Testing the Effectiveness of a Commercially Sold Probiotic on Restoring the Gut Microbiota of Honey Bees: a Field Study

Antibiotic use in apiculture is often necessary to ensure the survival of honey bee colonies. However, beekeepers are faced with the dilemma of needing to combat bacterial brood infections while also knowing that antibiotics kill beneficial bacteria important for bee health. In recent years, bee probiotics have become increasingly purchased by beekeepers because of product claims like being able to "replenish the microbes lost due to agricultural modifications of honey bees' environment" or "promote optimal gut health." Unfortunately, these products have little scientific evidence to support their efficacy, and previous lab experiments have refuted some of their claims. Here, we performed hive-level field experiments to test the effectiveness of SuperDFM-HoneyBee™ - the most commonly purchased honey bee probiotic in the United States - on restoring the honey bee gut microbiota after antibiotic treatment. We found slight but significant changes in the microbiota composition of bees following oxytetracycline (TerraPro) treatment and no difference between the microbiota of antibiotic treated bees with or without subsequent probiotic supplementation. Moreover, the microorganisms in the probiotic supplement were never found in the guts of the worker bee samples. These results highlight that more research is needed to test the efficacy and outcomes of currently available commercial honey bee probiotic supplements.

Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates

BACKGROUND

Sand flies vector several human pathogens, including Leishmania species, which cause leishmaniases. A leishmaniasis vaccine does not yet exist, so the most common prevention strategies involve personal protection and insecticide spraying. However, insecticides can impact non-target organisms and are becoming less effective because of the evolution of resistance. An alternative control strategy is the attract-and-kill approach, where the vector is lured to a lethal trap, ideally located in oviposition sites that will attract gravid females. Oviposition traps containing attractive microbes have proven successful for the control of some mosquito populations but have not been developed for sand flies. Gravid female sand flies lay their eggs in decomposing organic matter on which the larvae feed and develop. Studies have demonstrated that gravid females are particularly attracted to larval conditioned (containing eggs and larvae) and aged rearing substrates. An isolate-based study has provided some evidence that bacteria play a role in the attraction of sand flies to conditioned substrates. However, the overall bacterial community structure of conditioned and aged substrates and how they change over time has not been investigated.

METHODS

The goal of this study was to characterize the bacterial communities of rearing and oviposition substrates that have been shown to vary in attractiveness to gravid sand flies in previous behavioral studies. Using 16S rRNA amplicon sequencing we determined the bacterial composition in fresh, aged, and larval-conditioned substrates at four time points representing the main life-cycle stages of developing sand flies. We compared the diversity, presence, and abundance of taxa across substrate types and time points in order to identify how aging and larval-conditioning impact bacterial community structure.

RESULTS

We found that the bacterial communities significantly change within and between substrates over time. We also identified bacteria that might be responsible for attraction to conditioned and aged substrates, which could be potential candidates for the development of attract-and-kill strategies for sand flies.

CONCLUSION

This study demonstrated that both aging and larval conditioning induce shifts in the bacterial communities of sand fly oviposition and rearing substrates, which may explain the previously observed preference of gravid female sand flies to substrates containing second/third-instar larvae (conditioned) and substrates aged the same amount of time without larvae (aged).

High royal jelly production does not impact the gut microbiome of honey bees

Background

Honey bees are not only essential for pollination services, but are also economically important as a source of hive products (e.g., honey, royal jelly, pollen, wax, and propolis) that are used as foods, cosmetics, and alternative medicines. Royal jelly is a popular honey bee product with multiple potential medicinal properties. To boost royal jelly production, a long-term genetic selection program of Italian honey bees (ITBs) in China has been performed, resulting in honey bee stocks (here referred to as RJBs) that produce an order of magnitude more royal jelly than ITBs. Although multiple studies have investigated the molecular basis of increased royal jelly yields, one factor that has not been considered is the role of honey bee-associated gut microbes.

Results

Based on the behavioral, morphological, physiological, and neurological differences between RJBs and ITBs, we predicted that the gut microbiome composition of RJBs bees would differ from ITBs. To test this hypothesis, we investigated the bacterial composition of RJB and ITB workers from an urban location and RJBs from a rural location in China. Based on 16S rRNA gene profiling, we did not find any evidence that RJBs possess a unique bacterial gut community when compared to ITBs. However, we observed differences between honey bees from the urban versus rural sites.

Conclusions

Our results suggest that the environmental factors rather than stock differences are more important in shaping the bacterial composition in honey bee guts. Further studies are needed to investigate if the observed differences in relative abundance of taxa between the urban and rural bees correspond to distinct functional capabilities that impact honey bee health. Because the lifestyle, diet, and other environmental variables are different in rural and urban areas, controlled studies are needed to determine which of these factors are responsible for the observed differences in gut bacterial composition between urban and rural honeybees.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00124-1.

Larval Conditioning and Aging of Sand Fly Rearing Medium Affect Oviposition Site Selection in Phlebotomus papatasi (Diptera: Psychodidae) Sand Flies

Sand fly larvae develop in sheltered humid habitats containing decaying organic matter on which they feed. Previously, we showed that gravid females of Phlebotomus papatasi Scopoli (Diptera: Psychodidae) are attracted to and stimulated to lay eggs on larval rearing medium containing larvae. That study, however, did not control for the possible effect of medium aging. Our goal in this study was to evaluate the effect of larval substrate conditioning on attraction and oviposition responses of Ph. papatasi sand flies while controlling for the effect of substrate aging. Initially, we confirmed that the pretreatment fresh larval food sources (to be used as larval conditioned and unconditioned media) did not differ with respect to their effect on attraction and oviposition responses. The larval conditioned medium was produced by rearing larvae to the second/third-instar stage over 3 wk using the same larval food source. To produce larval unconditioned medium, the same amount of fresh larval food was added to a control rearing cup that did not contain larvae but was aged under identical time and conditions. Two-choice bioassays were conducted to evaluate gravid female's attraction and oviposition response to larval conditioned and unconditioned media. We found that gravid females were significantly attracted (P < 0.05) to larval conditioned medium when compared with unconditioned medium under the same amount of time and conditions. However, no such difference was found with respect to oviposition response. Both attraction and oviposition responses were significantly increased for larval conditioned and unconditioned media in comparison to the initial fresh larval food source.

CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

Glyphosate perturbs the gut microbiota of honey bees

Glyphosate, the primary herbicide used globally for weed control, targets the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme in the shikimate pathway found in plants and some microorganisms. Thus, glyphosate may affect bacterial symbionts of animals living near agricultural sites, including pollinators such as bees. The honey bee gut microbiota is dominated by eight bacterial species that promote weight gain and reduce pathogen susceptibility. The gene encoding EPSPS is present in almost all sequenced genomes of bee gut bacteria, indicating that they are potentially susceptible to glyphosate. We demonstrated that the relative and absolute abundances of dominant gut microbiota species are decreased in bees exposed to glyphosate at concentrations documented in the environment. Glyphosate exposure of young workers increased mortality of bees subsequently exposed to the opportunistic pathogen Serratia marcescens Members of the bee gut microbiota varied in susceptibility to glyphosate, largely corresponding to whether they possessed an EPSPS of class I (sensitive to glyphosate) or class II (insensitive to glyphosate). This basis for differences in sensitivity was confirmed using in vitro experiments in which the EPSPS gene from bee gut bacteria was cloned into Escherichia coli All strains of the core bee gut species, Snodgrassella alvi, encode a sensitive class I EPSPS, and reduction in S. alvi levels was a consistent experimental result. However, some S. alvi strains appear to possess an alternative mechanism of glyphosate resistance. Thus, exposure of bees to glyphosate can perturb their beneficial gut microbiota, potentially affecting bee health and their effectiveness as pollinators.

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

The role of the gut microbiome in animal health has become increasingly evident. Unlike most other insects, honey bees possess a highly conserved and specialized core gut microbiome, which consists of nine bacterial species and is acquired mostly through social transmission. Five of these species are ubiquitous in honey bees and are also present in bumble bees. Recent studies have shown that the bee gut microbiome plays a role in metabolism, immune function, growth and development, and protection against pathogens. Disruption of the gut microbiome has also been shown to have detrimental effects on bee health. Overall, evidence suggests that the gut microbiome plays an important role in bee health and disease.

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome

The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated. To address this gap, we used amplicon sequencing of protein-coding genes to assess effects of antibiotics on fine-scale genetic diversity of the honeybee gut microbiota. We followed the population dynamics of alleles within two dominant core species of the bee gut community, Gilliamella apicola and Snodgrassella alvi, following antibiotic perturbation. Whereas we observed a large reduction in genetic diversity in G. apicola, S. alvi diversity was mostly unaffected. The reduction in G. apicola diversity accompanied an increase in the frequency of several alleles, suggesting resistance to antibiotic treatment. We find that antibiotic perturbation can cause major shifts in diversity and that the extent of these shifts can vary substantially across species. Thus, antibiotics impact not only species composition, but also allelic diversity within species, potentially affecting hosts if variants with particular functions are reduced or eliminated. Overall, we show that amplicon sequencing of protein-coding genes, without clustering into operational taxonomic units, provides an accurate picture of the fine-scale dynamics of microbial communities over time.

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees

Gut microbiomes play crucial roles in animal health, and shifts in the gut microbial community structure can have detrimental impacts on hosts. Studies with vertebrate models and human subjects suggest that antibiotic treatments greatly perturb the native gut community, thereby facilitating proliferation of pathogens. In fact, persistent infections following antibiotic treatment are a major medical issue. In apiculture, antibiotics are frequently used to prevent bacterial infections of larval bees, but the impact of antibiotic-induced dysbiosis (microbial imbalance) on bee health and susceptibility to disease has not been fully elucidated. Here, we evaluated the effects of antibiotic exposure on the size and composition of honeybee gut communities. We monitored the survivorship of bees following antibiotic treatment in order to determine if dysbiosis of the gut microbiome impacts honeybee health, and we performed experiments to determine whether antibiotic exposure increases susceptibility to infection by opportunistic pathogens. Our results show that antibiotic treatment can have persistent effects on both the size and composition of the honeybee gut microbiome. Antibiotic exposure resulted in decreased survivorship, both in the hive and in laboratory experiments in which bees were exposed to opportunistic bacterial pathogens. Together, these results suggest that dysbiosis resulting from antibiotic exposure affects bee health, in part due to increased susceptibility to ubiquitous opportunistic pathogens. Not only do our results highlight the importance of the gut microbiome in honeybee health, but they also provide insights into how antibiotic treatment affects microbial communities and host health.

There is growing evidence for the importance of gut microbes in animal health. Unlike most other insects, honeybees possess a highly conserved gut microbial community, which is acquired through social contact, and several results have suggested that these microbes play an important role in honeybee health. Antibiotics, which can severely disrupt gut microbial communities, are commonly used in beekeeping in several countries. However, it is unknown how antibiotic treatment affects the gut microbial communities of honeybees. Here, we evaluated the effects of antibiotic treatment on the size and composition of the honeybee gut microbiome and on honeybee health. We found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survivorship of honeybees in the hive, likely due to increased susceptibility to infection by opportunistic pathogens.

Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea

The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

BACKGROUND

A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, "Candidatus Methanomethylophilus alvus", "Candidatus Methanomassiliicoccus intestinalis" and Methanomassiliicoccus luminyensis.

RESULTS

Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, "Ca. M. alvus" and "Ca. M. intestinalis" do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity.

CONCLUSIONS

This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata.

DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria

Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.