Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria

Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella

We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.

The Latitudinal Biotic Interaction Hypothesis revisited: contrasting latitudinal richness gradients in actively vs. passively accumulated interaction partners of honey bees

BACKGROUND

Contrasting hypotheses suggest that the number of biotic interactions per species could either increase towards the equator due to the increasing richness of potential interaction partners (Neutral theory), or decrease in the tropics due to increased biotic competition (Latitudinal Biotic Interaction Hypothesis). Empirical testing of these hypotheses remains limited due to practical limitations, differences in methodology, and species turnover across latitudes. Here, we focus on a single species with a worldwide distribution, the honey bee (Apis mellifera L.), to assess how the number of different types of interactions vary across latitudes. Foraging honey bees interact with many organisms in their local environment, including plants they actively select to visit and microbes that they largely encounter passively (i.e., unintentionally and more or less randomly). Tissue pieces and spores of these organisms are carried to the hive by foraging honey bees and end up preserved within honey, providing a rich record of the species honey bees encounter in nature.

RESULTS

Using honey samples from around the globe, we show that while honey bees visit more plant taxa at higher latitudes, they encounter more bacteria in the tropics.

CONCLUSIONS

These different components of honey bees' biotic niche support the latitudinal biotic interaction hypothesis for actively-chosen interactions, but are more consistent with neutral theory (assuming greater bacterial richness in the tropics) for unintentional interactions.

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

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

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

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

One-step genome engineering in bee gut bacterial symbionts

Mechanistic understanding of interactions in many host-microbe systems, including the honey bee microbiome, is limited by a lack of easy-to-use genome engineering approaches. To this end, we demonstrate a one-step genome engineering approach for making gene deletions and insertions in the chromosomes of honey bee gut bacterial symbionts. Electroporation of linear or non-replicating plasmid DNA containing an antibiotic resistance cassette flanked by regions with homology to a symbiont genome reliably results in chromosomal integration. This lightweight approach does not require expressing any exogenous recombination machinery. The high concentrations of large DNAs with long homology regions needed to make the process efficient can be readily produced using modern DNA synthesis and assembly methods. We use this approach to knock out genes, including genes involved in biofilm formation, and insert fluorescent protein genes into the chromosome of the betaproteobacterial bee gut symbiont Snodgrassella alvi. We are also able to engineer the genomes of multiple strains of S. alvi and another species, Snodgrassella communis, which is found in the bumble bee gut microbiome. Finally, we use the same method to engineer the chromosome of another bee symbiont, Bartonella apis, which is an alphaproteobacterium. As expected, gene knockout in S. alvi using this approach is recA-dependent, suggesting that this straightforward procedure can be applied to other microbes that lack convenient genome engineering methods.

IMPORTANCE

Honey bees are ecologically and economically important crop pollinators with bacterial gut symbionts that influence their health. Microbiome-based strategies for studying or improving bee health have utilized wild-type or plasmid-engineered bacteria. We demonstrate that a straightforward, single-step method can be used to insert cassettes and replace genes in the chromosomes of multiple bee gut bacteria. This method can be used for investigating the mechanisms of host-microbe interactions in the bee gut community and stably engineering symbionts that benefit pollinator health.

Eutrichophilus cordiceps Mjöberg, 1910 (Ischnocera: Trichodectidae) in Spiny Tree Porcupines (Coendou villosus): New locality records and the first molecular evidence of association with Bartonella sp

The chewing louse genus Eutrichophilus Mjöberg has 19 species only associated with porcupines (Rodentia: Erethizontidae). Of these species, E. cercolabes, E. cordiceps, E. emersoni, E. minor, E. moojeni, and E. paraguayensis have been recorded in Brazil. In the present study, we report E. cordiceps for the first time in the São Paulo State (Bauru Municipality) and for the second time in the Santa Catarina State (Lages Municipality), providing scanning electron images and light microscopy for the eggs, as well as the first molecular data (18S rRNA) for the genus. Additionally, Bartonella sp. was detected for the first time in this chewing lice species.

A novel Bartonella-like bacterium forms an interdependent mutualistic symbiosis with its host, the stored-product mite Tyrophagus putrescentiae

A novel Bartonella-like symbiont (BLS) of Tyrophagus putrescentiae was characterized. BLS formed a separate cluster from the Bartonella clade together with an ant symbiont. BLS was present in mite bodies (103 16S DNA copies/mite) and feces but was absent in eggs. This indicated the presence of the BLS in mite guts. The BLS showed a reduction in genome size (1.6 Mb) and indicates gene loss compared to Bartonella apis. The BLS can be interacted with its host by using host metabolic pathways (e.g., the histidine and arginine metabolic pathways) as well as by providing its own metabolic pathways (pantothenate and lipoic acid) to the host, suggesting the existence of a mutualistic association. Our experimental data further confirmed these potential mutualistic nutritional associations, as cultures of T. putrescentiae with low BLS abundance showed the strongest response after the addition of vitamins. Despite developing an arguably tight dependency on its host, the BLS has probably retained flagellar mobility, as evidenced by the 32 proteins enriched in KEGG pathways associated with flagellar assembly or chemotaxis (e.g., fliC, flgE, and flgK, as highly expressed genes). Some of these proteins probably also facilitate adhesion to host gut cells. The microcin C transporter was identified in the BLS, suggesting that microcin C may be used in competition with other gut bacteria. The 16S DNA sequence comparison indicated a mite clade of BLSs with a broad host range, including house dust and stored-product mites. Our phylogenomic analyses identified a unique lineage of arachnid specific BLSs in mites and scorpions.IMPORTANCEA Bartonella-like symbiont was found in an astigmatid mite of allergenic importance. We assembled the genome of the bacterium from metagenomes of different stored-product mite (T. putrescentiae) cultures. The bacterium provides pantothenate and lipoic acid to the mite host. The vitamin supply explains the changes in the relative abundance of BLSs in T. putrescentiae as the microbiome response to nutritional or pesticide stress, as observed previously. The phylogenomic analyses of available 16S DNA sequences originating from mite, scorpion, and insect samples identified a unique lineage of arachnid specific forming large Bartonella clade. BLSs associated with mites and a scorpion. The Bartonella clade included the previously described Ca. Tokpelaia symbionts of ants.

The honeybee microbiota and its impact on health and disease

Honeybees (Apis mellifera) are key pollinators that support global agriculture and are long-established models for developmental and behavioural research. Recently, they have emerged as models for studying gut microbial communities. Earlier research established that hindguts of adult worker bees harbour a conserved set of host-restricted bacterial species, each showing extensive strain variation. These bacteria can be cultured axenically and introduced to gnotobiotic hosts, and some have basic genetic tools available. In this Review, we explore the most recent research showing how the microbiota establishes itself in the gut and impacts bee biology and health. Microbiota members occupy specific niches within the gut where they interact with each other and the host. They engage in cross-feeding and antagonistic interactions, which likely contribute to the stability of the community and prevent pathogen invasion. An intact gut microbiota provides protection against diverse pathogens and parasites and contributes to the processing of refractory components of the pollen coat and dietary toxins. Absence or disruption of the microbiota results in altered expression of genes that underlie immunity, metabolism, behaviour and development. In the field, such disruption by agrochemicals may negatively impact bees. These findings demonstrate a key developmental and protective role of the microbiota, with broad implications for bee health.

Exploring the impact of fungicide exposure and nutritional stress on the microbiota and immune response of the Cape honey bee (Apis mellifera capensis)

Honey bees (Apis mellifera) harbour a stable core microbial community within their gut, that is suggested to play a role in metabolic functioning, immune regulation, and host homeostasis. This microbiota presents a unique opportunity to observe the effects of stressors on honey bee health. We examined the effects of two common honey bee stressors: indirect fungicide contamination and nutrient limitation. These effects were observed through changes in their hind- and midgut microbiota using Automated Ribosomal Intergenic Spacer Analysis (ARISA), alongside high-throughput amplicon sequencing. Expression of the honey bees' immune response was examined through the expression of three immune-related genes, namely, immune deficiency (imd), proPhenolOxidase (proPO), and spaetzle (spz). Additionally, longevity of the honey bees was monitored through observation of the expression levels of Vitellogenin (Vg). Both treatment groups were compared to a negative control, and a diseased positive control. There was no effect on the hindgut microbiota due to the stressors, while significant changes in the midgut was observed. This was also observed in the expression of the immune-related genes within the treatment groups. The Imd pathway was substantially downregulated, with upregulation in the prophenoloxidase pathway. However, no significant effect was observed in the expression of spz, and only the pollen treatment group showed reduced longevity through a downregulation of Vg. Overall, the effect of these two common stressors indicate a compromise in honey bee immunity, and potential vulnerabilities within the immune defence mechanisms.

An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment

The honey bee is a powerful model system to probe host-gut microbiota interactions, and an important pollinator species for natural ecosystems and for agriculture. While bacterial biosensors can provide critical insight into the complex interplay occurring between a host and its associated microbiota, the lack of methods to noninvasively sample the gut content, and the limited genetic tools to engineer symbionts, have so far hindered their development in honey bees. Here, we built a versatile molecular tool kit to genetically modify symbionts and reported for the first time in the honey bee a technique to sample their feces. We reprogrammed the native bee gut bacterium Snodgrassella alvi as a biosensor for IPTG, with engineered cells that stably colonize the gut of honey bees and report exposure to the molecules in a dose-dependent manner through the expression of a fluorescent protein. We showed that fluorescence readout can be measured in the gut tissues or noninvasively in the feces. These tools and techniques will enable rapid building of engineered bacteria to answer fundamental questions in host-gut microbiota research.

The Response of the Honey Bee Gut Microbiota to Nosema ceranae Is Modulated by the Probiotic Pediococcus acidilactici and the Neonicotinoid Thiamethoxam

The honey bee Apis mellifera is exposed to a variety of biotic and abiotic stressors, such as the highly prevalent microsporidian parasite Nosema (Vairimorpha) ceranae and neonicotinoid insecticides. Both can affect honey bee physiology and microbial gut communities, eventually reducing its lifespan. They can also have a combined effect on the insect's survival. The use of bacterial probiotics has been proposed to improve honey bee health, but their beneficial effect remains an open question. In the present study, western honey bees were experimentally infected with N. ceranae spores, chronically exposed to the neonicotinoid thiamethoxam, and/or supplied daily with the homofermentative bacterium Pediococcus acidilactici MA18/5M thought to improve the honey bees' tolerance to the parasite. Deep shotgun metagenomic sequencing allowed the response of the gut microbiota to be investigated with a taxonomic resolution at the species level. All treatments induced significant changes in honey bee gut bacterial communities. Nosema ceranae infection increased the abundance of Proteus mirabilis, Frischella perrara, and Gilliamella apicola and reduced the abundance of Bifidobacterium asteroides, Fructobacillus fructosus, and Lactobacillus spp. Supplementation with P. acidilactici overturned some of these alterations, bringing back the abundance of some altered species close to the relative abundance found in the controls. Surprisingly, the exposure to thiamethoxam also restored the relative abundance of some species modulated by N. ceranae. This study shows that stressors and probiotics may have an antagonistic impact on honey bee gut bacterial communities and that P. acidilactici may have a protective effect against the dysbiosis induced by an infection with N. ceranae.

Shotgun Metagenomics Reveals Minor Micro"bee"omes Diversity Defining Differences between Larvae and Pupae Brood Combs

Bees represent not only a valuable asset in agriculture, but also serve as a model organism within contemporary microbiology. The metagenomic composition of the bee superorganism has been substantially characterized. Nevertheless, traditional cultural methods served as the approach to studying brood combs in the past. Indeed, the comb microbiome may contribute to determining larval caste differentiation and hive immunity. To further this understanding, we conducted a shotgun sequencing analysis of the brood comb microbiome. While we found certain similarities regarding species diversity, it exhibits significant differentiation from all previously described hive metagenomes. Many microbiome members maintain a relatively constant ratio, yet taxa with the highest abundance level tend to be ephemeral. More than 90% of classified metagenomes were Gammaproteobacteria, Bacilli and Actinobacteria genetic signatures. Jaccard dissimilarity between samples based on bacteria genus classifications hesitate from 0.63 to 0.77, which for shotgun sequencing indicates a high consistency in bacterial composition. Concurrently, we identified antagonistic relationships between certain bacterial clusters. The presence of genes related to antibiotic synthesis and antibiotic resistance suggests potential mechanisms underlying the stability of comb microbiomes. Differences between pupal and larval combs emerge in the total metagenome, while taxa with the highest abundance remained consistent. All this suggests that a key role in the functioning of the comb microbiome is played by minor biodiversity, the function of which remains to be established experimentally.

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

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

The Effect of Residual Pesticide Application on Microbiomes of the Storage Mite Tyrophagus putrescentiae

Arthropods can host well-developed microbial communities, and such microbes can degrade pesticides and confer tolerance to most types of pests. Two cultures of the stored-product mite Tyrophagus putrescentiae, one with a symbiotic microbiome containing Wolbachia and the other without Wolbachia, were compared on pesticide residue (organophosphate: pirimiphos-methyl and pyrethroid: deltamethrin, deltamethrin + piperonyl butoxide)-containing diets. The microbiomes from mite bodies, mite feces and debris from the spent mite diet were analyzed using barcode sequencing. Pesticide tolerance was different among mite cultures and organophosphate and pyrethroid pesticides. The pesticide residues influenced the microbiome composition in both cultures but without any remarkable trend for mite cultures with and without Wolbachia. The most influenced bacterial taxa were Bartonella-like and Bacillus for both cultures and Wolbachia for the culture containing this symbiont. However, there was no direct evidence of any effect of Wolbachia on pesticide tolerance. The high pesticide concentration residues in diets reduced Wolbachia, Bartonella-like and Bacillus in mites of the symbiotic culture. This effect was low for Bartonella-like and Bacillus in the asymbiotic microbiome culture. The results showed that the microbiomes of mites are affected by pesticide residues in the diets, but the effect is not systemic. No actual detoxification effect by the microbiome was observed for the tested pesticides.

Insights into the effects of sublethal doses of pesticides glufosinate-ammonium and sulfoxaflor on honey bee health

Insect pollinators are threatened worldwide, being the exposure to multiple pesticides one of the most important stressor. The herbicide Glyphosate and the insecticide Imidacloprid are among the most used pesticides worldwide, although different studies evidenced their detrimental effects on non-target organisms. The emergence of glyphosate-resistant weeds and the recent ban of imidacloprid in Europe due to safety concerns, has prompted their replacement by new molecules, such as glufosinate-ammonium (GA) and sulfoxaflor (S). GA is a broad-spectrum and non-selective herbicide that inhibits a key enzyme in the metabolism of nitrogen, causing accumulation of lethal levels of ammonia; while sulfoxaflor is an agonist at insect nicotinic acetylcholine receptors (nAChRs) and generates excitatory responses including tremors, paralysis and mortality. Although those molecules are being increasingly used for crop protection, little is known about their effects on non-target organisms. In this study we assessed the impact of chronic and acute exposure to sublethal doses of GA and S on honey bee gut microbiota, immunity and survival. We found GA significantly reduced the number of gut bacteria, and decreased the expression of glucose oxidase, a marker of social immunity. On the other hand, S significantly increased the number of gut bacteria altering the microbiota composition, decreased the expression of lysozyme and increased the expression of hymenoptaecin. These alterations in gut microbiota and immunocompetence may lead to an increased susceptibility to pathogens. Finally, both pesticides shortened honey bee survival and increased the risk of death. Those results evidence the negative impact of GA and S on honey bees, even at single exposition to a low dose, and provide useful information to the understanding of pollinators decline.

Unraveling the Role of Antimicrobial Peptides in Insects

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

The promise of probiotics in honeybee health and disease management

Over the last decades, losses of bee populations have been observed worldwide. A panoply of biotic and abiotic factors, as well as the interplay among them, has been suggested to be responsible for bee declines, but definitive causes have not yet been identified. Among pollinators, the honeybee Apis mellifera is threatened by various diseases and environmental stresses, which have been shown to impact the insect gut microbiota that is known to be fundamental for host metabolism, development and immunity. Aimed at preserving the gut homeostasis, many researches are currently focusing on improving the honeybee health through the administration of probiotics e.g., by boosting the innate immune response against microbial infections. Here, we review the knowledge available on the characterization of the microbial diversity associated to honeybees and the use of probiotic symbionts as a promising approach to maintain honeybee fitness, sustaining a healthy gut microbiota and enhancing its crucial relationship with the host immune system.

Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members

The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether microbiota were influenced by host genotype and landscape composition. We also characterized the genotypes of individual bees and the land cover surrounding each colony. The literature-defined core taxa dominated across the region despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained much of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There were weak trends for colonies in more similar landscapes to have more similar microbiota, and for bees from more urban landscapes to have less diverse microbiota. To our knowledge, this is the first report for any species that the gut bacterial communities of individuals are influenced by the genotypes of others in the population.

Community Dynamics in Structure and Function of Honey Bee Gut Bacteria in Response to Winter Dietary Shift

Temperate honey bees (Apis mellifera) are challenged by low temperatures and abrupt dietary shifts associated with behavioral changes during winter. Case studies have revealed drastic turnover in the gut microbiota of winter bees, highlighted by the seasonal dominance of a non-core bacterium Bartonella. However, neither biological consequence nor underlying mechanism of this microbial turnover is clear. In particular, we ask whether such changes in gut profile are related to winter dietary shift and possibly beneficial to host and associated gut microbiome? Here, we integrated evidences from genomics, metagenomics, and metabolomics in three honey bee subspecies maintained at the same locality of northern China to profile both diversity and functional variations in gut bacteria across seasons. Our results showed that winter dominance of Bartonella was shared in all tested honey bee lineages. This seasonal change was likely a consequence of winter dietary shifts characterized by greatly reduced pollen consumption and accumulation of metabolic waste due to restricted excretion. Bartonella showed expanded genomic capacity in utilizing more diverse energy substrates, such as converting metabolic wastes lactate and ethanol into pyruvate, an energy source for self-utilization and possibly also for host and other symbionts. Furthermore, Bartonella was the only bacterium capable of both producing and secreting tryptophan and phenylalanine, whose metabolic products were detected in bee guts, even though all gut bacteria lacked relevant digestion enzymes. These results thus suggested a possible mechanism where the gut bacteria might benefit the host by supplementing them with essential amino acids lacking in a protein shortage diet.

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee

To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.

Emerging rodent-associated Bartonella: a threat for human health?

Background

Species of the genus Bartonella are facultative intracellular alphaproteobacteria with zoonotic potential. Bartonella infections in humans range from mild with unspecific symptoms to life threatening, and can be transmitted via arthropod vectors or through direct contact with infected hosts, although the latter mode of transmission is rare. Among the small mammals that harbour Bartonella spp., rodents are the most speciose group and harbour the highest diversity of these parasites. Human–rodent interactions are not unlikely as many rodent species live in proximity to humans. However, a surprisingly low number of clinical cases of bartonellosis related to rodent-associated Bartonella spp. have thus far been recorded in humans.

Methods

The main purpose of this review is to determine explanatory factors for this unexpected finding, by taking a closer look at published clinical cases of bartonellosis connected with rodent-associated Bartonella species, some of which have been newly described in recent years. Thus, another focus of this review are these recently proposed species.

Conclusions

Worldwide, only 24 cases of bartonellosis caused by rodent-associated bartonellae have been reported in humans. Possible reasons for this low number of cases in comparison to the high prevalences of Bartonella in small mammal species are (i) a lack of awareness amongst physicians of Bartonella infections in humans in general, and especially those caused by rodent-associated bartonellae; and (ii) a frequent lack of the sophisticated equipment required for the confirmation of Bartonella infections in laboratories that undertake routine diagnostic testing. As regards recently described Bartonella spp., there are presently 14 rodent-associated Candidatus taxa. In contrast to species which have been taxonomically classified, there is no official process for the review of proposed Candidatus species and their names before they are published. This had led to the use of malformed names that are not based on the International Code of Nomenclature of Prokaryotes. Researchers are thus encouraged to propose Candidatus names to the International Committee on Systematics of Prokaryotes for approval before publishing them, and only to propose new species of Bartonella when the relevant datasets allow them to be clearly differentiated from known species and subspecies.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05162-5.

Long-Read Sequencing Reveals Genetic Adaptation of Bartonella Adhesin A Among Different Bartonella henselae Isolates

Bartonella henselae is the causative agent of cat scratch disease and other clinical entities such as endocarditis and bacillary angiomatosis. The life cycle of this pathogen, with alternating host conditions, drives evolutionary and host-specific adaptations. Human, feline, and laboratory adapted B. henselae isolates often display genomic and phenotypic differences that are related to the expression of outer membrane proteins, for example the Bartonella adhesin A (BadA). This modularly-structured trimeric autotransporter adhesin is a major virulence factor of B. henselae and is crucial for the initial binding to the host via the extracellular matrix proteins fibronectin and collagen. By using next-generation long-read sequencing we demonstrate a conserved genome among eight B. henselae isolates and identify a variable genomic badA island with a diversified and highly repetitive badA gene flanked by badA pseudogenes. Two of the eight tested B. henselae strains lack BadA expression because of frameshift mutations. We suggest that active recombination mechanisms, possibly via phase variation (i.e., slipped-strand mispairing and site-specific recombination) within the repetitive badA island facilitate reshuffling of homologous domain arrays. The resulting variations among the different BadA proteins might contribute to host immune evasion and enhance long-term and efficient colonisation in the differing host environments. Considering the role of BadA as a key virulence factor, it remains important to check consistently and regularly for BadA surface expression during experimental infection procedures.

Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate : Seasonal Dynamics of Honey Bee Gut Microbiota

Honey bees (Apis mellifera) provide invaluable benefits for food production and maintenance of biodiversity of natural environments through pollination. They are widely spread across the world, being adapted to different climatic conditions. To survive the winter in cold temperate regions, honey bees developed different strategies including storage of honey and pollen, confinement of individuals during the winter, and an annual cycle of colony growth and reproduction. Under these conditions, winter honey bees experience physiological changes, including changes in immunity and the composition of honey bee gut microbiota. However, under tropical or subtropical climates, the life cycle can experience alterations, i.e., queens lay eggs during almost all the year and new honey bees emerge constantly. In the present study, we characterized nurses' honey bee gut microbiota in colonies under subtropical region through a year, combining qPCR, PCR-DGGE, and 16S rDNA high-throughput sequencing. We also identified environmental variables involved in those changes. Our results showed that under the mentioned conditions, the number of bacteria is stable throughout the year. Diversity of gut microbiota is higher in spring and lower in summer and winter. Gradual changes in compositions occur between seasons: Lactobacillus spp. predominate in spring while Gilliamella apicola and Snodgrasella alvi predominate in summer and winter. Environmental variables (mainly precipitations) affected the composition of the honey bee gut microbiota. Our findings provide new insights into the dynamics of honey bee gut microbiota and may be useful to understand the adaptation of bees to different environmental conditions.

Cardinium inhibits Wolbachia in its mite host, Tyrophagus putrescentiae, and affects host fitness

Interactions among endosymbiotic bacteria inside their eukaryotic hosts are poorly understood, particularly in mites. The mite Tyrophagus putrescentiae is a common, medically important generalist species that has many intracellular and gut bacterial symbionts. In the experiments, we examined bacterial abundances and composition in mite populations obtained by controlled mixing of stock mite populations that differed in the presence/absence of the major intracellular bacteria Wolbachia and Cardinium. Changes in microbial communities were characterized using 16S ribosomal RNA high-throughput sequencing (pooled mite individuals) and quantitative PCR for key microbial taxa (individual mites). Mite fitness was estimated as a parameter of population growth. We detected that in mixed mite populations, Cardinium and Wolbachia can co-occur in the same mite individual. The presence of Cardinium was negatively correlated with the presence of Wolbachia and Bartonella, while the Bartonella and Wolbachia were positively correlated in individual level samples. Since mixed populations had lower abundances of Wolbachia, while the abundance of Cardinium did not change, we suggest that the presence of Cardinium inhibits the growth of Wolbachia. The mixed mite populations had lower population growth than parental populations. The possible effect of symbionts on the fitness of mixed population is discussed.

Resistance and Vulnerability of Honeybee (Apis mellifera) Gut Bacteria to Commonly Used Pesticides

Agricultural and apicultural practices expose honeybees to a range of pesticides that have the potential to negatively affect their physiology, neurobiology, and behavior. Accumulating evidence suggests that these effects extend to the honeybee gut microbiome, which serves important functions for honeybee health. Here we test the potential effects of the pesticides thiacloprid, acetamiprid, and oxalic acid on the gut microbiota of honeybees, first in direct in vitro inhibition assays and secondly in an in vivo caged bee experiment to test if exposure leads to gut microbiota community changes. We found that thiacloprid did not inhibit the honeybee core gut bacteria in vitro, nor did it affect overall community composition or richness in vivo. Acetamiprid did also not inhibit bacterial growth in vitro, but it did affect community structure within bees. The eight bacterial genera tested showed variable levels of susceptibility to oxalic acid in vitro. In vivo, treatment with this pesticide reduced amplicon sequence variant (ASV) richness and affected gut microbiome composition, with most marked impact on the common crop bacteria Lactobacillus kunkeei and the genus Bombella. We conducted network analyses which captured known associations between bacterial members and illustrated the sensitivity of the microbiome to environmental stressors. Our findings point to risks of honeybee exposure to oxalic acid, which has been deemed safe for use in treatment against Varroa mites in honeybee colonies, and we advocate for more extensive assessment of the long-term effects that it may have on honeybee health.

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

The core gut microbiome of adult honeybee comprises a set of recurring bacterial phylotypes, accompanied by lineage-specific, variable, and less abundant environmental bacterial phylotypes. Several mutual interactions and functional services to the host, including the support provided for growth, hormonal signaling, and behavior, are attributed to the core and lineage-specific taxa. By contrast, the diversity and distribution of the minor environmental phylotypes and fungal members in the gut remain overlooked. In the present study, we hypothesized that the microbial components of forager honeybees (i.e., core bacteria, minor environmental phylotypes, and fungal members) are compartmentalized along the gut portions. The diversity and distribution of such three microbial components were investigated in the context of the physico-chemical conditions of different gut compartments. We observed that changes in the distribution and abundance of microbial components in the gut are consistently compartment-specific for all the three microbial components, indicating that the ecological and physiological interactions among the host and microbiome vary with changing physico-chemical and metabolic conditions of the gut.

Characterization of Apis mellifera Gastrointestinal Microbiota and Lactic Acid Bacteria for Honeybee Protection-A Review

Numerous honeybee (Apis mellifera) products, such as honey, propolis, and bee venom, are used in traditional medicine to prevent illness and promote healing. Therefore, this insect has a huge impact on humans’ way of life and the environment. While the population of A. mellifera is large, there is concern that widespread commercialization of beekeeping, combined with environmental pollution and the action of bee pathogens, has caused significant problems for the health of honeybee populations. One of the strategies to preserve the welfare of honeybees is to better understand and protect their natural microbiota. This paper provides a unique overview of the latest research on the features and functioning of A. mellifera. Honeybee microbiome analysis focuses on both the function and numerous factors affecting it. In addition, we present the characteristics of lactic acid bacteria (LAB) as an important part of the gut community and their special beneficial activities for honeybee health. The idea of probiotics for honeybees as a promising tool to improve their health is widely discussed. Knowledge of the natural gut microbiota provides an opportunity to create a broad strategy for honeybee vitality, including the development of modern probiotic preparations to use instead of conventional antibiotics, environmentally friendly biocides, and biological control agents.

Acute and chronic effects of Titanium dioxide (TiO2) PM1 on honey bee gut microbiota under laboratory conditions

Apis mellifera is an important provider of ecosystem services, and during flight and foraging behaviour is exposed to environmental pollutants including airborne particulate matter (PM). While exposure to insecticides, antibiotics, and herbicides may compromise bee health through alterations of the gut microbial community, no data are available on the impacts of PM on the bee microbiota. Here we tested the effects of ultrapure Titanium dioxide (TiO₂) submicrometric PM (i.e., PM₁, less than 1 µm in diameter) on the gut microbiota of adult bees. TiO₂ PM₁ is widely used as a filler and whitening agent in a range of manufactured objects, and ultrapure TiO₂ PM₁ is also a common food additive, even if it has been classified by the International Agency for Research on Cancer (IARC) as a possible human carcinogen in Group 2B. Due to its ubiquitous use, honey bees may be severely exposed to TiO₂ ingestion through contaminated honey and pollen. Here, we demonstrated that acute and chronic oral administration of ultrapure TiO₂ PM₁ to adult bees alters the bee microbial community; therefore, airborne PM may represent a further risk factor for the honey bee health, promoting sublethal effects against the gut microbiota.

Overwintering Honey Bee Colonies: Effect of Worker Age and Climate on the Hindgut Microbiota

Honey bee overwintering health is essential to meet the demands of spring pollination. Managed honey bee colonies are overwintered in a variety of climates, and increasing rates of winter colony loss have prompted investigations into overwintering management, including indoor climate controlled overwintering. Central to colony health, the worker hindgut gut microbiota has been largely ignored in this context. We sequenced the hindgut microbiota of overwintering workers from both a warm southern climate and controlled indoor cold climate. Congruently, we sampled a cohort of known chronological age to estimate worker longevity in southern climates, and assess age-associated changes in the core hindgut microbiota. We found that worker longevity over winter in southern climates was much lower than that recorded for northern climates. Workers showed decreased bacterial and fungal load with age, but the relative structure of the core hindgut microbiome remained stable. Compared to cold indoor wintering, collective microbiota changes in the southern outdoor climate suggest compromised host physiology. Fungal abundance increased by two orders of magnitude in southern climate hindguts and was positively correlated with non-core, likely opportunistic bacteria. Our results contribute to understanding overwintering honey bee biology and microbial ecology and provide insight into overwintering strategies.

Characterization of the Kenyan Honey Bee (Apis mellifera) Gut Microbiota: A First Look at Tropical and Sub-Saharan African Bee Associated Microbiomes

Gut microbiota plays important roles in many physiological processes of the host including digestion, protection, detoxification, and development of immune responses. The honey bee (Apis mellifera) has emerged as model for gut-microbiota host interaction studies due to its gut microbiota being highly conserved and having a simple composition. A key gap in this model is understanding how the microbiome differs regionally, including sampling from the tropics and in particular from Africa. The African region is important from the perspective of the native diversity of the bees, and differences in landscape and bee management. Here, we characterized the honey bee gut microbiota in sub-Saharan Africa using 16S rRNA amplicon sequencing. We confirm the presence of the core gut microbiota members and highlight different compositions of these communities across regions. We found that bees from the coastal regions harbor a higher relative abundance and diversity on core members. Additionally, we showed that Gilliamella, Snodgrassella, and Frischella dominate in all locations, and that altitude and humidity affect Gilliamella abundance. In contrast, we found that Lactobacillus was less common compared temperate regions of the world. This study is a first comprehensive characterization of the gut microbiota of honey bees from sub-Saharan Africa and underscores the need to study microbiome diversity in other indigenous bee species and regions.

Impact of Nutritional Stress on Honeybee Gut Microbiota, Immunity, and Nosema ceranae Infection

Honeybees are important pollinators, having an essential role in the ecology of natural and agricultural environments. Honeybee colony losses episodes reported worldwide and have been associated with different pests and pathogens, pesticide exposure, and nutritional stress. This nutritional stress is related to the increase in monoculture areas which leads to a reduction of pollen availability and diversity. In this study, we examined whether nutritional stress affects honeybee gut microbiota, bee immunity, and infection by Nosema ceranae, under laboratory conditions. Consumption of Eucalyptus grandis pollen was used as a nutritionally poor-quality diet to study nutritional stress, in contraposition to the consumption of polyfloral pollen. Honeybees feed with Eucalyptus grandis pollen showed a lower abundance of Lactobacillus mellifer and Lactobacillus apis (Firm-4 and Firm-5, respectively) and Bifidobacterium spp. and a higher abundance of Bartonella apis, than honeybees fed with polyfloral pollen. Besides the impact of nutritional stress on honeybee microbiota, it also decreased the expression levels of vitellogenin and genes associated to immunity (glucose oxidase, hymenoptaecin and lysozyme). Finally, Eucalyptus grandis pollen favored the multiplication of Nosema ceranae. These results show that nutritional stress impacts the honeybee gut microbiota, having consequences on honeybee immunity and pathogen development. Those results may be useful to understand the influence of modern agriculture on honeybee health.

Oral or Topical Exposure to Glyphosate in Herbicide Formulation Impacts the Gut Microbiota and Survival Rates of Honey Bees

Honey bees are important agricultural pollinators that rely on a specific gut microbiota for the regulation of their immune system and defense against pathogens. Environmental stressors that affect the bee gut microbial community, such as antibiotics and glyphosate, can indirectly compromise bee health. Most of the experiments demonstrating these effects have been done under laboratory conditions with pure chemicals. Here, we investigated the oral and topical effects of various concentrations of glyphosate in a herbicide formulation on the honey bee gut microbiota and health under laboratory and field conditions. Under all of these conditions, the formulation, dissolved in sucrose syrup or water, affected the abundance of beneficial bacteria in the bee gut in a dose-dependent way. Mark-recapture experiments also demonstrated that bees exposed to the formulation were more likely to disappear from the colony, once reintroduced after exposure. Although no visible effects were observed for hives exposed to the formulation in field experiments, challenge trials with the pathogen Serratia marcescens, performed under laboratory conditions, revealed that bees from hives exposed to the formulation exhibited increased mortality compared with bees from control hives. In the field experiments, glyphosate was detected in honey collected from exposed hives, showing that worker bees transfer xenobiotics to the hive, thereby extending exposure and increasing the chances of exposure to recently emerged bees. These findings show that different routes of exposure to glyphosate-based herbicide can affect honey bees and their gut microbiota.IMPORTANCE The honey bee gut microbial community plays a vital role in immune response and defense against opportunistic pathogens. Environmental stressors, such as the herbicide glyphosate, may affect the gut microbiota, with negative consequences for bee health. Glyphosate is usually sprayed in the field mixed with adjuvants, which enhance herbicidal activity. These adjuvants may also enhance undesired effects in nontargeted organisms. This seems to be the case for glyphosate-based herbicide on honey bees. As we show in this study, oral exposure to either pure glyphosate or glyphosate in a commercial herbicide formulation perturbs the gut microbiota of honey bees, and topical exposure to the formulation also has a direct effect on honey bee health, increasing mortality in a dose-dependent way and leaving surviving bees with a perturbed microbiota. Understanding the effects of herbicide formulations on honey bees may help to protect these important agricultural pollinators.

Bartonella spp. detection in ticks, Culicoides biting midges and wild cervids from Norway

Bartonella spp. are fastidious, gram-negative, aerobic, facultative intracellular bacteria that infect humans, and domestic and wild animals. In Norway, Bartonella spp. have been detected in cervids, mainly within the distribution area of the arthropod vector deer ked (Lipoptena cervi). We used PCR to survey the prevalence of Bartonella spp. in blood samples from 141 cervids living outside the deer ked distribution area (moose [Alces alces, n = 65], red deer [Cervus elaphus, n = 41] and reindeer [Rangifer tarandus, n = 35]), in 44 pool samples of sheep tick (Ixodes ricinus, 27 pools collected from 74 red deer and 17 from 45 moose) and in biting midges of the genus Culicoides (Diptera: Ceratopogonidae, 120 pools of 6,710 specimens). Bartonella DNA was amplified in moose (75.4%, 49/65) and in red deer (4.9%, 2/41) blood samples. All reindeer were negative. There were significant differences in Bartonella prevalence among the cervid species. Additionally, Bartonella was amplified in two of 17 tick pools collected from moose and in 3 of 120 biting midge pool samples. The Bartonella sequences amplified in moose, red deer and ticks were highly similar to B. bovis, previously identified in cervids. The sequence obtained from biting midges was only 81.7% similar to the closest Bartonella spp. We demonstrate that Bartonella is present in moose across Norway and present the first data on northern Norway specimens. The high prevalence of Bartonella infection suggests that moose could be the reservoir for this bacterium. This is the first report of bacteria from the Bartonella genus in ticks from Fennoscandia and in Culicoides biting midges worldwide.

Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut

Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.

Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment

Some lineages of ants, termites, and beetles independently evolved a symbiotic association with lignocellulolytic fungi cultivated for food, in a lifestyle known as fungiculture. Fungus-growing insects' symbiosis also hosts a bacterial community thought to integrate their physiology. Similarities in taxonomic composition support the microbiota of fungus-growing insects as convergent, despite differences in fungus-rearing by these insects. Here, by comparing fungus-growing insects to several hosts ranging diverse dietary patterns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of the fungiculture environment. Compared to other hosts, the microbiota associated with fungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at class level and by Pseudomonas at genera level. Even with a functional profile presenting similarities with the gut microbiota of herbivorous and omnivorous hosts, some differentially abundant features codified by the microbiota of fungus-growing insects suggest these communities occupying microhabitats that are characteristic of fungiculture. These features include metabolic pathways involved in lignocellulose breakdown, detoxification of plant secondary metabolites, metabolism of simple sugars, fungal cell wall deconstruction, biofilm formation, antimicrobials biosynthesis, and metabolism of diverse nutrients. Our results suggest that the microbiota could be functionally adapted to the fungiculture environment, codifying metabolic pathways potentially relevant to the fungus-growing insects' ecosystems functioning.

Investigation of Bartonella spp. in brazilian mammals with emphasis on rodents and bats from the Atlantic Forest

The Bartonella species are zoonotic agents that infect mammals and are transmitted by arthropod vectors. Approximately 18 distinct genotypes cause diseases in humans, and may be spread by both domestic and wild animals. In Brazil, Bartonella genotypes have been identified in several species of wild mammals, and in the present study, we analyzed samples from non-human primates (marmosets), marsupials, rodents, and bats, and compared them with the genotypes described in mammals from Brazil, to examine the distribution of Bartonella genotypes in two impacted areas of Rio de Janeiro state, in southeastern Brazil. We used polymerase chain reaction (PCR) methods to detect the Bartonella DNA using partial sequences of the gltA, ftsZ, and groEL genes. We generated Bayesian inference and maximum likelihood trees to characterize the positive PCR samples and infer the phylogenetic relationships of the genotypes. A total of 276 animals were captured, including 110 bats, 91 rodents, 38 marsupials, and 37 marmosets. The DNA of Bartonella was amplified from tissue samples collected from 12 (4.34%) of the animals, including eight rodents – Akodon cursor (5/44) and Nectomys squamipes (3/27) – and four bats, Artibeus lituratus (3/58) and Carollia perspicillata (1/15). We identified Bartonella genotypes closely related to those described in previous studies, as well as new genotypes in both the rodent and the bat samples. Considering the high diversity of the Bartonella genotypes and hosts identified in the present study, further research is needed to better understand the relationships between the different Bartonella genotypes and their vectors and host species. The presence of Bartonella in the wild rodents and bats from the study area indicates that the local human populations may be at risk of infection by Bartonella due to the spillover of these strains from the wild environment to domestic and peri-domestic environments.

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First record of wild mammals with Bartonella DNA at northwestern of Rio de Janeiro.

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The genotypes of Bartonella were characterized in two species of cricetid rodents and two species of phyllostomid bats from Rio de Janeiro.

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The genotype of Bartonella in Akodon cursor was identified closely related to B. rochalimae.

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This is the first report of Bartonella in C. perspicillata from Rio de Janeiro state, based on the analysis of tissue samples.

Genomic Characterization of the Novel Bartonella refiksaydamii sp. Isolated from the Blood of a Crocidura suaveolens (Pallas, 1811)

Bartonella species are reemerging infectious agents that are transmitted by arthropod vectors among animals and/or humans. At least 13 of the 35 currently recognized Bartonella species are pathogenic for humans. Most of the pathogenic species, except Bartonella quintana and Bartonella bacilliformis, are zoonotic agents with animal reservoirs, including cats, dogs, coyotes, foxes, cattle, and rodents. In this study, a novel Bartonella species was isolated from the blood of a Crocidura suaveolens (Pallas, 1811) Lesser shrew that was captured in the Bartın region of Northwestern Turkey. The strain, RSKK 19006, was characterized using whole-genome sequencing and comparison, multilocus sequence typing (gltA, rpoB, ssrA, nuoG, and 16S rRNA) and internal transcribed spacer sequencing, electron microscopy scanning, biochemical tests, and MALDI-TOF MS (matrix assisted laser desorption ionization-time of flight mass spectrometry). This novel Bartonella is a Gram-negative, rod-shaped, microaerophilic bacterium and has neither flagella nor pilus. As a consequence, we propose to name this new species Bartonella refiksaydamii sp. nov. in Bartonella genus. The zoonotic potential of this novel Bartonella species is as yet unknown.

Isolation of Candidatus Bartonella rousetti and Other Bat-associated Bartonellae from Bats and Their Flies in Zambia

Bat-associated bartonellae, including Bartonella mayotimonensis and Candidatus Bartonella rousetti, were recently identified as emerging and potential zoonotic agents, respectively. However, there is no report of bat-associated bartonellae in Zambia. Thus, we aimed to isolate and characterize Bartonella spp. from bats and bat flies captured in Zambia by culturing and PCR. Overall, Bartonella spp. were isolated from six out of 36 bats (16.7%), while Bartonella DNA was detected in nine out of 19 bat flies (47.3%). Subsequent characterization using a sequence of five different genes revealed that three isolates obtained from Egyptian fruit bats (Rousettus aegyptiacus) were Ca. B. rousetti. The isolates obtained from insectivorous bats (Macronycteris vittatus) were divided into two previously unclassified bat-associated bartonellae. A phylogenetic analysis of the six genotypes of Bartonella gltA sequences from nine pathogen-positive bat flies revealed that three genotypes belonged to the same clades as bat-associated bartonellae, including Ca. B. rousetti. The other three genotypes represented arthropod-associated bartonellae, which have previously been isolated only from ectoparasites. We demonstrated that Ca. B. rousetti is maintained between bats (R. aegyptiacus) and bat flies in Zambia. Continuous surveillance of Bartonella spp. in bats and serological surveys in humans in Africa are warranted to evaluate the public health importance of bat-associated bartonellae.

Bartonella species in medically important mosquitoes, Central Europe

Here, we provide the first mass molecular screening of medically important mosquitoes for Bartonella species using multiple genetic markers. We examined a total of 72,115 mosquito specimens, morphologically attributed to Aedes vexans (61,050 individuals), Culex pipiens (10,484 individuals) and species of the Anopheles maculipennis complex (581 individuals) for Bartonella spp. The initial screening yielded 63 Bartonella-positive A. vexans mosquitoes (mean prevalence 0.1%), 34 Bartonella-positive C. pipiens mosquitoes (mean prevalence 0.3%) and 158 Bartonella-positive A. maculipennis group mosquitoes (mean prevalence 27.2%). Several different Bartonella ITS sequences were recovered. This study highlights the need for molecular screening of mosquitoes, the most important vectors of arthropod-borne pathogens, for potential bacterial agents.

Comparative analysis of microbial community in the whole body and midgut from fully engorged and unfed female adult Melophagus ovinus

Melophagus ovinus is a type of ectoparasite infesting sheep. Data regarding the comprehensive bacterial community associated with the whole body and midgut of M. ovinus under different engorged statuses are required. Melophagus ovinus were collected from the city of Jiuquan, China. Bacterial DNA was extracted from the whole body and midgut of fully engorged female adults, or newly hatched and unfed adult female M. ovinus. The 16S rRNA gene V3-V4 hypervariable regions were sequenced using the IonS5™XL platform (Thermo Fisher Scientific, Waltham, MA, U.S.A.). The whole body bacterial diversity of the newly hatched, unfed adult females was greater compared with that of the other three samples. Proteobacteria was the dominant bacterial phylum in all of the samples. Of the 42 total bacterial genera present in all of the experimental samples, Arsenophonus, Bartonella and Wolbachia were the dominant genera. The relative abundance of Arsenophonus in midgut was greater than that in the whole body. The relative abundance of Bartonella in fully engorged adults was far greater than those in newly hatched, unfed adults. The relative abundance of Wolbachia was highest in the whole body of newly hatched, unfed adults. Seventeen bacterial species were identified in all experimental samples. Bartonella chomelii, Streptococcus hyointestinalis and Escherichia coli were the first species reported in M. ovinus.

Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas

The genus Bartonella (Family: Bartonellaceae; Order: Rhizobiales; Class: Alphaproteobacteria) comprises facultative intracellular Gram-negative, haemotropic, slow-growing, vector-borne bacteria. Wild rodents and their fleas harbor a great diversity of species and strains of the genus Bartonella, including several zoonotic ones. This genetic diversity coupled with a fastidious nature of the organism results in a taxonomic challenge that has led to a massive collection of uncharacterized strains. Here, we report the genomic and phenotypic characterization of two strains, members of the genus Bartonella (namely Tel Aviv and OE 1-1), isolated from Rattus rattus rats and Synosternus cleopatrae fleas, respectively. Scanning electron microscopy revealed rod-shaped bacteria with polar pili, lengths ranging from 1.0 to 2.0 µm and widths ranging from 0.3 to 0.6 µm. OE 1-1 and Tel Aviv strains contained one single chromosome of 2.16 and 2.23 Mbp and one plasmid of 29.0 and 41.5 Kbp, with average DNA G+C contents of 38.16 and 38.47 mol%, respectively. These strains presented an average nucleotide identity (ANI) of 89.9 %. Bartonella elizabethae was found to be the closest phylogenetic relative of both strains (ANI=90.9-93.6 %). The major fatty acids identified in both strains were C_18:1ω7c, C_18 : 0 and C_16 : 0. They differ from B. elizabethae in their C_17 : 0 and C_15 : 0 compositions. Both strains are strictly capnophilic and their biochemical profiles resembled those of species of the genus Bartonella with validly published names, whereas differences in arylamidase activities partially assisted in their speciation. Genomic and phenotypic differences demonstrate that OE 1-1 and Tel Aviv strains represent novel individual species, closely related to B. elizabethae, for which we propose the names Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov.

Honeybee microbiome is stabilized in the presence of propolis

Honeybees have developed many unique mechanisms to help ensure the proper maintenance of homeostasis within the hive. One method includes the collection of chemically complex plant resins combined with wax to form propolis, which is deposited throughout the hive. Propolis is believed to play a significant role in reducing disease load in the colony due to its antimicrobial and antiseptic properties. However, little is known about how propolis may interact with bee-associated microbial symbionts, and if propolis alters microbial community structure. In this study, we found that propolis appears to maintain a stable microbial community composition and reduce the overall taxonomic diversity of the honeybee microbiome. Several key members of the gut microbiota were significantly altered in the absence of propolis, suggesting that it may play an important role in maintaining favourable abundance and composition of gut symbionts. Overall, these findings suggest that propolis may help to maintain honeybee colony microbial health by limiting changes to the overall microbial community.

Gene Transfer Agents in Symbiotic Microbes

Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera)

Bacteria within the digestive tract of adult honey bees are likely to play a key role in the digestion of sugar-rich foods. However, the influence of diet on honey bee gut bacteria is not well understood. During periods of low floral abundance, beekeepers often supplement the natural sources of carbohydrate that honey bees collect, such as nectar, with various forms of carbohydrates such as sucrose (a disaccharide) and invert sugar (a mixture of the monosaccharides glucose and fructose). We compared the effect of these sugar supplements on the relative abundance of bacteria in the gut of bees by feeding bees from a single colony, two natural diets: mānuka honey, a monofloral honey with known antibacterial properties, and a hive diet; and artificial diets of invert sugar, sucrose solution, and sucrose solutions containing synthesised compounds associated with the antibacterial properties of mānuka honey. 16S ribosomal RNA (rRNA)-based sequencing showed that dietary regimes containing mānuka honey, sucrose and invert sugar did not alter the relative abundance of dominant core bacteria after 6 days of being fed these diets. However, sucrose-rich diets increased the relative abundances of three sub-dominant core bacteria, Rhizobiaceae, Acetobacteraceae, and Lactobacillus kunkeei, and decreased the relative abundance of Frischella perrara, all which significantly altered the bacterial composition. Acetogenic bacteria from the Rhizobiaceae and Acetobacteraceae families increased two- to five-fold when bees were fed sucrose. These results suggest that sucrose fuels the proliferation of specific low abundance primary sucrose-feeders, which metabolise sugars into monosaccharides, and then to acetate.

Honey bee microbiome associated with different hive and sample types over a honey production season

Western honey bees (Apis mellifera) are important pollinators in natural and agricultural ecosystems, and yet are in significant decline due to several factors including parasites, pathogens, pesticides, and habitat loss. A new beehive construction called the Flow^TM hive was developed in 2015 to allow honey to be harvested directly from the hive without opening it, resulting in an apparent decrease in stress to the bees. Here, we compared the Flow and traditional Langstroth hive constructions to determine if there were any significant differences in the bee microbiome. The bee-associated bacterial communities did not differ between hive constructions and varied only slightly over the course of a honey production season. Samples were dominated by taxa belonging to the Lactobacillus, Bifidobacterium, Bartonella, Snodgrassella, Gilliamella, and Frischella genera, as observed in previous studies. The top ten most abundant taxa made up the majority of the sequence data; however, many low abundance organisms were persistent across the majority of samples regardless of sampling time or hive type. We additionally compared different preparations of whole bee and dissected bee samples to elaborate on previous bee microbiome research. We found that bacterial sequences were overwhelming derived from the bee guts, and microbes on the bee surfaces (including pollen) contributed little to the overall microbiome of whole bees. Overall, the results indicate that different hive constructions and associated disturbance levels do not influence the bee gut microbiome, which has broader implications for supporting hive health.

Effects of Tropilaelaps mercedesae on midgut bacterial diversity of Apis mellifera

Tropilaelaps mercedesae is an ectoparasite of Apis mellifera in Asia and is considered a major threat to honey bee health. Herein, we used the Illumina MiSeq platform 16S rDNA Amplicon Sequencing targeting the V3-V4 regions and analysed the effects on the midgut bacterial communities of honey bees infested with T. mercedesae. The overall bacterial community in honey bees infested with T. mercedesae were observed at different developmental stages. Honey bee core intestinal bacterial genera such as Gilliamella, Lactobacillus and Frischella were detected. Tropilaelapsmercedesae infestation changed the bacterial communities in the midgut of A. mellifera. Tropilaelapsmercedesae-infested pupae had greatly increased relative abundances of Micrococcus and Sphingomonas, whereas T. mercedesae-infested 15-day-old workers had significantly reduced relative abundance of non-core microbes: Corynebacterium, Sphingomonas, Acinetobacter and Enhydrobacter compared to T. mercedesae-infested newly emerged bees. The bacterial community was significantly changed at the various T. mercedesae-infested developmental stages of A. mellifera. Tropilaelapsmercedesae infestation also changed the non-core bacterial community from larvae to newly emerged honey bees. Bacterial communities were significantly different between T. mercedesa-infested and non-mite-infested 15-day-old workers. Lactobacillus was dominant in T. mercedesae-infested 15-day-old workers compared to non-mite-infested 15-day-old workers.

Molecular Detection of Bartonella bacilliformis in Lutzomyia maranonensis in Cajamarca, Peru: A New Potential Vector of Carrion's Disease in Peru?

Carrion's disease is a neglected, vector-borne illness that affects Colombia, Ecuador, and especially Peru. The phlebotomine sand flies Lutzomyia verrucarum and Lutzomyia peruensis are the main illness vectors described, although other species may be implicated in endemic areas such as some northern Peruvian regions, in which Carrion's disease vector has not been established. The aim of this study was to evaluate the presence of Bartonella bacilliformis DNA in Lutzomyia maranonensis from Cajamarca, northern Peru. This sand fly has not been defined as a vector yet. Centers for Disease Control and Prevention light traps were used to collect adult phlebotomine sand flies from 2007 to 2008 in the Cajamarca department. Female specimens were identified using morphological keys and were grouped into pools of five sand flies, taking into account district and sampling site (intradomicile or peridomicile). DNA was extracted, and then conventional and real-time polymerase chain reaction (RT-PCR) were performed to detect B. bacilliformis and subsequently confirmed by sequencing. A total of 383 specimens of L. maranonensis species were analyzed. Two of 76 pools were positive for B. bacilliformis by sequencing; all positives pools were from Querocotillo district. In addition, Mesorhizobium spp. were identified in two pools of sand flies, which is an α-proteobacteria phylogenetically very close to B. bacilliformis. This study presents molecular evidence that suggests L. maranonensis is naturally infected by B. bacilliformis in the Cajamarca department. Further research should determine if L. maranonensis is a vector and could transmit B. bacilliformis.

The honey bee gut microbiota: strategies for study and characterization

Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of Ap. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general and to aid design of future experiments in this growing field.