways, in which Relish and dorsal-1 may regulate Dual Oxidase (Duox) for ROS production. Therefore, the honeybee maintains symbiotic specificity by creating a hostile gut environment to exotic bacteria, through differential regulation of its immune system, reflecting a co-opting of existing machinery evolved to combat pathogens.

Extracts of Talaromyces purpureogenus Strains from Apis mellifera Bee Bread Inhibit the Growth of Paenibacillus spp. In Vitro

Honey bees coexist with fungi that colonize hive surfaces and pollen. Some of these fungi are opportunistic pathogens, but many are beneficial species that produce antimicrobial compounds for pollen conservation and the regulation of pathogen populations. In this study, we tested the in vitro antimicrobial activity of Talaromyces purpureogenus strains isolated from bee bread against Paenibacillus alvei (associated with European foulbrood disease) and three Aspergillus species that cause stonebrood disease. We found that methanol extracts of T. purpureogenus strains B18 and B195 inhibited the growth of P. alvei at a concentration of 0.39 mg/mL. Bioactivity-guided dereplication revealed that the activity of the crude extracts correlated with the presence of diketopiperazines, a siderophore, and three unknown compounds. We propose that non-pathogenic fungi such as Talaromyces spp. and their metabolites in bee bread could be an important requirement to prevent disease. Agricultural practices involving the use of fungicides can disrupt the fungal community and thus negatively affect the health of bee colonies.

Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats

The gut microbiota affects the health and overall fitness of bumblebees. It can enhance the host's ecological range by leveraging their metabolic capacities. However, the diversity of the gut microbiota and adaptive functional evolution in high-altitude regions remain unclear. To explore how the gut microbiota helps the host adapt to high-altitude environments, we analyzed the differences in diversity and function of the gut microbiota between high- and low-altitude regions through full-length 16S rRNA sequencing. Our results show that high-altitude regions have a lower abundance of Fructobacillus and Saccharibacter compared to low-altitude regions. Additionally, some individuals in low-altitude regions were invaded by opportunistic pathogens. The gut microbiota in high-altitude regions has a greater number of pathways involved in "Protein digestion and absorption" and "Biosynthesis of amino acids," while fewer carbohydrate pathways are involved in "digestion and absorption" and "Salmonella infection." Our finding suggests that plateau hosts typically reduce energy metabolism and enhance immunity in response to adverse environments. Correspondingly, the gut microbiota also makes changes, such as reducing carbohydrate degradation and increasing protein utilization in response to the host. Additionally, the gut microbiota regulates their abundance and function to help the host adapt to adverse high-altitude environments.

Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees

Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.

Effect of honey bee forage plants in Tunisia on diversity and antibacterial potential of lactic acid bacteria and bifidobacteria from Apis mellifera intermissa and its products

Lactic acid bacteria and bifidobacteria (LAB and Bifido), isolated from the gastrointestinal tract of Apis mellifera intermissa (BGIT), honey (H), propolis (P) and bee bread (BB) of hives set in different vegetations (wildflowers, caraway, orange blossom, Marrubium vulgare, Eucalyptus and Erica cinerea), were subjected to analysis of their antibacterial potential. Isolates able to inhibit Staphylococcus aureus were selected and identified with MALDI-TOF MS leading to 154 strains representing 12 LAB and Bifido species. Lactiplantibacillus plantarum, Pediococcus pentosaceus and Enterococcus faecalis were predominantly found in all matrices. BGIT showed the highest LAB and Bifido diversity with exclusive occurrences of five species (including Bifidobacterium asteroides and Limosilactobacillus fermentum). Honey was the second origin harboring an important variety of LAB species of which Apilactobacillus kunkeei and Enterococcus mundtii were characteristic of both H and BGIT. Principal components analysis revealed associations between antibacterial activities of LAB and Bifido, matrices and honey bee forage plants. Inhibition trends of S. aureus and Citrobacter freundii were highlighted with: L. plantarum from BGIT, P, H of bees feeding on E. cinerea; Pediococcus pentosaceus from BGIT, P, BB associated with E. cinerea; and Bifidobacterium asteroides from BGIT/orange blossom system. However, Enterococcus faecium associated with BGIT/Eucalyptus system antagonized Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. Our findings highlighted noteworthy effects of bee forage plants on the antibacterial activity of LAB and Bifido. Our approach could be useful to identify multiple conditions promoting antibacterial potency of LAB and Bifido under the combined effects of feeding plants and living matrices.

Effects of different temperatures on growth and intestinal microbial composition of juvenile Eriocheir sinensis

The change in temperature will change the composition of intestinal microorganisms of juvenile Eriocheir sinensis, and the composition of intestinal microorganisms will affect the growth and development of juvenile crabs. In order to explore the relationship between intestinal microorganisms and growth of E. sinensis at different temperatures, the status of growth and intestinal microflora of juvenile E. sinensis reared at different water temperatures (15 °C, 23 °C, and 30 °C) were compared in this study. The results showed that the respective survival rate of juvenile E. sinensis in the three water temperature groups was 100%, 87.5%, and 64.44%. Moreover, the molting rate increased with an increase in water temperature, which was at 0%, 10%, and 71.11% for the three respective temperature groups. The average weight gain rate showed an overall increasing trend with the increase of water temperature. Moreover, the final fatness of the crabs in the 30 °C water temperature group was significantly lower than that in the 15 °C and 23 °C groups (p < 0.05); there was no significant difference in the liver-to-body ratio among the three groups. The results of the alpha diversity analysis of the 16S rRNA data revealed that there was no significant difference in the intestinal microbial abundance among the three water temperature groups; however, the intestinal microbial diversity in the 23 °C water temperature group was significantly lower than that in the 15 °C and 30 °C groups. At the phylum level, the dominant flora of the three groups was Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, the abundance of Parabacteroides and Aeromonas in the intestine of the crabs in the 30 °C water temperature group was significantly higher than that in the 15 °C and 23 °C groups (p < 0.05). The function prediction showed that the main functional diversity of intestinal microflora of juvenile E. sinensis in the three water temperature groups was similar and mainly involved in metabolic-related functions, but there were still differences in the effects of water temperature on functional pathways such as metabolism, immunity, and growth among each group, either promoting or inhibiting. In conclusion, different water temperatures can affect the composition and function of intestinal flora of E. sinensis, and 23 °C-30 °C is the optimal water temperature for the growth of juvenile E. sinensis.

Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders

Disentangling modes and fidelity of symbiont transmission are key for understanding host-symbiont associations in wild populations. In group-living animals, social transmission may evolve to ensure high-fidelity transmission of symbionts, since non-reproducing helpers constitute a dead-end for vertical transmission. We investigated symbiont transmission in the social spider Stegodyphus dumicola, which lives in family groups where the majority of females are non-reproducing helpers, females feed offspring by regurgitation, and individuals feed communally on insect prey. Group members share temporally stable microbiomes across generations, while distinct variation in microbiome composition exists between groups. We hypothesized that horizontal transmission of symbionts is enhanced by social interactions, and investigated transmission routes within (horizontal) and across (vertical) generations using bacterial 16S rRNA gene amplicon sequencing in three experiments: (i) individuals were sampled at all life stages to assess at which life stage the microbiome is acquired. (ii) a cross-fostering design was employed to test whether offspring carry the microbiome from their natal nest, or acquire the microbiome of the foster nest via social transmission. (iii) adult spiders with different microbiome compositions were mixed to assess whether social transmission homogenizes microbiome composition among group members. We demonstrate that offspring hatch symbiont-free, and bacterial symbionts are transmitted vertically across generations by social interactions with the onset of regurgitation feeding by (foster)mothers in an early life stage. Social transmission governs horizontal inter-individual mixing and homogenization of microbiome composition among nest mates. We conclude that temporally stable host-symbiont associations in social species can be facilitated and maintained by high-fidelity social transmission.

Caffeine Consumption Helps Honey Bees Fight a Bacterial Pathogen

Caffeine has long been used as a stimulant by humans. Although this secondary metabolite is produced by some plants as a mechanism of defense against herbivores, beneficial or detrimental effects of such consumption are usually associated with dose. The Western honey bee, Apis mellifera, can also be exposed to caffeine when foraging at Coffea and Citrus plants, and low doses as are found in the nectar of these plants seem to boost memory learning and ameliorate parasite infection in bees. In this study, we investigated the effects of caffeine consumption on the gut microbiota of honey bees and on susceptibility to bacterial infection. We performed in vivo experiments in which honey bees, deprived of or colonized with their native microbiota, were exposed to nectar-relevant concentrations of caffeine for a week, then challenged with the bacterial pathogen Serratia marcescens. We found that caffeine consumption did not impact the gut microbiota or survival rates of honey bees. Moreover, microbiota-colonized bees exposed to caffeine were more resistant to infection and exhibited increased survival rates compared to microbiota-colonized or microbiota-deprived bees only exposed to the pathogen. Our findings point to an additional benefit of caffeine consumption in honey bee health by protecting against bacterial infections. IMPORTANCE The consumption of caffeine is a remarkable feature of the human diet. Common drinks, such as coffee and tea, contain caffeine as a stimulant. Interestingly, honey bees also seem to like caffeine. They are usually attracted to the low concentrations of caffeine found in nectar and pollen of Coffea plants, and consumption improves learning and memory retention, as well as protects against viruses and fungal parasites. In this study, we expanded these findings by demonstrating that caffeine can improve survival rates of honey bees infected with Serratia marcescens, a bacterial pathogen known to cause sepsis in animals. However, this beneficial effect was only observed when bees were colonized with their native gut microbiota, and caffeine seemed not to directly affect the gut microbiota or survival rates of bees. Our findings suggest a potential synergism between caffeine and gut microbial communities in protection against bacterial pathogens.

Atrazine exposure can dysregulate the immune system and increase the susceptibility against pathogens in honeybees in a dose-dependent manner

Recently, concerns regarding the impact of agrochemical pesticides on non-target organisms have increased. The effect of atrazine, the second-most widely used herbicide in commercial farming globally, on honeybees remains poorly understood. Here, we evaluated how atrazine impacts the survival of honeybees and pollen and sucrose consumption, investigating the morphology and mRNA expression levels of midgut tissue, along with bacterial composition (relative abundance) and load (absolute abundance) in the whole gut. Atrazine did not affect mortality, but high exposure (37.3 mg/L) reduced pollen and sucrose consumption, resulting in peritrophic membrane dysplasia. Sodium channels and chitin synthesis were considered potential atrazine targets, with the expression of various genes related to lipid metabolism, detoxification, immunity, and chemosensory activity being inhibited after atrazine exposure. Importantly, 37.3 mg/L atrazine exposure substantially altered the composition and size of the gut microbial community, clearly reducing both the absolute and relative abundance of three core gram-positive taxa, Lactobacillus Firm-5, Lactobacillus Firm-4, and Bifidobacterium asteroides. With altered microbiome composition and a weakened immune system following atrazine exposure, honeybees became more susceptible to infection by the opportunistic pathogen Serratia marcescens. Thus, considering its scale of use, atrazine could negatively impact honeybee populations worldwide, which may adversely affect global food security.

Keady M, Lim HC. Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections

The gut microbiome of bees is vital for the health of their hosts. Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections. We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey bees (Apis mellifera, N = 49) and bumble bees (Bombus spp., N = 66) in a suburban-rural landscape. We identified a total of 233 amplicon sequence variants (ASVs) and found simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus. The average number of ASVs per species ranged from 4.00-15.00 (8.79 ± 3.84, mean ± SD). Amplicon sequence variant of one bacterial species, G. apicola (ASV 1), was widely shared across honey bees and bumble bees. However, we detected another ASV of G. apicola that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees. Other than ASV 1, honey bees and bumble bees rarely share gut bacteria, even ones likely derived from outside environments (e.g., Rhizobium spp., Fructobacillus spp.). Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities than those of bumble bees, likely a result of the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria (G. apicola, Acinetobacter sp. and Pluralibacter sp.) that associate with Trypanosome and/or Vairimorpha infections in bees. Such insights help to determine bees' susceptibility to infections should gut microbiomes become disrupted by chemical pollutants and contribute to our understanding of what constitutes a state of dysbiosis.

Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome

The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.

No impacts of glyphosate or Crithidia bombi, or their combination, on the bumblebee microbiome

Pesticides are recognised as a key threat to pollinators, impacting their health in many ways. One route through which pesticides can affect pollinators like bumblebees is through the gut microbiome, with knock-on effects on their immune system and parasite resistance. We tested the impacts of a high acute oral dose of glyphosate on the gut microbiome of the buff tailed bumblebee (Bombus terrestris), and glyphosate's interaction with the gut parasite (Crithidia bombi). We used a fully crossed design measuring bee mortality, parasite intensity and the bacterial composition in the gut microbiome estimated from the relative abundance of 16S rRNA amplicons. We found no impact of either glyphosate, C. bombi, or their combination on any metric, including bacterial composition. This result differs from studies on honeybees, which have consistently found an impact of glyphosate on gut bacterial composition. This is potentially explained by the use of an acute exposure, rather than a chronic exposure, and the difference in test species. Since A. mellifera is used as a model species to represent pollinators more broadly in risk assessment, our results highlight that caution is needed in extrapolating gut microbiome results from A. mellifera to other bee species.

Gut microbiota assembly of Gotland varroa-surviving honey bees excludes major viral pathogens

The spread of the parasite Varroa destructor and associated viruses has resulted in massive honey bee colony losses with considerable economic and ecological impact. The gut microbiota has a major role in shaping honey bees tolerance and resistance to parasite infestation and viral infection, but the contribution of viruses to the assembly of the host microbiota in the context of varroa resistance and susceptibility remains unclear. Here, we used a network approach including viral and bacterial nodes to characterize the impact of five viruses, Apis Rhabdovirus-1 (ARV-1), Black Queen Cell virus (BQCV), Lake Sinai virus (LSV), Sacbrood virus (SBV) and Deformed wing virus (DWV) on the gut microbiota assembly of varroa-susceptible and Gotland varroa-surviving honey bees. We found that microbiota assembly was different in varroa-surviving and varroa-susceptible honey bees with the network of the latter having a whole module not present in the network of the former. Four viruses, ARV-1, BQCV, LSV, and SBV, were tightly associated with bacterial nodes of the core microbiota of varroa-susceptible honey bees, while only two viruses BQCV and LSV, appeared correlated with bacterial nodes in varroa-surviving honey bees. In silico removal of viral nodes caused major re-arrangement of microbial networks with changes in nodes centrality and significant reduction of the networks' robustness in varroa-susceptible, but not in varroa-surviving honey bees. Comparison of predicted functional pathways in bacterial communities using PICRUSt2 showed the superpathway for heme b biosynthesis from uroporphyrinogen-III and a pathway for arginine, proline, and ornithine interconversion as significantly increased in varroa-surviving honey bees. Notably, heme and its reduction products biliverdin and bilirubin have been reported as antiviral agents. These findings show that viral pathogens are differentially nested in the bacterial communities of varroa-surviving and varroa-susceptible honey bees. These results suggest that Gotland honey bees are associated with minimally-assembled and reduced bacterial communities that exclude viral pathogens and are resilient to viral nodes removal, which, together with the production of antiviral compounds, may explain the resiliency of Gotland honey bees to viral infections. In contrast, the intertwined virus-bacterium interactions in varroa-susceptible networks suggest that the complex assembly of microbial communities in this honey bee strain favor viral infections, which may explain viral persistence in this honey bee strain. Further understanding of protective mechanisms mediated by the microbiota could help developing novel ways to control devastating viral infections affecting honey bees worldwide.

Diesel exhaust particles alter gut microbiome and gene expression in the bumblebee Bombus terrestris

Insect decline is a major threat to ecosystems around the world as they provide many important functions, such as pollination or pest control. Pollution is one of the main reasons for the decline, alongside changes in land use, global warming, and invasive species. While negative impacts of pesticides are well-studied, there is still a lack of knowledge about the effects of other anthropogenic pollutants, such as airborne particulate matter, on insects. To address this, we exposed workers of the bumblebee Bombus terrestris to sublethal doses of diesel exhaust particles (DEPs) and brake dust, orally or via air. After 7 days, we looked at the composition of the gut microbiome and tracked changes in gene expression. While there were no changes in the other treatments, oral DEP exposure significantly altered the structure of the gut microbiome. In particular, the core bacterium Snodgrassella had a decreased abundance in the DEP treatment. Similarly, transcriptome analysis revealed changes in gene expression after oral DEP exposure, but not in the other treatments. The changes are related to metabolism and signal transduction, which indicates a general stress response. Taken together, our results suggest potential health effects of DEP exposure on insects, here shown in bumblebees, as gut dysbiosis may increase the susceptibility of bumblebees to pathogens, while a general stress response may lower available energy resources. Those effects may exacerbate under natural conditions where insects face a multiple-stressor environment.

Probiotic candidates for controlling Paenibacillus larvae, a causative agent of American foulbrood disease in honey bee

BACKGROUND

American foulbrood (AFB) disease caused by Paenibacillus larvae is dangerous, and threatens beekeeping. The eco-friendly treatment method using probiotics is expected to be the prospective method for controlling this pathogen in honey bees. Therefore, this study investigated the bacterial species that have antimicrobial activity against P. larvae.

RESULTS

Overall, 67 strains of the gut microbiome were isolated and identified in three phyla; the isolates had the following prevalence rates: Firmicutes 41/67 (61.19%), Actinobacteria 24/67 (35.82%), and Proteobacteria 2/67 (2.99%). Antimicrobial properties against P. larvae on agar plates were seen in 20 isolates of the genus Lactobacillus, Firmicutes phylum. Six representative strains from each species (L. apis HSY8_B25, L. panisapium PKH2_L3, L. melliventris HSY3_B5, L. kimbladii AHS3_B36, L. kullabergensis OMG2_B25, and L. mellis OMG2_B33) with the largest inhibition zones on agar plates were selected for in vitro larvae rearing challenges. The results showed that three isolates (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) had the potential to be probiotic candidates with the properties of safety to larvae, inhibition against P. larvae in infected larvae, and high adhesion ability.

CONCLUSIONS

Overall, 20 strains of the genus Lactobacillus with antimicrobial properties against P. larvae were identified in this study. Three representative strains from different species (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) were evaluated to be potential probiotic candidates and were selected for probiotic development for the prevention of AFB. Importantly, the species L. panisapium isolated from larvae was identified with antimicrobial activity for the first time in this study.

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees

Nosema ceranae is an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find that Snodgrassella alvi inhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly, N. ceranae employs the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of the N. ceranae parasite. Finally, we genetically modify the symbiotic S. alvi to deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineered S. alvi induces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically, N. ceranae is most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts against N. ceranae and provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes

Pollen is the primary source of dietary protein for honey bees. It also includes complex polysaccharides in its outer coat, which are largely indigestible by bees but can be metabolized by bacterial species within the gut microbiota. During periods of reduced availability of floral pollen, supplemental protein sources are frequently provided to managed honey bee colonies. The crude proteins in these supplemental feeds are typically byproducts from food manufacturing processes and are rarely derived from pollen. Our experiments on the impact of different diets showed that a simplified pollen-free diet formulated to resemble the macronutrient profile of a monofloral pollen source resulted in larger microbial communities with reduced diversity, reduced evenness, and reduced levels of potentially beneficial hive-associated bacteria. Furthermore, the pollen-free diet sharply reduced the expression of genes central to honey bee development. In subsequent experiments, we showed that these shifts in gene expression may be linked to colonization by the gut microbiome. Lastly, we demonstrated that for bees inoculated with a defined gut microbiota, those raised on an artificial diet were less able to suppress infection from a bacterial pathogen than those that were fed natural pollen. Our findings demonstrate that a pollen-free diet significantly impacts the gut microbiota and gene expression of honey bees, indicating the importance of natural pollen as a primary protein source.

The Ascosphaera apis Infection (Chalkbrood Disease) Alters the Gut Bacteriome Composition of the Honeybee

The declining honeybee populations are a significant risk to the productivity and security of agriculture worldwide. Although there are many causes of these declines, parasites are a significant one. Disease glitches in honeybees have been identified in recent years and increasing attention has been paid to addressing the issue. Between 30% and 40% of all managed honeybee colonies in the USA have perished annually over the past few years. American foulbrood (AFB) and European foulbrood (EFB) have been reported as bacterial diseases, Nosema as a protozoan disease, and Chalkbrood and Stonebrood as fungal diseases. The study aims to compare the bacterial community related to the Nosema ceranae and Ascosphaera apis infection on the gut of the honeybee and compare it with the weakly active honeybees. The Nosema-infected honeybees contain the phyla Proteobacteria as the significantly dominant bacterial phyla, similar to the weakly active honeybees. In contrast, the Ascosphaera (Chalkbrood) infected honeybee contains large amounts of Firmicutes rather than Proteobacteria.

Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees

Background

Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown.

Methods

We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis.

Results

A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism.

Conclusions

Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.

Gut microbial diversity in Apis cerana indica and Apis florea colonies: a comparative study

Introduction

Honey bee gut microbiota have an important role in host health, nutrition, host-symbiont interaction, and interaction behavior with the surrounding environment. Recent discoveries of strain-level variation, characteristics of protective and nutritional capabilities, and reports of eco-physiological significance to the microbial community have emphasized the importance of honey bee gut microbiota. Many regions of Asia and Africa are inhabited by the dwarf honey bee, Apis florea. Studying its microflora and potential for pollination is therefore of foremost importance.

Methods

In the present investigation, we aimed to explore the gut bacteriobiome composition of two distinct honey bee species, Apis florea and Apis cerana indica using high throughput sequencing. Functional predictions of bee gut bacterial communities using PICRUSt2 was carried out.

Results and discussion

The phylum Proteobacteria dominated the bacterial community in both A. cerana indica (50.1%) and A. florea (86.7%), followed by Firmicutes (26.29 and 12.81%), Bacteroidetes (23.19 and 0.04%) and Actinobacteria (0.4 and 0.02%) respectively. The gut bacteria of A. cerana indica was more diverse than that of A. florea. The observed variations in bacterial genomic diversity among these critical pollinator species may have been influenced by the apiary management techniques, ecological adaptation factors or habitat size. These variations can have a significant effect in understanding host-symbiont interactions and functioning of gut microbiota highlighting the importance of metagenomic survey in understanding microbial community ecology and evolution. This is the first comparative study on variation in bacterial diversity between two Asian honey bees.

The effects of glyphosate, pure or in herbicide formulation, on bumble bees and their gut microbial communities

The widespread use of glyphosate-based formulations to eliminate unwanted vegetation has increased concerns regarding their effects on non-target organisms, such as honey bees and their gut microbial communities. These effects have been associated with both glyphosate and co-formulants, but it is still unknown whether they translate to other bee species. In this study, we tested whether glyphosate, pure or in herbicide formulation, can affect the gut microbiota and survival rates of the eastern bumble bee, Bombus impatiens. We performed mark-recapture experiments with bumble bee workers from four different commercial colonies, which were exposed to field relevant concentrations of glyphosate or a glyphosate-based formulation (0.01 mM to 1 mM). After a 5-day period of exposure, we returned the bees to their original colonies, and they were sampled at days 0, 3 and 7 post-exposure to investigate changes in microbial community and microbiota resilience by 16S rRNA amplicon sequencing and quantitative PCR. We found that exposure to glyphosate, pure or in herbicide formulation, reduced the relative abundance of a beneficial bee gut bacterium, Snodgrassella, in bees from two of four colonies when compared to control bees at day 0 post-exposure, but this reduction became non-significant at days 3 and 7 post-exposure, suggesting microbiota resilience. We did not find significant changes in total bacteria between control and exposed bees. Moreover, we observed an overall trend in decreased survival rates in bumble bees exposed to 1 mM herbicide formulation during the 7-day post-exposure period, suggesting a potential negative effect of this formulation on bumble bees.

Basic Structures of Gut Bacterial Communities in Eusocial Insects

Gut bacterial communities assist host animals with numerous functions such as food digestion, nutritional provision, or immunity. Some social mammals and insects are unique in that their gut microbial communities are stable among individuals. In this review, we focus on the gut bacterial communities of eusocial insects, including bees, ants, and termites, to provide an overview of their community structures and to gain insights into any general aspects of their structural basis. Pseudomonadota and Bacillota are prevalent bacterial phyla commonly detected in those three insect groups, but their compositions are distinct at lower taxonomic levels. Eusocial insects harbor unique gut bacterial communities that are shared within host species, while their stability varies depending on host physiology and ecology. Species with narrow dietary habits, such as eusocial bees, harbor highly stable and intraspecific microbial communities, while generalists, such as most ant species, exhibit relatively diverse community structures. Caste differences could influence the relative abundance of community members without significantly altering the taxonomic composition.

The impact of early-life exposure to three agrochemicals on survival, behavior, and gut microbiota of stingless bees (Partamona helleri)

Over the last few decades, agrochemicals have been partially associated with a global reduction in bees' population. Toxicological assessment is therefore crucial for understanding the overall agrochemical risks to stingless bees. Therefore, the lethal and sublethal effects of agrochemicals commonly used in crops (copper sulfate, glyphosate, and spinosad) on the behavior and gut microbiota of the stingless bee, Partamona helleri, were assessed using chronic exposure during the larval stage. When used at the field-recommended rates, both copper sulfate (200 µg of active ingredient/bee; a.i µg bee^-1) and spinosad (8.16 a.i µg bee^-1) caused a decrease in bee survival, while glyphosate (148 a.i µg bee^-1) did not show any significant effects. No significant adverse effects on bee development were observed in any treatment with CuSO₄ or glyphosate, but spinosad (0.08 or 0.03 a.i µg bee ^-1) increased the number of deformed bees and reduced their body mass. Agrochemicals changed the behavior of bees and composition of the gut microbiota of adult bees, and metals such as copper accumulated in the bees' bodies. The response of bees to agrochemicals depends on the class or dose of the ingested compound. In vitro rearing of stingless bees' larvae is a useful tool to elucidate the sublethal effects of agrochemicals.

Gut microbiota composition and gene expression changes induced in the Apis cerana exposed to acetamiprid and difenoconazole at environmentally realistic concentrations alone or combined

Apis cerana is an important pollinator of agricultural crops in China. In the agricultural environment, A. cerana may be exposed to acetamiprid (neonicotinoid insecticide) and difenoconazole (triazole fungicide), alone or in combination because they are commonly applied to various crops. At present, our understanding of the toxicological effects of acetamiprid and difenoconazole on honey bee gut microbiomes is limited. The primary objective of this study was to explore whether these two pesticides affect honey bees' gut microbiota and to analyze the transcriptional effects of these two pesticides on honey bees' head and gut. In this study, adults of A. cerana were exposed to acetamiprid and/or difenoconazole by contaminated syrup at field-realistic concentrations for 10 days. Results indicated that acetamiprid and/or difenoconazole chronic exposure did not affect honey bees' survival and food consumption, whereas difenoconazole decreased the weight of honey bees. 16S rRNA sequencing suggested that difenoconazole and the mixture of difenoconazole and acetamiprid decreased the diversity index and shaped the composition of gut bacteria microbiota, whereas acetamiprid did not impact the gut bacterial community. The ITS sequence data showed that neither of the two pesticides affected the fungal community structure. Meanwhile, we also observed that acetamiprid or difenoconazole significantly altered the expression of genes related to detoxification and immunity in honey bees' tissues. Furthermore, we observed that the adverse effect of the acetamiprid and difenoconazole mixture on honey bees' health was greater than that of a single mixture. Taken together, our study demonstrates that acetamiprid and/or difenoconazole exposure at field-realistic concentrations induced changes to the honey bee gut microbiome and gene expression.

Effect of Chronic Exposure to Sublethal Doses of Imidacloprid and Nosema ceranae on Immunity, Gut Microbiota, and Survival of Africanized Honey Bees

Large-scale honey bee colony losses reported around the world have been associated with intoxication with pesticides, as with the presence of pests and pathogens. Among pesticides, neonicotinoid insecticides are the biggest threat. Due to their extensive use, they can be found in all agricultural environments, including soil, water, and air, are persistent in the environment, and are highly toxic for honey bees. In addition, infection by different pests and pathogens can act synergistically, weakening bees. In this study, we investigated the effects of chronic exposure to sublethal doses of imidacloprid alone or combined with the microsporidia Nosema ceranae on the immune response, deformed wing virus infection (DWV), gut microbiota, and survival of Africanized honey bees. We found that imidacloprid affected the expression of some genes associated with immunity generating an altered physiological state, although it did not favor DWV or N. ceranae infection. The pesticide alone did not affect honey bee gut microbiota, as previously suggested, but when administered to N. ceranae infected bees, it generated significant changes. Finally, both stress factors caused high mortality rates. Those results illustrate the negative impact of imidacloprid alone or combined with N. ceranae on Africanized honey bees and are useful to understand colony losses in Latin America.

Social Interaction is Unnecessary for Hindgut Microbiome Transmission in Honey Bees: The Effect of Diet and Social Exposure on Tissue-Specific Microbiome Assembly

Honey bees are a model for host-microbial interactions with experimental designs evolving towards conventionalized worker bees. Research on gut microbiome transmission and assembly has examined only a fraction of factors associated with the colony and hive environment. Here, we studied the effects of diet and social isolation on tissue-specific bacterial and fungal colonization of the midgut and two key hindgut regions. We found that both treatment factors significantly influenced early hindgut colonization explaining similar proportions of microbiome variation. In agreement with previous work, social interaction with older workers was unnecessary for core hindgut bacterial transmission. Exposure to natural eclosion and fresh stored pollen resulted in gut bacterial communities that were taxonomically and structurally equivalent to those produced in the natural colony setting. Stressed diets of no pollen or autoclaved pollen in social isolation resulted in decreased fungal abundance and bacterial diversity, and atypical microbiome structure and tissue-specific variation of functionally important core bacteria. Without exposure to the active hive environment, the abundance and strain diversity of keystone ileum species Gilliamella apicola was markedly reduced. These changes were associated with significantly larger ileum microbiotas suggesting that extended exposure to the active hive environment plays an antibiotic role in hindgut microbiome establishment. We conclude that core hindgut microbiome transmission is facultative horizontal with 5 of 6 core hindgut species readily acquired from the built hive structure and natural diet. Our findings contribute novel insights into factors influencing assembly and maintenance of honey bee gut microbiota and facilitate future experimental designs.

Impact of a Microbial Pest Control Product Containing Bacillus thuringiensis on Brood Development and Gut Microbiota of Apis mellifera Worker Honey Bees

To avoid potential adverse side effects of chemical plant protection products, microbial pest control products (MPCP) are commonly applied as biological alternatives. This study aimed to evaluate the biosafety of a MPCP with the active organism Bacillus thuringiensis ssp. aizawai (strain: ABTS-1857). An in-hive feeding experiment was performed under field-realistic conditions to examine the effect of B. thuringiensis (B. t.) on brood development and the bacterial abundance of the core gut microbiome (Bifidobacterium asteroids, Gilliamella apicola, the group of Lactobacillus and Snodgrasella alvi) in Apis mellifera worker bees. We detected a higher brood termination rate and a non-successful development into worker bees of treated colonies compared to those of the controls. For the gut microbiome, all tested core members showed a significantly lower normalized abundance in bees of the treated colonies than in those of the controls; thus, a general response of the gut microbiome may be assumed. Consequently, colony exposure to B. t. strain ABTS-1857 had a negative effect on brood development under field-realistic conditions and caused dysbiosis of the gut microbiome. Further studies with B. t.-based products, after field-realistic application in bee attractive crops, are needed to evaluate the potential risk of these MPCPs on honey bees.

A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont

BACKGROUND

To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis.

RESULTS

The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont.

CONCLUSION

The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.

Microplastics and Nanoplastics Effects on Plant-Pollinator Interaction and Pollination Biology

Microplastics and nanoplastics (MNPs) contamination is an emerging environmental and public health concern, and these particles have been reported both in aquatic and terrestrial ecosystems. Recent studies have expanded our understanding of the adverse effects of MNPs pollution on human, terrestrial, and aquatic animals, insects, and plants. In this perspective, we describe the adverse effects of MNPs particles on pollinator and plant health and discuss the mechanisms by which MNPs disrupt the pollination process. We discuss the evidence and integrate transcriptome studies to investigate the negative effects of MNPs on the molecular biology of pollination, which may cause delay or inhibit the pollination services. We conclude by addressing challenges to plant-pollinator health from MNPs pollution and argue that such harmful effects disrupt the communication between plant and pollinator for a successful pollination process.

Ecotoxicological effects of common fungicides on the eastern honeybee Apis cerana cerana (Hymenoptera)

The widespread use of fungicides for plant protection has increased the potential for pollinator exposure. This study therefore aimed at assessing the acute and chronic effects of fungicides on pollinators. For this purpose, the acute oral toxicity of the common fungicides azoxystrobin, pyraclostrobin, and boscalid to Eastern honeybee Apis cerana cerena was first evaluated, and the chronic effects on multiple aspects were investigated after exposure to a one-tenth medium lethal dose (LD₅₀) for 10 days. This study revealed that the LD₅₀ values of azoxystrobin, pyraclostrobin and boscalid for adult Eastern honeybees were 12.7 μg/bee, 36.6 μg/bee, and >119 μg/bee, respectively. Midgut epithelial cells revealed that fungicide exposure caused increased intercellular spaces and varying degrees of vacuolization. Exposure to these three fungicides and their binary mixtures significantly affected glycerophospholipid, alanine, aspartate, and glutamate metabolism in Eastern honeybee midguts. Additionally, the relative composition of Lactobacillus, the dominant functional genus in Eastern honeybee guts decreased and microbial balance was disrupted. All fungicides and their mixtures induced strong transcriptional upregulation of genes associated with the immune response and encoding enzymes related to oxidative phosphorylation and metabolism, including abaecin, apidaecin, hymenotaecin, cyp4c3, cyp6a2 and hbg3. Our study provides important insight for understanding the effects of commonly used fungicides on nontarget pollinator and contributes to a more comprehensive assessment of fungicide effects on ecological and environmental safety.

Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees

Pathogens and parasites of solitary bees have been studied for decades, but the microbiome as a whole is poorly understood for most taxa. Comparative analyses of microbiome features such as composition, abundance, and specificity, can shed light on bee ecology and the evolution of host–microbe interactions. Here we study microbiomes of ground-nesting cellophane bees (Colletidae: Diphaglossinae). From a microbial point of view, the diphaglossine genus Ptiloglossa is particularly remarkable: their larval provisions are liquid and smell consistently of fermentation. We sampled larval provisions and various life stages from wild nests of Ptiloglossa arizonensis and two species of closely related genera: Caupolicana yarrowi and Crawfordapis luctuosa. We also sampled nectar collected by P. arizonensis. Using 16S rRNA gene sequencing, we find that larval provisions of all three bee species are near-monocultures of lactobacilli. Nectar communities are more diverse, suggesting ecological filtering. Shotgun metagenomic and phylogenetic data indicate that Ptiloglossa culture multiple species and strains of Apilactobacillus, which circulate among bees and flowers. Larval lactobacilli disappear before pupation, and hence are likely not vertically transmitted, but rather reacquired from flowers as adults. Thus, brood cell microbiomes are qualitatively similar between diphaglossine bees and other solitary bees: lactobacilli-dominated, environmentally acquired, and non-species-specific. However, shotgun metagenomes provide evidence of a shift in bacterial abundance. As compared with several other bee species, Ptiloglossa have much higher ratios of bacterial to plant biomass in larval provisions, matching the unusually fermentative smell of their brood cells. Overall, Ptiloglossa illustrate a path by which hosts can evolve quantitatively novel symbioses: not by acquiring or domesticating novel symbionts, but by altering the microenvironment to favor growth of already widespread and generalist microbes.

Isolation and characterization of Lactobacillus casei A14.2, a strain with immunomodulating activity on Apis mellifera

Considering the economic and environmental role played by bees and their present threats it is necessary to develop food supplements favoring their health. The aim of this work was to isolate and characterize an immunomodulating probiotic capable to improve the health of honeybee colonies. For this purpose, bacterial strains were isolated from Apis mellifera bees (N = 180) obtained at three apiaries. A total of 44 strains were isolated and 9 of them were identified as Lactobacillus having the capacity to grow under saccharose osmotic stress, at pH 4.0 and possessing a wide susceptibility to antibiotics. Results allowed to select two strains but finally only one of them, strain A14.2 showed a very significant immunomodulating activity. This strain increased the expression of mRNA codifying the antimicrobial peptides 24 h post-administration. We evaluated its growth kinetics under aerobic and microaerobic conditions and its survival in the presence of high concentrations of saccharose. Results demonstrated that Lactobacillus casei A14.2 strain was highly tolerant to oxygen and that it was able to adapt to saccharose enriched environments (50% and 100% w/v). Finally, L. casei A14.2 strain was administered monthly during summer and early fall to 4 honeybee colonies (2 controls and 2 treatments). The results showed a gradual sustained decrease of infestation (p < 0.05) by the pathogenic Nosema spp. but no reduction in the infestation by the mite Varroa destructor. These results suggest that the administration of this potential probiotic, may increase the resistance of honeybee colonies to infectious diseases caused by Nosema spp.

Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees

Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.

Unraveling the Role of Antimicrobial Peptides in Insects

Antimicrobial peptides (AMPs) are short, mainly positively charged, amphipathic molecules. AMPs are important effectors of the immune response in insects with a broad spectrum of antibacterial, antifungal, and antiparasitic activity. In addition to these well-known roles, AMPs exhibit many other, often unobvious, functions in the host. They support insects in the elimination of viral infections. AMPs participate in the regulation of brain-controlled processes, e.g., sleep and non-associative learning. By influencing neuronal health, communication, and activity, they can affect the functioning of the insect nervous system. Expansion of the AMP repertoire and loss of their specificity is connected with the aging process and lifespan of insects. Moreover, AMPs take part in maintaining gut homeostasis, regulating the number of endosymbionts as well as reducing the number of foreign microbiota. In turn, the presence of AMPs in insect venom prevents the spread of infection in social insects, where the prey may be a source of pathogens.

Ternary Mixture of Azoxystrobin, Boscalid and Pyraclostrobin Disrupts the Gut Microbiota and Metabolic Balance of Honeybees (Apis cerana cerana)

There is a growing risk of pollinators being exposed to multiple fungicides due to the widespread use of fungicides for plant protection. A safety assessment of honeybees exposed to multiple commonly used fungicides is urgently required. Therefore, the acute oral toxicity of the ternary mixed fungicide of ABP (azoxystrobin: boscalid: pyraclostrobin = 1:1:1, m/m/m) was tested on honeybees (Apis cerana cerana), and its sublethal effect on foragers’ guts was evaluated. The results showed that the acute oral median lethal concentration (LD50) of ABP for foragers was 12.6 μg a.i./bee. ABP caused disorder of the morphological structure of midgut tissue and affected the intestinal metabolism; the composition and structure of the intestinal microbial community was perturbed, which altered its function. Moreover, the transcripts of genes involved in detoxification and immunity were strongly upregulated with ABP treatment. The study implies that exposure to a fungicide mixture of ABP can cause a series of negative effects on the health of foragers. This work provides a comprehensive understanding of the comprehensive effects of common fungicides on non-target pollinators in the context of ecological risk assessment and the future use of fungicides in agriculture.

Microbial diversity in stingless bee gut is linked to host wing size and influenced by the environment

Stingless bees are important social corbiculate bees, fulfilling critical pollination roles in many ecosystems. However, their gut microbiota, particularly the fungal communities associated with them, remains inadequately characterised. This knowledge gap hinders our understanding of bee gut microbiomes and their impacts on the host fitness. We collected 121 samples from two species, Tetragonula carbonaria and Austroplebeia australis across 1200 km of eastern Australia. We characterised their gut microbiomes and investigated potential correlations between bee gut microbiomes and various geographical and morphological factors. We found their core microbiomes consisted of the abundant bacterial taxa Snodgrassella, Lactobacillus and Acetobacteraceae, and the fungal taxa Didymellaceae, Monocilium mucidum and Aureobasidium pullulans, but variances of their abundances among samples were large. Furthermore, gut bacterial richness of T. carbonaria was positively correlated to host forewing length, an established correlate to body size and fitness indicator in insects relating to flight capacity. This result indicates that larger body size/longer foraging distance of bees could associate with greater microbial diversity in gut. Additionally, both host species identity and management approach significantly influenced gut microbial diversity and composition, and similarity between colonies for both species decreased as the geographic distance between them increased. We also quantified the total bacterial and fungal abundance of the samples using qPCR analyses and found that bacterial abundance was higher in T. carbonaria compared to A. australis, and fungi were either lowly abundant or below the threshold of detection for both species. Overall, our study provides novel understanding of stingless bee gut microbiomes over a large geographic span and reveals that gut fungal communities likely not play an important role in host functions due to their low abundances.

Honey bee functional genomics using symbiont-mediated RNAi

Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.

Microbial community profiling and culturing reveal functional groups of bacteria associated with Thai commercial stingless worker bees (Tetragonula pagdeni)

Stingless bees play a crucial role in the environment and agriculture as they are effective pollinators. Furthermore, they can produce various products that can be exploited economically, such as propolis and honey. Despite their economic value, the knowledge of microbial community of stingless bees, and their roles on the bees' health, especially in Thailand, are in its infancy. This study aimed to investigate the composition and the functions of bacterial community associated with Tetragonula pagdeni stingless bees using culture-independent and culture-dependent approaches with emphasis on lactic acid bacteria. The culture-independent results showed that the dominant bacterial phyla were Firmicutes, Proteobacteria and Actinobacteria. The most abundant families were Lactobacillaceae and Halomonadaceae. Functional prediction indicated that the prevalent functions of bacterial communities were chemoheterotrophy and fermentation. In addition, the bacterial community might be able to biosynthesize amino acid and antimicrobial compounds. Further isolation and characterization resulted in isolates that belonged to the dominant taxa of the community and possessed potentially beneficial metabolic activity. This suggested that they are parts of the nutrient acquisition and host defense bacterial functional groups in Thai commercial stingless bees.

Beneficial bacteria as biocontrol agents for American foulbrood disease in honey bees (Apis mellifera)

American foulbrood (AFB) is a cosmopolitan bacterial disease that affects honey bee (Apis mellifera) larvae and causes great economic losses in apiculture. Currently, no satisfactory methods are available for AFB treatment mainly due to the difficulties to eradicate the tenacious spores produced by the etiological agent of AFB, Paenibacillus larvae (Bacillales, Paenibacillaceae). This present review focused on the beneficial bacteria that displayed antagonistic activities against P. larvae and demonstrated potential in AFB control. Emphases were placed on commensal bacteria (genus Bacillus and lactic acid bacteria in particular) in the alimentary tract of honey bees. The probiotic roles lactic acid bacteria play in combating the pathogenic P. larvae and the limitations referring to the application of these beneficial bacteria were addressed.

The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans

The present research investigated whether accidental contact through stinging with honeybees, wasps, and hornets could represent a microbial hazard for humans. It has been previously suggested that such contact may transmit pathogens causing infections that could even be fatal for some susceptible individuals. Stinging simulation experiments were performed in the lab with live insects collected from the environment in Lemnos Island (north-eastern Greece), while different selective agar media targeting some clinically important bacteria (i.e., Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis/faecium, and Pseudomonas aeruginosa) were used as substrates for microbial recovery and identification. Results revealed none of the target pathogenic bacterial species in the honeybee samples, with bacilli, staphylococci, and micrococci dominating their surveyed microbiota. However, most of the suspect colonies isolated from wasps and hornets belonged to important hygienic indicators (i.e., enterococci, Proteus mirabilis, and coliforms), implying possible contact of these insects with fecal origin materials. To sum up, the microbiota that may be transmitted to humans through stinging appears to differ between honeybees and wasps/hornets, while the isolation from the latter samples of some other important opportunistic pathogens, such as Enterobacter spp. and Klebsiella spp., also known for multidrug resistance, could be an additional reason of concern.

Synergy in symbiosis

Honeybees rely on their microbial gut symbionts to overcome a potent toxin found in pollen and nectar.

Geographical and Seasonal Analysis of the Honeybee Microbiome

We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.

Nasonia-microbiome associations: a model for evolutionary hologenomics research

In recent years, with the development of microbial research technologies, microbiota research has received widespread attention. The parasitoid wasp genus Nasonia is a good model organism for studying insect behavior, development, evolutionary genetics, speciation, and symbiosis. This review describes key advances and progress in the field of the Nasonia-microbiome interactions. We provide an overview of the advantages of Nasonia as a model organism for microbiome studies, list research methods to study the Nasonia microbiome, and discuss recent discoveries in Nasonia microbiome research. This summary of the complexities of Nasonia-microbiome relationships will help to contribute to a better understanding of the interactions between animals and their microbiomes and establish a clear research direction for Nasonia-microbiome interactions in the future.