The bumble bee microbiome increases survival of bees exposed to selenate toxicity

With a little help from my friends: the roles of microbial symbionts in insect populations and communities

To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Microbial Symbiont-Based Detoxification of Different Phytotoxins and Synthetic Toxic Chemicals in Insect Pests and Pollinators

Insects are the most diverse form of life, and as such, they interact closely with humans, impacting our health, economy, and agriculture. Beneficial insect species contribute to pollination, biological control of pests, decomposition, and nutrient cycling. Pest species can cause damage to agricultural crops and vector diseases to humans and livestock. Insects are often exposed to toxic xenobiotics in the environment, both naturally occurring toxins like plant secondary metabolites and synthetic chemicals like herbicides, fungicides, and insecticides. Because of this, insects have evolved several mechanisms of resistance to toxic xenobiotics, including sequestration, behavioral avoidance, and enzymatic degradation, and in many cases had developed symbiotic relationships with microbes that can aid in this detoxification. As research progresses, the important roles of these microbes in insect health and function have become more apparent. Bacterial symbionts that degrade plant phytotoxins allow host insects to feed on otherwise chemically defended plants. They can also confer pesticide resistance to their hosts, especially in frequently treated agricultural fields. It is important to study these interactions between insects and the toxic chemicals they are exposed to in order to further the understanding of pest insect resistance and to mitigate the negative effect of pesticides on nontarget insect species like Hymenopteran pollinators.

Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees

Strain LMG 33000T was isolated from a Bombus lapidarius gut sample. It shared the highest percentage 16S rRNA sequence identity, average amino acid identity, and amino acid identity of conserved genes with Convivina intestini LMG 28291T (95.86 %, 69.9 and 76.2 %, respectively), and the highest percentage OrthoANIu value with Fructobacillus fructosus DSM 20349T (71.4 %). Phylogenomic analyses by means of 107 or 120 conserved genes consistently revealed Convivina as nearest neighbour genus. The draft genome of strain LMG 33000T was 1.44 Mbp in size and had a DNA G+C content of 46.1 mol%. Genomic and physiological analyses revealed that strain LMG 33000T was a typical obligately fructophilic lactic acid bacterium that lacked the adhE and aldh genes and that did not produce ethanol during glucose or fructose metabolism. In contrast, Convivina species have the adhE and aldh genes in their genomes and produced ethanol from glucose and fructose metabolism, which is typical for heterofermentative lactic acid bacteria. Moreover, strain LMG 33000T exhibited catalase activity, an unusual characteristic among lactic acid bacteria, that is not shared with Convivina species. Given its position in the phylogenomic trees, and the difference in genomic percentage G+C content and in physiological and metabolic characteristics between strain LMG 33000T and Convivina species, we considered it most appropriate to classify strain LMG 33000T into a novel genus and species within the Lactobacillaceae family for which we propose the name Eupransor demetentiae gen. nov., sp. nov., with LMG 33000T (=CECT 30958T) as the type strain.

Microbiome and floral associations of a wild bee using biodiversity survey collections

The health of bees can be assessed through their microbiome, which serves as a biomarker indicating the presence of both beneficial and harmful microorganisms within a bee community. This study presents the characterisation of the bacterial, fungal, and plant composition on the cuticle of adult bicoloured sweat bees (Agapostemon virescens). These bees were collected using various methods such as pan traps, blue vane traps and sweep netting across the northern extent of their habitat range. Non-destructive methods were employed to extract DNA from the whole pinned specimens of these wild bees. Metabarcoding of the 16S rRNA, ITS and rbcL regions was then performed. The study found that the method of collection influenced the detection of certain microbial and plant taxa. Among the collection methods, sweep net samples showed the lowest fungal alpha diversity. However, minor differences in bacterial or fungal beta diversity suggest that no single method is significantly superior to others. Therefore, a combination of techniques can cater to a broader spectrum of microbial detection. The study also revealed regional variations in bacterial, fungal and plant diversity. The core microbiome of A. virescens comprises two bacteria, three fungi and a plant association, all of which are commonly detected in other wild bees. These core microbes remained consistent across different collection methods and locations. Further extensive studies of wild bee microbiomes across various species and landscapes will help uncover crucial relationships between pollinator health and their environment.

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis

BACKGROUND

The gut microbiota and their hosts profoundly affect each other's physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria.

RESULTS

We established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host.

CONCLUSIONS

Using the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions. Video Abstract.

A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees

The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.

Discussion: Harnessing microbiome-mediated adaptations in insect pollinators to mitigate climate change impact on crop pollination

Insect pollinators, vital for agriculture and biodiversity, face escalating threats from climate change. We argue and explore the pivotal role of the microbiomes in shaping adaptations of insect pollinator resilience amid climate-induced challenges (climate change and habitat alteration). Examining diverse taxonomic groups, we unravel the interplay between insect physiology, microbiomes, and adaptive mechanisms. Climate-driven alterations in microbiomes impact insect health, behavior, and plant interactions, posing significant effects on agricultural ecosystems. We propose harnessing microbiome-mediated adaptations as a strategic approach to mitigate climate change impacts on crop pollination. Insights into insect-pollinator microbiomes offer transformative avenues for sustainable agriculture, including probiotic interventions (use of EM PROBIOTIC) and microbiome engineering (such as engineering gut bacteria) to induce immune responses and enhanced pollination services. Integrating microbiome insights into conservation practices elucidates strategies for preserving pollinator habitats, optimizing agricultural landscapes, and developing policies to safeguard pollinator health in the face of environmental changes. Finally, we stress interdisciplinary collaboration and the urgency of understanding pollinator microbiome dynamics under climate change in future research.

Antagonistic effect of the beneficial bacterium Enterobacter hormaechei against the heavy metal Cu2+ in housefly larvae

Vermicomposting via housefly larvae can be used to efficiently treat manure and regenerate biofertilizer; however, the uptake of heavy metals could negatively influence the growth and development of larvae. Intestinal bacteria play an important role in the development of houseflies, but their effects on resistance to heavy metal damage in houseflies are still poorly understood. In this study, the life history traits and gut microbiota of housefly larvae were evaluated after exposure to an environment with Cu2+ -Enterobacter hormaechei. The data showed that exposure to 300 μg/mL Cu2+ significantly inhibited larval development and locomotor activity and reduced immune capacity. However, dietary supplementation with a Cu2+ -Enterobacter hormaechei mixture resulted in increased body weight and length, and the immune capacity of the larvae returned to normal levels. The abundances of Providencia and Klebsiella increased when larvae were fed Cu2+ -contaminated diets, while the abundances of Enterobacter and Bacillus increased when larvae were exposed to a Cu2+ -Enterobacter hormaechei mixture-contaminated environment. In vitro scanning electron microscopy analysis revealed that Enterobacter hormaechei exhibited obvious adsorption of Cu2+ when cultured in the presence of Cu2+, which reduced the damage caused by Cu2+ to other bacteria in the intestine and protected the larvae from Cu2+ injury. Overall, our results showed that Enterobacter hormaechei can absorb Cu2+ and increase the abundance of beneficial bacteria, thus protecting housefly larvae from damage caused by Cu2+. These results may fill the gaps in our understanding of the interactions between heavy metals and beneficial intestinal bacteria, offering valuable insights into the interplay between housefly larvae and metal contaminants in the environment. This approach could enhance the efficiency of converting manure contaminated with heavy metals to resources using houseflies.

Exposure to a fungicide for a field-realistic duration does not alter bumble bee fecal microbiota structure

Social bees are frequently exposed to pesticides when foraging on nectar and pollen. Recent research has shown that pesticide exposure not only impacts social bee host health but can also alter the community structure of social bee gut microbiotas. However, most research on pesticide-bee gut microbiota interactions has been conducted in honey bees; bumble bees, native North American pollinators, have received less attention and, due to differences in their ecology, may be exposed to certain pesticides for shorter durations than honey bees. Here, we examine how exposure to the fungicide chlorothalonil for a short, field-realistic duration alters bumble bee fecal microbiotas (used as a proxy for gut microbiotas) and host performance. We expose small groups of Bombus impatiens workers (microcolonies) to field-realistic chlorothalonil concentrations for 5 days, track changes in fecal microbiotas during the exposure period and a recovery period, and compare microcolony offspring production between treatments at the end of the experiment. We also assess the use of fecal microbiotas as a gut microbiota proxy by comparing community structures of fecal and gut microbiotas. We find that chlorothalonil exposure for a short duration does not alter bumble bee fecal microbiota structure or affect microcolony production at any concentration but that fecal and gut microbiotas differ significantly in community structure. Our results show that, at least when exposure durations are brief and unaccompanied by other stressors, bumble bee microbiotas are resilient to fungicide exposure. Additionally, our work highlights the importance of sampling gut microbiotas directly, when possible.IMPORTANCEWith global pesticide use expected to increase in the coming decades, studies on how pesticides affect the health and performance of animals, including and perhaps especially pollinators, will be crucial to minimize negative environmental impacts of pesticides in agriculture. Here, we find no effect of exposure to chlorothalonil for a short, field-realistic period on bumble bee fecal microbiota community structure or microcolony production regardless of pesticide concentration. Our results can help inform pesticide use practices to minimize negative environmental impacts on the health and fitness of bumble bees, which are key native, commercial pollinators in North America. We also find that concurrently sampled bumble bee fecal and gut microbiotas contain similar microbes but differ from one another in community structure and consequently suggest that using fecal microbiotas as a proxy for gut microbiotas be done cautiously; this result contributes to our understanding of proxy use in gut microbiota research.

Microbes, the 'silent third partners' of bee-angiosperm mutualisms

While bee-angiosperm mutualisms are widely recognized as foundational partnerships that have shaped the diversity and structure of terrestrial ecosystems, these ancient mutualisms have been underpinned by 'silent third partners': microbes. Here, we propose reframing the canonical bee-angiosperm partnership as a three-way mutualism between bees, microbes, and angiosperms. This new conceptualization casts microbes as active symbionts, processing and protecting pollen-nectar provisions, consolidating nutrients for bee larvae, enhancing floral attractancy, facilitating plant fertilization, and defending bees and plants from pathogens. In exchange, bees and angiosperms provide their microbial associates with food, shelter, and transportation. Such microbial communities represent co-equal partners in tripartite mutualisms with bees and angiosperms, facilitating one of the most important ecological partnerships on land.

A case study of the diet-microbiota-parasite interplay in bumble bees

AIMS

Diets and parasites influence the gut bacterial symbionts of bumble bees, but potential interactive effects remain overlooked. The main objective of this study was to assess the isolated and interactive effects of sunflower pollen, its phenolamides, and the widespread trypanosomatid Crithidia sp. on the gut bacterial symbionts of Bombus terrestris males.

METHODS AND RESULTS

Bumble bee males emerged in microcolonies fed on either (i) willow pollen (control), (ii) sunflower pollen, or (iii) willow pollen spiked with phenolamide extracts from sunflower pollen. These microcolonies were infected by Crithidia sp. or were pathogen-free. Using 16S rRNA amplicon sequencing (V3-V4 region), we observed a significant alteration of the beta diversity but not of the alpha diversity in the gut microbial communities of males fed on sunflower pollen compared to males fed on control pollen. Similarly, infection by the gut parasite Crithidia sp. altered the beta diversity but not the alpha diversity in the gut microbial communities of males, irrespective of the diet. By contrast, we did not observe any significant alteration of the beta or alpha diversity in the gut microbial communities of males fed on phenolamide-enriched pollen compared to males fed on control pollen. Changes in the beta diversity indicate significant dissimilarities of the bacterial taxa between the treatment groups, while the lack of difference in alpha diversity demonstrates no significant changes within each treatment group.

CONCLUSIONS

Bumble bees harbour consistent gut microbiota worldwide, but our results suggest that the gut bacterial communities of bumble bees are somewhat shaped by their diets and gut parasites as well as by the interaction of these two factors. This study confirms that bumble bees are suitable biological surrogates to assess the effect of diet and parasite infections on gut microbial communities.

Wild bee and pollen microbiomes across an urban-rural divide

Wild pollinators and their microbiota are sensitive to land use changes from anthropogenic activities that disrupt landscape and environmental features. As urbanization and agriculture affect bee habitats, human-led disturbances are driving changes in bee microbiomes, potentially leading to dysbiosis detrimental to bee fitness. This study examines the bacterial, fungal, and plant compositions of the small carpenter bee, Ceratina calcarata, and its pollen provisions across an urban-rural divide. We performed metabarcoding of C. calcarata and provisions in Toronto by targeting the 16S rRNA, ITS, and rbcL regions. Despite similar plant composition and diversity across bees and their provisions, there was a greater microbial diversity in pollen provisions than in bees. By characterizing the differences in land use, climate, and pesticide residues that differentiate urban and rural landscapes, we find that urban areas support elevated levels of microbial diversity and more complex networks between microbes and plants than rural areas. However, urban areas may lead to lower relative abundances of known beneficial symbionts and increased levels of pathogens, such as Ascosphaera and Alternaria fungi. Further, rural pollen provisions indicate elevated pesticide residues that may dysregulate symbiosis. As anthropogenic activities continue to alter land use, ever changing environments threaten microbiota crucial in maintaining bee health.

Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

This study revealed that primer selection substantially influences the taxonomic and predicted functional composition and the characterization of microecological patterns, which was not alleviated by close-reference clustering. Biases were relatively consistent across different habitats in community profiling but not in microecological patterns. These primer biases could be attributed to multiple aspects, including taxa specificity, regional hypervariability, and amplification efficiency.

The impact of selenium on insects

Selenium, a naturally occurring metalloid, is an essential trace element for many higher organisms, including humans. Humans primarily become exposed to selenium by ingesting food products containing trace amounts of selenium compounds. Although essential in these small amounts, selenium exhibits toxic effects at higher doses. Previous studies investigating the effects on insects of order Blattodea, Coleoptera, Diptera, Ephemeroptera, Hemiptera, Hymenoptera, Lepidoptera, Odonata, and Orthoptera revealed impacts on mortality, growth, development, and behavior. Nearly every study examining selenium toxicity has shown that insects are negatively affected by exposure to selenium in their food. However, there were no clear patterns of toxicity between insect orders or similarities between insect species within families. At this time, the potential for control will need to be determined on a species-by-species basis. We suspect that the multiple modes of action, including mutation-inducing modification of important amino acids as well as impacts on microbiome composition, influence this variability. There are relatively few studies that have examined the potential effects of selenium on beneficial insects, and the results have ranged from increased predation (a strong positive effect) to toxicity resulting in reduced population growth or even the effective elimination of the natural enemies (more common negative effects). As a result, in those pest systems where selenium use is contemplated, additional research may be necessary to ascertain if selenium use is compatible with key biological control agents. This review explores selenium as a potential insecticide and possible future directions for research.

Effect of selenium accumulation on foraging behavior of pollinators and seed yield in Trifolium alexandrinum L

Selenium (Se) is an essential nutrient for both plants and animals and is usually provided as a supplement to livestock. Se bioaccumulation promotes plant growth by enhancing the accumulation of organic solutes and the activation of antioxidant system. In animals, the Se supplements reduce the chances of mastitis and white muscle disease, and improve the immunity, health, and reproduction, particularly in lactating dairy cows. Therefore, the enrichment or biofortification of fodder crops with Se may improve the nutritional quality of forages and thereby reduce malnutrition in cattle. However, Se hyper-accumulation in plants or plant parts can cause direct toxic effects on insects especially bees. Berseem is a highly cross-pollinated fodder crop that attracts a large number of pollinators. However, little or no reports are available regarding the effects of Se biofortification on the foraging behavior of pollinators in berseem. Therefore, the current study was planned to evaluate the effect of exogenous application of Se on the foraging behavior of native pollinators visiting the berseem crop. Five different doses of Se were applied to evaluate its effect on abundance, foraging behavior (visit duration and visitation rate), and single-visit efficacy of native pollinators that may affect berseem seed yield. Our results showed maximum abundance of pollinators in plants supplemented with low Se level, i.e., 5 g ha^-1 while the minimum abundance was observed at high Se doses (15 and 20 g ha^-1). Also, the seed yield attributes, i.e., the number of seeds per head, seed weight per head, 1000 seed weight, were the highest in plants treated with a low dose of Se, whereas the seed yield of berseem decreased with an increase in Se concentrations. Hence, our study provides evidence that high doses of Se negatively affect the foraging behavior of pollinators (visitation rate and visit duration) in plants. We conclude that the application of moderate Se dose positively influences the pollination ecology of berseem, consequently improving seed yield. HIGHLIGHTS: Selenium (Se) is essential for animals and beneficial for plants and may become toxic at high level. Se is delivered to the environment due to agriculture. Se toxicity affected berseem growth and considerably reduced the seed yield. High dose of Se reduced the abundance of pollinators and negatively affected their foraging behavior.

The effects of urban land use gradients on wild bee microbiomes

Bees and their microbes interact in complex networks in which bees form symbiotic relationships with their bacteria and fungi. Microbial composition and abundance affect bee health through nutrition, immunity, and fitness. In ever-expanding urban landscapes, land use development changes bee habitats and floral resource availability, thus altering the sources of microbes that wild bees need to establish their microbiome. Here, we implement metabarcoding of the bacterial 16S and fungal ITS regions to characterize the diversity and composition of the microbiome in 58 small carpenter bees, Ceratina calcarata, across urban land use gradients (study area 6,425 km2). By categorizing land use development, green space, precipitation, and temperature variables as indicators of habitat across the city, we found that land use variables can predict microbial diversity. Microbial composition was also found to vary across urban land use gradients, with certain microbes such as Acinetobacter and Apilactobacillus overrepresented in less urban locations and Penicillium more abundant in developed areas. Environmental features may also lead to differences in microbe interactions, as co-occurrences between bacteria and fungi varied across percent land use development, exemplified by the correlation between Methylobacterium and Sphingomonas being more prevalent in areas of higher urban development. Surrounding landscapes change the microbial landscape in wild bees and alter the relationships they have with their microbiome. As such, urban centres should consider the impact of growing cities on their pollinators' health and protect wild bees from the effects of anthropogenic activities.

Effects of in situ experimental selenium exposure on finescale dace (Phoxinus neogaeus) gut microbiome

Selenium (Se) is an environmental contaminant of global concern that can cause adverse effects in fish at elevated levels. Fish gut microbiome play essential roles in gastrointestinal function and host health and can be perturbed by environmental contaminants, including metals and metalloids. Here, an in-situ Se exposure of female finescale dace (Phoxinus neogaeus) using mesocosms was conducted to determine the impacts of Se accumulation on the gut microbiome and morphometric endpoints. Prior to this study, the gut microbiome of finescale dace, a widespread Cyprinid throughout North America, had not been characterized. Exposure to Se caused a hormetic response of alpha diversity of the gut microbiome, with greater diversity at the lesser concentration of 1.6 μg Se/L, relative to that of fish exposed to the greater concentration of 5.6 μg Se/L. Select gut microbiome taxa of fish were differentially abundant between aqueous exposure concentrations and significantly correlated with liver-somatic index (LSI). The potential effects of gut microbiome dysbiosis on condition of wild fish might be a consideration when assessing adverse effects of Se in aquatic environments. More research regarding effects of Se on field-collected fish gut microbiome and the potential adverse effects or benefits on the host is warranted.

Prospects for probiotics in social bees

Social corbiculate bees are major pollinators. They have characteristic bacterial microbiomes associated with their hives and their guts. In honeybees and bumblebees, worker guts contain a microbiome composed of distinctive bacterial taxa shown to benefit hosts. These benefits include stimulating immune and metabolic pathways, digesting or detoxifying food, and defending against pathogens and parasites. Stressors including toxins and poor nutrition disrupt the microbiome and increase susceptibility to opportunistic pathogens. Administering probiotic bacterial strains may improve the health of individual bees and of hives, and several commercial probiotics are available for bees. However, evidence for probiotic benefits is lacking or mixed. Most bacterial species used in commercial probiotics are not native to bee guts. We present new experimental results showing that cultured strains of native bee gut bacteria colonize robustly while bacteria in a commercial probiotic do not establish in bee guts. A defined community of native bee gut bacteria resembles unperturbed native gut communities in its activation of genes for immunity and metabolism in worker bees. Although many questions remain unanswered, the development of natural probiotics for honeybees, or for commercially managed bumblebees, is a promising direction for protecting the health of managed bee colonies.

This article is part of the theme issue ‘Natural processes influencing pollinator health: from chemistry to landscapes’.

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes

The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism’s microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.

Global wild bee metagenomes provide insights into microbiome, sociality and pollinator health.

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity

Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes.

IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee’s microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.

Novel application of survival models for predicting microbial community transitions with variable selection for eDNA

Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is under-utilized in microbiome research to predict microbial community mediated events, partly due to the sparsity and high dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA (eDNA) data with feature selection suitable for filtering irrelevant and redundant taxonomic variables. Selection methods are compared in terms of false positives, sensitivity, and survival estimation accuracy in simulation and in a real data setting to forecast harmful cyanobacterial blooms. A novel extension of a method for selecting microbial biomarkers with survival data (SuRFCox) reliably outperforms other methods. We determine Cox PH models with SuRFCox selected predictors are more robust to varied signal, noise, and data correlation structure. SuRFCox also yields the most accurate and consistent prediction of blooms according to cross-validated testing by year over eight different bloom seasons. Identification of common biomarkers among validated survival forecasts over changing conditions has clear biological significance. Survival models with such biomarkers inform risk assessment and provide insight into the causes of critical community transitions. Importance In this paper, we report on a novel approach of selecting microorganisms for model-based prediction of the time to critical microbially-modulated events (e.g., harmful algal blooms, clinical outcomes, community shifts, etc.). Our novel method for identifying biomarkers from large, dynamic communities of microbes has broad utility to environmental and ecological impact risk assessment and public health. Results will also promote theoretical and practical advancements relevant to the biology of specific organisms. To address the unique challenge posed by diverse environmental conditions and sparse microbes, we developed a novel method of selecting predictors for modelling time-to-event data. Competing methods for selecting predictors are rigorously compared to determine which is the most accurate and generalizable. Model forecasts are applied to show suitable predictors can precisely quantify the risk over time of biological events like harmful cyanobacterial blooms.

Pesticide-induced disturbances of bee gut microbiotas

Social bee gut microbiotas play key roles in host health and performance. Worryingly, a growing body of literature shows that pesticide exposure can disturb these microbiotas. Most studies examine changes in taxonomic composition in Western honey bee (Apis mellifera) gut microbiotas caused by insecticide exposure. Core bee gut microbiota taxa shift in abundance after exposure but are rarely eliminated, with declines in Bifidobacteriales and Lactobacillus near melliventris abundance being the most common shifts. Pesticide concentration, exposure duration, season and concurrent stressors all influence whether and how bee gut microbiotas are disturbed. Also, the mechanism of disturbance-i.e. whether a pesticide directly affects microbial growth or indirectly affects the microbiota by altering host health-likely affects disturbance consistency. Despite growing interest in this topic, important questions remain unanswered. Specifically, metabolic shifts in bee gut microbiotas remain largely uninvestigated, as do effects of pesticide-disturbed gut microbiotas on bee host performance. Furthermore, few bee species have been studied other than A. mellifera, and few herbicides and fungicides have been examined. We call for these knowledge gaps to be addressed so that we may obtain a comprehensive picture of how pesticides alter bee gut microbiotas, and of the functional consequences of these changes.

Critical links between biodiversity and health in wild bee conservation

Wild bee populations are declining due to human activities, such as land use change, which strongly affect the composition and diversity of available plants and food sources. The chemical composition of food (i.e., nutrition) in turn determines the health, resilience, and fitness of bees. For pollinators, however, the term 'health' is recent and is subject to debate, as is the interaction between nutrition and wild bee health. We define bee health as a multidimensional concept in a novel integrative framework linking bee biological traits (physiology, stoichiometry, and disease) and environmental factors (floral diversity and nutritional landscapes). Linking information on tolerated nutritional niches and health in different bee species will allow us to better predict their distribution and responses to environmental change, and thus support wild pollinator conservation.

Why Did the Bee Eat the Chicken? Symbiont Gain, Loss, and Retention in the Vulture Bee Microbiome

Diet and gut microbiomes are intricately linked on both short and long timescales. Changes in diet can alter the microbiome, while microbes in turn allow hosts to access novel diets. Bees are wasps that switched to a vegetarian lifestyle, and the vast majority of bees feed on pollen and nectar. Some stingless bee species, however, also collect carrion, and a few have fully reverted to a necrophagous lifestyle, relying on carrion for protein and forgoing flower visitation altogether. These “vulture” bees belong to the corbiculate apid clade, which is known for its ancient association with a small group of core microbiome phylotypes. Here, we investigate the vulture bee microbiome, along with closely related facultatively necrophagous and obligately pollinivorous species, to understand how these diets interact with microbiome structure. Via deep sequencing of the 16S rRNA gene and subsequent community analyses, we find that vulture bees have lost some core microbes, retained others, and entered into novel associations with acidophilic microbes found in the environment and on carrion. The abundance of acidophilic bacteria suggests that an acidic gut is important for vulture bee nutrition and health, as has been found in other carrion-feeding animals. Facultatively necrophagous bees have more variable microbiomes than strictly pollinivorous bees, suggesting that bee diet may interact with microbiomes on both short and long timescales. Further study of vulture bees promises to provide rich insights into the role of the microbiome in extreme diet switches.

Host species identity shapes the diversity and structure of insect microbiota

As for most of the life that inhabits our planet, microorganisms play an essential role in insect nutrition, reproduction, defence, and support their host in many other functions. More recently, we assisted to an exponential growth of studies describing the taxonomical composition of bacterial communities across insects' phylogeny. However, there is still an outstanding question that needs to be answered: Which factors contribute most to shape insects' microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin and treatment). However, when specifically testing for signatures of codiversification of insect species and their microbiota, analyses found weak support for this, suggesting that while insect species strongly drive the structure and diversity of insect microbiota, the diversification of those microbial communities did not follow their host's phylogeny. Furthermore, a parallel survey of the literature highlights several methodological limitations that need to be considered in the future research endeavours.

The gut microbiota of bumblebees

Bumblebees (Bombus) are charismatic and important pollinators. They are one of the best studied insect groups, especially in terms of ecology, behavior, and social structure. As many species are declining, there is a clear need to understand more about them. Microbial symbionts, which can influence many dimensions of animal life, likely have an outsized role in bumblebee biology. Recent research has shown that a conserved set of beneficial gut bacterial symbionts is ubiquitous across bumblebees. These bacteria are related to gut symbionts of honeybees, but have not been studied as intensively. Here we synthesize studies of bumblebee gut microbiota, highlight major knowledge gaps, and suggest future directions. Several patterns emerge, such as symbiont-host specificity maintained by sociality, frequent symbiont loss from individual bees, symbiont-conferred protection from trypanosomatid parasites, and divergence between bumblebee and honeybee microbiota in several key traits. For many facets of bumblebee-microbe interactions, however, underlying mechanisms and ecological functions remain unclear. Such information is important if we are to understand how bumblebees shape, and are shaped by, their gut microbiota. Bumblebees may provide a useful system for microbiome scientists, providing insights into general principles of host-microbe interactions. We also note how microbiota could influence bumblebee traits and responses to stressors. Finally, we propose that tinkering with the microbiota could be one way to aid bumblebee resilience in the face of global change.

Bacterial communities of indoor surface of stingless bee nests

Microbes have been identified as fundamental for the good health of bees, acting as pathogens, protective agent against infection/inorganic toxic compounds, degradation of recalcitrant secondary plant metabolites, definition of social group membership, carbohydrate metabolism, honey and bee pollen production. However, study of microbiota associated with bees have been largely confined to the honeybees and solitary bees. Here, I characterized the microbiota of indoor surface nest of four brazilian stingless bee species (Apidae: Meliponini) with different construction behaviors and populations. Bees that use predominantly plant material to build the nest (Frieseomelitta varia and Tetragonisca angustula) have a microbiome dominated by bacteria found in the phylloplane and flowers such as Pseudomonas sp. and Sphingomonas sp. Species that use mud and feces (Trigona spinipes) possess a microbiome dominated by coliforms such as Escherichia coli and Alcaligenes faecalis. Melipona quadrifasciata, which uses both mud / feces and plant resin, showed a hybrid microbiome with microbes found in soil, feces and plant material. These findings indicate that indoor surface microbiome varies widely among bees and reflects the materials used in the construction of the nests.

Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees

Animal-microbe symbioses are often stable for millions of years. An example is the clade consisting of social corbiculate bees-honeybees, bumblebees, and stingless bees-in which a shared ancestor acquired specialized gut bacteria that subsequently diversified with hosts. This model may be incomplete, however, as few microbiomes have been characterized for stingless bees, which are diverse and ecologically dominant pollinators in the tropics. We surveyed gut microbiomes of Brazilian stingless bees, focusing on the genus Melipona, for which we sampled multiple species and biomes. Strikingly, Melipona lacks Snodgrassella and Gilliamella, bacterial symbionts ubiquitous in other social corbiculate bees. Instead, Melipona species harbor more environmental bacteria and bee-specific Starmerella yeasts. Loss of Snodgrassella and Gilliamella may stem from ecological shifts in Melipona or the acquisition of new symbionts as functional replacements. Our findings demonstrate the value of broadly sampling microbiome biodiversity and show that even ancient symbioses can be lost.

BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to "bxid" placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species-two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors.IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on "in-house" reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.

Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees

Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.

The direct and indirect effects of environmental toxicants on the health of bumblebees and their microbiomes

Bumblebees (Bombus spp.) are important and widespread insect pollinators, but the act of foraging on flowers can expose them to harmful pesticides and chemicals such as oxidizers and heavy metals. How these compounds directly influence bee survival and indirectly affect bee health via the gut microbiome is largely unknown. As toxicants in floral nectar and pollen take many forms, we explored the genomes of bee-associated microbes for their potential to detoxify cadmium, copper, selenate, the neonicotinoid pesticide imidacloprid, and hydrogen peroxide-which have all been identified in floral nectar and pollen. We then exposed Bombus impatiens workers to varying concentrations of these chemicals via their diet and assayed direct effects on bee survival. Using field-realistic doses, we further explored the indirect effects on bee microbiomes. We found multiple putative genes in core gut microbes that may aid in detoxifying harmful chemicals. We also found that while the chemicals are largely toxic at levels within and above field-realistic concentrations, the field-realistic concentrations-except for imidacloprid-altered the composition of the bee microbiome, potentially causing gut dysbiosis. Overall, our study shows that chemicals found in floral nectar and pollen can cause bee mortality, and likely have indirect, deleterious effects on bee health via their influence on the bee microbiome.

Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts

Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.

Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees

Simple Summary

Solitary bees are important pollinators in managed and wild ecosystems. Across the bee phylogeny, bees may forage on a single species of plant, few plant species, or a broad diversity of plants. During foraging, these bees are often exposed to microbes, and in turn, may inoculate the brood cell and pollen provision of their offspring with these microbes. It is becoming evident that pollen-associated microbes are important to bee health, but it is not known how diet breadth impacts bees’ exposure to microbes. In this study, we collected pollen provisions from the bees Osmia lignaria and Osmia ribifloris at four different sites, then characterized the bacterial populations within the pollen provisions with 16S rRNA gene sequencing. We found that diet breadth did not have large effects on the bacteria found in the pollen provisions. We also note that the bacterial communities were slightly different between bee species and site, and there was minimal overlap in the unique bacterial variants between sites and bee species too. Our research supports the hypothesis of environmental transmission for solitary bee microbes, and we suggest future studies investigate the impacts of microbes on larval health.

Abstract

Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.

The Gut-Brain-Microbiome Axis in Bumble Bees

The brain-gut–microbiome axis is an emerging area of study, particularly in vertebrate systems. Existing evidence suggests that gut microbes can influence basic physiological functions and that perturbations to the gut microbiome can have deleterious effects on cognition and lead to neurodevelopmental disorders. While this relationship has been extensively studied in vertebrate systems, little is known about this relationship in insects. We hypothesized that because of its importance in bee health, the gut microbiota influences learning and memory in adult bumble bees. As an initial test of whether there is a brain-gut–microbiome axis in bumble bees, we reared microbe-inoculated and microbe-depleted bees from commercial Bombus impatiens colonies. We then conditioned experimental bees to associate a sucrose reward with a color and tested their ability to learn and remember the rewarding color. We found no difference between microbe-inoculated and microbe-depleted bumble bees in performance during the behavioral assay. While these results suggest that the brain-gut–microbiome axis is not evident in Bombus impatiens, future studies with different invertebrate systems are needed to further investigate this phenomenon.

Microbial symbionts expanding or constraining abiotic niche space in insects

In addition to their well-studied contributions to their host's nutrition, digestion, and defense, microbial symbionts of insects are increasingly found to affect their host's response toward abiotic stressors. In particular, symbiotic microbes can reduce or enhance tolerance to temperature extremes, improve desiccation resistance by aiding cuticle biosynthesis and sclerotization, and detoxify heavy metals. As such, individual symbionts or microbial communities can expand or constrain the abiotic niche space of their host and determine its adaptability to fluctuating environments. In light of the increasing impact of humans on climate and environment, a better understanding of host-microbe interactions is necessary to predict how different insect species will respond to changes in abiotic conditions.

Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa

Microbiome communities are complex assemblages of bacteria. The dissection of their assembly dynamics is challenging because it requires repeated sampling of both host and source communities. We used the nematode Caenorhabditis elegans as a model to study these dynamics. We characterized microbiome variation from natural worm populations and their substrates for two consecutive years using 16S rDNA amplicon sequencing. We found conservation in microbiome composition across time at the genus, but not amplicon sequencing variant (ASV) level. Only three ASVs were consistently present across worm samples (Comamonas ASV10859, Pseudomonas ASV7162 and Cellvibrio ASV9073). ASVs were more diverse in worms from different rather than the same substrates, indicating an influence of the source community on microbiome assembly. Surprisingly, almost 50% of worm-associated ASVs were absent in corresponding substrates, potentially due to environmental filtering. Ecological network analysis revealed strong effects of bacteria-bacteria interactions on community composition: While a dominant Erwinia strain correlated with decreased alpha-diversity, predatory bacteria of the Bdellovibrio and like organisms associated with increased alpha-diversity. High alpha-diversity was further linked to high worm population growth, especially on species-poor substrates. Our results highlight that microbiomes are individually shaped and sensitive to dramatic community shifts in response to particular competitive species.

Bombus (Hymenoptera: Apidae) Microcolonies as a Tool for Biological Understanding and Pesticide Risk Assessment

Bumble bees provide valuable pollination services to many wild and agricultural plants. Populations of some bumble bee species are in decline, prompting the need to better understand bumble bee biology and to develop methodologies for assessing the effects of environmental stressors on these bees. Use of bumble bee microcolonies as an experimental tool is steadily increasing. This review closely examines the microcolony model using peer-reviewed published literature identified by searching three databases through November 2018. Microcolonies have been successfully used for investigating a range of endpoints including behavior, the gut microbiome, nutrition, development, pathogens, chemical biology, and pesticides/xenobiotics. Methods for the initiation and monitoring of microcolonies, as well as the recorded variables were catalogued and described. From this information, we identified a series of recommendations for standardizing core elements of microcolony studies. Standardization is critical to establishing the foundation needed to support use of this model for biological response investigations and particularly for supporting use in pesticide risk assessment.

Cadmium and Selenate Exposure Affects the Honey Bee Microbiome and Metabolome, and Bee-Associated Bacteria Show Potential for Bioaccumulation

Honey bees are important insect pollinators used heavily in agriculture and can be found in diverse environments. Bees may encounter toxicants such as cadmium and selenate by foraging on plants growing in contaminated areas, which can result in negative health effects. Honey bees are known to have a simple and consistent microbiome that conveys many benefits to the host, and toxicant exposure may impact this symbiotic microbial community. We used 16S rRNA gene sequencing to assay the effects that sublethal cadmium and selenate treatments had over 7 days and found that both treatments significantly but subtly altered the composition of the bee microbiome. Next, we exposed bees to cadmium and selenate and then used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to show that chemical exposure changed the bees' metabolite profiles and that compounds which may be involved in detoxification, proteolysis, and lipolysis were more abundant in treatments. Finally, we exposed several strains of bee-associated bacteria in liquid culture and found that each strain removed cadmium from its medium but that only Lactobacillus Firm-5 microbes assimilated selenate, indicating the possibility that these microbes may reduce the metal and metalloid burden on their host. Overall, our report shows that metal and metalloid exposure can affect the honey bee microbiome and metabolome and that strains of bee-associated bacteria can bioaccumulate these toxicants.IMPORTANCE Bees are important insect pollinators that may encounter environmental pollution when foraging upon plants grown in contaminated areas. Despite the pervasiveness of pollution, little is known about the effects of these toxicants on honey bee metabolism and their symbiotic microbiomes. Here, we investigated the impact of selenate and cadmium exposure on the gut microbiome and metabolome of honey bees. We found that exposure to these chemicals subtly altered the overall composition of the bees' microbiome and metabolome and that exposure to toxicants may negatively impact both host and microbe. As the microbiome of animals can reduce mortality upon metal or metalloid challenge, we grew bee-associated bacteria in media spiked with selenate or cadmium. We show that some bacteria can remove these toxicants from their media in vitro and suggest that bacteria may reduce metal burden in their hosts.