Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera

Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics

The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species-Pipistrellus (PB), Rhinolophus (RB), and Myotis (MB)-in Liping County, collecting rectal samples for 16S rRNA amplicon sequencing. Data processing involved Trimmomatic, Flash, and Qiime2 for operational taxonomic unit (OTU) standardization and species annotation via the Greengenes database. Differential abundance was analyzed using LEfSe, and diversity metrics were assessed through alpha and beta diversity analyses. The RB group was predominantly composed of Proteobacteria (80.99%), while MB and PB exhibited diverse compositions with significant OTU richness (729 in MB). Notable genera included Hafnia and Yersinia in RB and Cosenzaea myxofaciens in MB. High proportions of unclassified taxa were observed, particularly in RB (83.81%). Functional predictions indicated metabolic pathways, with a significant representation of human diseases in PB. Culturomics revealed the successful cultivation of Huaxiibacter chinensis and Enterobacter chengduensis from bats for the first time and appears to have identified a new bacterium that is likely closely related to Clostridium paraputrificum.IMPORTANCEOur research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions.

Strain diversity and host specificity of the gut symbiont Gilliamella in Apis mellifera, Apis cerana and Bombus terrestris

Social bees, with their specialized gut microbiota and societal transmission between individuals, provide an ideal model for studying host-gut microbiota interactions. While the functional disparities arising from strain-level diversity of gut symbionts and their effects on host health have been studied in Apis mellifera and bumblebees, studies focusing on host-specific investigations of individual strains across different honeybee hosts remain relatively unexplored. In this study, the complete genomic sequences of 17 strains of Gilliamella from A. mellifera, Apis cerana and Bombus terrestris were analyzed. The analysis revealed that the strains of A. mellifera display a more expansive genomic and functional content compared to the strains of A. cerana and B. terrestris. Phylogenetic analysis showed a deep divergence among the Gilliamella strains from different hosts. Additionally, biochemistry tests and antibiotic susceptibility tests revealed that gut strains from A. mellifera exhibited a more extensive pathway for carbohydrate metabolism and a greater resistance to antibiotics than gut strains from A. cerana and B. terrestris. Strains from A. mellifera and A. cerana showed higher colonization efficiency and competitive ability whithin their respective host species, indicating a higher degree of host-specific adaptation of local gut microbiota. In addition, colonization by A. mellifera-derived strain triggers a stronger transcriptional response in the host than A. cerana-derived strain. The variation in the number of differentially expressed genes and the involvement of distinct signaling pathways across these two host species suggest species-specific adaptations to Gilliamella strains. These findings suggest that despite occupying similar niches in the bee gut, strain-level variations can influence microbial functions, and their impact on host physiological functions may vary across different strains.

Host specificity of gut microbiota associated with social bees: patterns and processes

SUMMARYGut microbes provide benefits to some animals, but their distribution and effects across diverse hosts are still poorly described. There is accumulating evidence for host specificity (i.e., a pattern where different microbes tend to associate with distinct host lineages), but the causes and consequences of this pattern are unclear. Combining experimental tests in the laboratory with broad surveys in the wild is a promising approach to gaining a comprehensive and mechanistic understanding of host specificity prevalence, origin, and importance. Social bees represent an ideal testbed for this endeavor because they are phylogenetically and functionally diverse, with host-specific, stable, and tractable gut microbiota. Furthermore, the western honeybee (Apis mellifera) is an emerging experimental model system for studying microbiota-host interactions. In this review, we summarize data on the prevalence and strength of host specificity of the social bee gut microbiota (bumblebees, stingless bees, and honeybees), as well as the potential and proven ecological and molecular mechanisms that maintain host specificity. Overall, we found that host specificity in bees is relatively strong and likely results from several processes, including host filtering mediated by the immune system and priority effects. However, more research is needed across multiple social bee species to confirm these findings. To help future research, we summarize emerging hypotheses in the field and propose several experimental and comparative tests. Finally, we conclude this review by highlighting the need to understand how host specificity can influence host health.

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

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

Captive-rearing changes the gut microbiota of the bumblebee Bombus lantschouensis native to China

Bumblebees play crucial roles as pollinators in both natural agricultural and ecological systems. Their health and overall fitness are significantly affected by the gut microbiota, which can maintain intestinal homeostasis in hosts by regulating their nutritional metabolism. However, information about the diversity of the gut microbiota and related functional changes during artificial rearing of native species is currently limited. This study investigated the dynamic remodeling of gut microbiota in the Chinese native bumblebee Bombus lantschouensis under captive rearing, supported by 16S rRNA amplicon sequencing of bacterial DNA. The typical microbial community composition of the bumblebee was detected in the gut of wild B. lantschouensis, with species of genus Gilliamella and Snodgrassella identified as the dominant strains. Conversely, the microbiota of the captive-reared group showed increased diversity and decreased abundance of certain species of microorganisms. The populations of Bifidobacterium, Saccharibacter, and Lactobacillus, including Firm-4 and Firm-5, were dramatically increased after captive-rearing and became the dominant bacteria, while Gilliamella and Snodgrassella were strikingly reduced. Notably, this study found that pathogenic bacteria appeared in the intestines of wild-caught B. lantschouensis and disappeared when the host was reared under captive conditions. This study shows microbial community changes in bumblebees and facilitates the study of physiological metabolism in the commercial rearing of insects.

Dietary Quercetin Regulates Gut Microbiome Diversity and Abundance in Apis cerana (Hymenoptera Apidae)

Honeybee gut microbiota plays a crucial role in maintaining their health and digestive function. Studies have confirmed that quercetin improves honeybee health by enhancing their pesticide tolerance and survival rates. This study aimed to examine the effects of quercetin on the bee gut microbiome by absolute quantification sequencing. We included 1800 bees from the experimental apiary and exposed them to 151.2, 75.6, and 37.8 mg/L of quercetin. Gut samples were collected on the 5th and 9th days, subjected to a polymerase chain reaction and 16S rRNA sequencing, and analyzed. After 5 days of quercetin treatment, the diversity of the honeybee gut microbiota was altered, and total bacterial copies and Lactobacillus abundance significantly decreased at high quercetin concentrations (151.2 and 75.6 mg/L). On day 9, the gut microbial community had recovered from the adverse effects, and Gilliamella abundance increased in response to 37.8 mg/L quercetin treatment. However, quercetin had no noticeable effects on survival rate, food consumption, and gut structure. Our study confirmed the effect of short-term quercetin intake on the gut microbiota of A. cerana, providing valuable insights into how phytochemicals alter the bee gut microbiome, and their repercussions on host physiology.

Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system

Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.

Temporospatial dynamics and host specificity of honeybee gut bacteria

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

Honeybee symbiont Bombella apis could restore larval-to-pupal transition disrupted by antibiotic treatment

Numerous studies have demonstrated the vital roles of gut microbes in the health, immunity, nutrient metabolism, and behavior of adult worker honeybees. However, a few studies have been conducted on gut microbiota associated with the larval stage of honeybees. In the present study, we explored the role of a gut bacterium in larval development and larval-pupal transition in the Asian honeybee, Apis cerana. First, our examination of gut microbial profiling showed that Bombella apis, a larvae-associated bacterium, was the most dominant bacterium colonized in the fifth instar larvae. Second, we demonstrated that tetracycline, an antibiotic used to treat a honeybee bacterial brood disease, could cause the complete depletion of gut bacteria. This antibiotic-induced gut microbiome depletion in turn, significantly impacted the survivorship, pupation rate and emergence rate of the treated larvae. Furthermore, our analysis of gene expression pattens revealed noteworthy changes in key genes. The expression of genes responsible for encoding storage proteins vitellogenin (vg) and major royal jelly protein 1 (mrjp1) was significantly down-regulated in the tetracycline-treated larvae. Concurrently, the expression of krüppel homolog 1(kr-h1), a pivotal gene in endocrine signaling, increased, whilethe expression of broad-complex (br-c) gene that plays a key role in the ecdysone regulation decreased. These alterations indicated a disruption in the coordination of juvenile hormone and ecdysteroid synthesis. Finally, we cultivated B. apis isolated from the fifth instar worker larval of A. cerana and fed tetracycline-treated larvae with a diet replenished by B. apis. This intervention resulted in a significant improvement in the pupation rate, emergence rate, and overall survival rate of the treated larvae. Our findings demonstrate the positive impact of B. apis on honeybee larvae development, providing new evidence of the functional capacities of gut microbes in honeybee growth and development.

Toxic effects of the heavy metal Cd on Apis cerana cerana (Hymenoptera: Apidae): Oxidative stress, immune disorders and disturbance of gut microbiota

Cadmium (Cd) is a toxic non-essential metal element that can enter the honey bee body through air, water and soil. Currently, there is a lack of sufficient research on the effects of Cd on A. cerana cerana, especially the potential risks of long-term exposure to sublethal concentrations. In order to ascertain the toxicological effects of the heavy metal Cd on bees, we performed laboratory-based toxicity experiments on worker bees and conducted analyses from three distinctive facets: antioxidative, immunological, and gut microbiota. The results showed that exposure of bees to high concentrations of Cd resulted in acute mortality, and the increase in mortality was concentration dependent. In long-term exposure to sublethal concentrations, Cd reduced the number of transcripts of antioxidant genes (AccSOD1, AccTPx3 and AccTPx4) and superoxide dismutase activity, causing an increase in malondialdehyde content. Simultaneously, the transcription of immune-related genes (AccAbaecin and AccApidaecin) and acetylcholinesterase activities was inhibited. Furthermore, Cd changes the structural characteristics of bacterial and fungal communities in the gut, disrupting the balance of microbial communities. In conclusion, the health and survival of honey bees are affected by Cd. This study provides a scientific basis for investigating the toxicological mechanisms and control strategies of the heavy metal Cd on honey bees, while facilitating a better understanding and protection of these valuable honey bees.

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

BACKGROUND

Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.

RESULTS

Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states.

CONCLUSIONS

Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.

Fungicides and insecticides can alter the microbial community on the cuticle of honey bees

Honey bees are crucial for our ecosystems as pollinators, but the intensive use of plant protection products (PPPs) in agriculture poses a risk for them. PPPs do not only affect target organisms but also affect non-targets, such as the honey bee Apis mellifera and their microbiome. This study is the first of its kind, aiming to characterize the effect of PPPs on the microbiome of the cuticle of honey bees. We chose PPPs, which have frequently been detected in bee bread, and studied their effects on the cuticular microbial community and function of the bees. The effects of the fungicide Difcor® (difenoconazole), the insecticide Steward® (indoxacarb), the combination of both (mix A) and the fungicide Cantus® Gold (boscalid and dimoxystrobin), the insecticide Mospilan® (acetamiprid), and the combination of both (mix B) were tested. Bacterial 16S rRNA gene and fungal transcribed spacer region gene-based amplicon sequencing and quantification of gene copy numbers were carried out after nucleic acid extraction from the cuticle of honey bees. The treatment with Steward® significantly affected fungal community composition and function. The fungal gene copy numbers were lower on the cuticle of bees treated with Difcor®, Steward®, and PPP mix A in comparison with the controls. However, bacterial and fungal gene copy numbers were increased in bees treated with Cantus® Gold, Mospilan®, or PPP mix B compared to the controls. The bacterial cuticular community composition of bees treated with Cantus® Gold, Mospilan®, and PPP mix B differed significantly from the control. In addition, Mospilan® on its own significantly changed the bacterial functional community composition. Cantus® Gold significantly affected fungal gene copy numbers, community, and functional composition. Our results demonstrate that PPPs show adverse effects on the cuticular microbiome of honey bees and suggest that PPP mixtures can cause stronger effects on the cuticular community than a PPP alone. The cuticular community composition was more diverse after the PPP mix treatments. This may have far-reaching consequences for the health of honey bees.

MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes

The reconstruction of microbial genome sequences by bioinformatic pipelines and the consequent functional annotation of their genes' repertoire are fundamental activities aiming at unveiling their biological mechanisms, such as metabolism, virulence factors, and antimicrobial resistances. Here, we describe the development of the MEGAnnotator2 pipeline able to manage all next-generation sequencing methodologies producing short- and long-read DNA sequences. Starting from raw sequencing data, the updated pipeline can manage multiple analyses leading to the assembly of high-quality genome sequences and the functional classification of their genetic repertoire, providing the user with a useful report constituting features and statistics related to the microbial genome. The updated pipeline is fully automated from the installation to the delivery of the output, thus requiring minimal bioinformatics knowledge to be executed.

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.

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.

Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes

Bifidobacterium asteroides is considered the ancestor of the genus Bifidobacterium, which has evolved in close touch with the hindgut of social insects. However, recent studies revealed high intraspecies biodiversity within this taxon, uncovering the putative existence of multiple bifidobacterial species, thus, suggesting its reclassification. Here, a genomic investigation of 98 B. asteroides-related genomes retrieved from public repositories and reconstructed from metagenomes of the hindgut of Apis mellifera and Apis cerana was performed to shed light on the genetic variability of this taxon. Phylogenetic and genomic analyses revealed the existence of eight clusters, of which five have been recently characterized with a representative type strain of the genus and three were represented by putative novel bifidobacterial species inhabiting the honeybee gut. Then, the dissection of 366 shotgun metagenomes of honeybee guts revealed a pattern of seven B. asteroides-related taxa within A. mellifera that co-exist with the host, while A. cerana microbiome was characterized by the predominance of one of the novel species erroneously classified as B. asteroides. A further glycobiome analysis unveiled a conserved repertoire of glycosyl hydrolases (GHs) reflecting degradative abilities towards a broad range of simple carbohydrates together with genes encoding specific GHs of each B. asteroides-related taxa.

Distinct gut microbiota profiles of Asian honey bee (Apis cerana) foragers

Bee gut microbial communities have been studied extensively and linked to honey bee biology in terms of stages of bee development and behavior. Associations of bee gut microbiota in health and disease have also been explored. A large number of studies have centered on the gut microbiome of Apis mellifera, with similar investigations lagging far behind in Asian honey bee foragers. In this study, we characterized and compared the gut bacterial profiles of foragers and nurse bees of A. cerana and A. mellifera. Analysis of 16S rRNA partial gene sequences revealed significant differences in gut bacterial communities between the two honey bee species. Despite sharing dominant taxa, Bacteroides was more abundant in A. cerana, while Proteobacteria was higher in A. mellifera. Specific gut members are distinctly associated with hosts performing different tasks (i.e. nurse bees versus foragers). An exclusive abundance of Apibacter detected in Asian honey bee seemed to be a microbial signature of A. cerana foragers. Overall, our study highlights that variations in gut microbiota could be linked to task-specific (nurse bees and foragers) bacterial species associated with honey bees. Future investigations on the symbiotic relationship between host and the resident microbiota would be beneficial for improving honey bee health.

The Pass-on Effect of Tetracycline-Induced Honey Bee (Apis mellifera) Gut Community Dysbiosis

Gut microbial community plays an important role in the regulation of insect health. Antibiotic treatment is powerful to fight bacterial infections, while it also causes collateral damage to gut microbiome, which may have long-lasting consequences for host health. However, current studies on honey bees mainly focus on the impact of direct exposure to antibiotics on individual bees, and little is known about the impact of social transmission of antibiotic-induced gut community disorder in honey bee colonies. In order to provide insight into the potential pass-on effect of antibiotic-induced dysbiosis, we colonized newly emerged germ-free workers with either normal or tetracycline-treated gut community and analyzed the gut bacteria composition. We also treated workers with low dosage of tetracycline to evaluate its impact on honey bee gut microbiota. Our results showed that the tetracycline-treated gut community caused disruption of gut community in their receivers, while the direct exposure to the low dosage of tetracycline had no significant effect. In addition, no significant difference was observed on the mortality rate of A. mellifera workers with different treatments. These results suggest that though the residue of antibiotic treatment may not have direct effect on honey bee gut community, the gut microbiota dysbiosis caused by high dosage of antibiotic treatment has a cascade effect on the gut community of the nestmates in honeybee colonies.