Honey Bee Gut Research Articles

An amitraz-based miticide does not appear to affect the bacterial microbiota of Apis mellifera (Apidae: Hymenoptera, Linnaeus, 1758) or Varroa destructor (Acari: Varroidae, Anderson & Trueman, 2000)

ABSTRACT The use of pesticides in beehives constitutes an important health issue for honey bees (Apis mellifera). Miticide treatments are not lethal to bees but could still impose significant sublethal costs. This study examined the impacts of amitraz, a commonly used miticide, on the bacterial communities of the honey bee gut and Varroa destructor mites. We sequenced and compared gut 16S rDNA composition pre – and post-amitraz treatment. Amitraz did not significantly influence bacterial gut communities in either honey bees or mites during the first six weeks following treatment. The gut bacterial community of bees was mainly dominated by the commonly observed microbiota in bees, which included species in the genera Gilliamella, Snodgrassella, and Frischella. Deformed wing virus (DWV) loads were analysed but were also unaffected by amitraz treatment over the six-week period studied. The bacterial community of Varroa destructor mites was heavily dominated by Bartonella spp., in contrast to results observed elsewhere. Our results indicating that amitraz does not appear to affect honey bee microbiota should be helpful for beekeepers who rely on this pesticide for mite control.

Effect of host genetics on gut microbiota composition in an italian honeybee breeding population

Honeybees host a specialised gut microbiota composed of five ever-present bacteria, which undergo seasonal variation in their proportions. The objective of this study was to investigate how host genetics can affect the microbial composition of the honeybee gut over a 5-month sampling period. Seventy-seven colonies from eight maternal genetic lines were sampled from a breeding population located in Lombardy, Italy. The colonies have been selected since 2015 for three different traits, using isolated mating stations for reproduction. Worker bees were sampled three times: June, July and October 2021. From each colony, gut from ten worker bees were pooled, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Statistical analyses were conducted in the R environment to assess the impact of genetic lines, timepoints, and their interaction on α-diversity and β-diversity. Results for α-diversity showed a significant effect of genetic line on the Simpson index, as well as a consistent effect of the timepoint. Specifically, genetic line H showed a lower Simpson index, and this line also produced less honey in the same years, suggesting a genetic influence on both microbiota richness and honey yield. For β-diversity, results revealed that the month of sampling had the strongest effect, while no significant differences were identified for the genetic line or their interaction.

Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont

The Type VI Secretion System (T6SS) is a sophisticated mechanism utilized by gram-negative bacteria to deliver toxic effector proteins into target cells, influencing microbial community dynamics and host interactions. In this study, we investigated the role of T6SSs in Snodgrassella alvi wkB2, a core bacterial symbiont of the honey bee gut microbiota. We generated single- and double-knockout mutants targeting essential genes (tssD and tssE) in both T6SS-1 and T6SS-2 and assessed their colonization and competition capabilities in vivo. Our results indicate that T6SSs are nonessential for colonization of the bee gut, although T6SS-2 mutant strains exhibited significantly lower colonization levels compared to the wild-type (WT) strain. Further, a defined community experiment showed that S. alvi wkB2 T6SSs do not significantly impact interspecific competition among core gut bacteria. However, cocolonization experiments with closely related S. alvi strains demonstrated that T6SS-1 plays a role in mediating intraspecific competition. Transcriptomic analysis of bee guts monocolonized by WT or T6SS mutants revealed differential expression of host immunity-related genes relative to microbiota-deprived bees, such as upregulation of the antimicrobial peptide apidaecin in the presence of WT S. alvi and the antimicrobial peptide defensin in the presence of T6SS-2 mutant S. alvi, suggesting that T6SSs contribute to shaping host immune responses. These findings provide insight into the ecological roles of T6SSs in the honey bee gut microbiota, emphasizing their importance in maintaining competitive dynamics and influencing host-bacterial interactions.

Biological damage of monocrotaline on the brain and intestinal tissues of Apis mellifera

Monocrotaline (MCT) is a toxic alkaloid present in plants, posing a threat to animals in terrestrial ecosystems. However, little is known about its potential impacts on pollinating insects. Here, we report the effects of of MCT on the brains and intestines of foraging honeybees (Apis mellifera). MCT exposure resulted in a reduction in head weight and swelling of the abdomen in honeybees. Additionally, MCT exposure caused morphological damage to the brain, characterized by decreased antioxidant capacity and increased apoptosis, along with intestinal tissue damage that was accompanied by increased antioxidant capacity and apoptosis. Moreover, MCT altered the core gut microbial community structure in honeybees and increased the expression of antimicrobial peptide (AMP) genes in the midgut. These findings indicate that exposure to MCT activates the immune response in the honeybee gut, while the brain does not exhibit an immune response but instead experiences oxidative stress. This study provides a resource for future research exploring interactions between MCT and other insects, and can help deepen our understanding of MCT's potential impacts in ecosystems.

The IMPACT OF HONEYBEE GUT BACTERIA ON THE SURVIVAL OF HONEYBEES EXPOSED TO INSECTICIDES

The widespread use of insecticides poses a significant threat to the health and sustainability of honeybees (Apis mellifera). This study aimed to isolate, identify, and investigate the potential of honeybee gut bacterial strains in mitigating the detrimental effects of insecticides on honeybees and extending their lifespan. The efficacy of seven honeybee gut bacterial strains in reducing insecticide toxicity was evaluated. Through the identification of honeybee gut bacterial isolates using 16s rRNA, seven strains were identified, namely Priestia endophytica, Bacillus subtilis, Bacillus pumilus, Peribacillus frigoritolerans, B. subtilis, Bacillus pumilus, and Bacillus tequilensis. The experimental results revealed that bees treated with these gut bacteria significantly reduced oxidative stress markers and detoxification enzyme levels compared to untreated bees. Moreover, the treated bees demonstrated enhanced immune responses. The bees treated with deltamethrin + intestinal bacteria showed an increase in bees' lifespan to 6.33 days compared to a lifespan of 4 days with deltamethrin only. Similarly, bees treated with acetamiprid intestinal bacteria had further extended to 10.33 days compared to a lifespan of 7.67 days with acetamiprid. These findings suggest that using honeybee gut bacterial strains may serve as a sustainable strategy to mitigate the harmful impacts of insecticides on honeybees, thereby promoting their overall health and contributing to the preservation of pollination services and apiculture. Further research is warranted to elucidate the underlying mechanisms and optimize the application of these natural products in honeybee management practices.

Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera)

Flumethrin mitigates Varroa’s harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.

Colonies under dysbiosis benefit from oxalic acid application: the role of landscape and beekeeping practices in microbiota response to treatment

AbstractThe Varroa destructor mite causes severe losses of Apis mellifera colonies, requiring recurring treatments. One such treatment is oxalic acid (OA), considered ecological. However, it is unclear whether OA affects the honey bee gut microbiota or other hive-associated microbiotas. Herein, we studied the effect of three OA treatments (trickling at 2.1% or 4.2%, and sublimation through Varrox®) upon microbial communities associated with workers’ gut, hive bee bread and pupae, sampled from conventionally or ecologically managed colonies under different anthropization levels (located in urban, rural or mountainous landscapes). We hypothesized that treatment with OA would impact the diversity and composition of bacteria and/or eukaryotic communities, and that the effect would be dose-dependent and specific to the beehive niche. Results showed that the microbiomes of apiaries under different anthropization levels and management strategies differed prior to OA application. Neither the bacterial nor the fungal communities of bee bread and pupae shifted due to OA treatment. Independent of the dosage and the application method (trickling or sublimation), OA induced slight compositional changes in the bacterial profiles of honeybee guts. Those changes were stronger the higher the anthropization (in colonies from urban areas under conventional management). OA treatment reduced the relative abundance of several pathogens, such as Nosema ceranae, and decreased the overall bacterial diversity down to values found in less anthropized colonies. Thus, our results suggest that, aside from managing Varroa infestations, OA could have beneficial effects for stressed colonies while not impairing honey bee resilience from a microbial point of view.

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome

Managed colonies of the European honey bee, Apis mellifera, have faced considerable losses in recent years. A widespread contributing factor is a microsporidian pathogen, Nosema ceranae, which occurs worldwide, is increasingly resistant to antibiotic treatment, and can alter the host’s immune response and nutritional uptake. These obligate gut pathogens share their environment with a natural honey bee microbiome whose composition can affect pathogen resistance. We tested the effect of N. ceranae infection on this microbiome by feeding 5 day-old adult bees that had natural, fully developed microbiomes with live N. ceranae spores (40,000 per bee) or a sham inoculation, sterile 2.0 M sucrose solution. We caged and reared these bees in a controlled lab environment and tracked their mortality over 12 d, after which we dissected them, measured their infection levels (gut spore counts), and analyzed their microbiomes. Bees fed live spores had two-fold higher mortality by 12 d and 36.5-fold more spores per bee than controls. There were also strong colony effects on infection levels, and 9% of spore-inoculated bees had no spore counts at all (defined as fed-spores-but-not-infected). Nosema ceranae infection had significant but subtle effects on the gut microbiomes of experimentally infected bees, bees with different infection levels, and fed-spores-but-not-infected vs. bees with gut spores. Specific bacteria, including Gilliamella ASVs, were positively associated with infection, indicating that multiple strains of core gut microbes either facilitate or resist N. ceranae infection. Future studies on the interactions between bacterial, pathogen, and host genotypes would be illuminating.

Honeybee gut bacterial strain improved survival and gut microbiota homeostasis in Apis mellifera exposed in vivo to clothianidin.

The present work suggests that administration of bacterial strains isolated from honeybee gut may promote recovery of gut microbiota homeostasis after prolonged clothianidin exposure, while improving survival. This study highlights that gut bacterial strains hold promise for developing efficient microbial formulations to mitigate environmental pesticide exposure in honeybee colonies.

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria

The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.

Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria.

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

Tetracycline-induced gut community dysbiosis and Israeli Acute Paralysis Virus infection synergistically negatively affect honeybees

Antibiotics are frequently employed to control bacterial diseases in honeybees, but their broad-spectrum action can disrupt the delicate balance of the gut microbiome, leading to dysbiosis. This imbalance in the gut microbiota of honeybees adversely affects their physiological health and weakens their resistance to pathogens, including viruses that significantly threaten honeybee health. In this study, we investigated whether tetracycline-induced gut microbiome dysbiosis promotes the replication of Israeli acute paralysis virus (IAPV), a key virus associated with colony losses and whether IAPV infection exacerbates gut microbiome dysbiosis. Our results demonstrated that tetracycline-induced gut microbiome dysbiosis increases the susceptibility of honeybees to IAPV infection. The viral titer in worker bees with antibiotic-induced gut microbiome dysbiosis prior to IAPV inoculation was significantly higher than in those merely inoculated with IAPV. Furthermore, we observed a synergistic effect between tetracycline and IAPV on the disruption of the honeybee gut microbiome balance. The progression of IAPV replication could, in turn, exacerbate antibiotic-induced gut microbiome dysbiosis in honeybees. Our research provides novel insights into the role of the gut microbiota in host-virus interactions, emphasizing the complex interplay between antibiotic use, gut microbiome health, and viral susceptibility in honeybees. We highlight the crucial role of a balanced gut microbiota in honey bees for their immune response against pathogens and emphasize the importance of careful, safe antibiotic use in beekeeping to protect these beneficial microbes.

Improving bee feed recipes to safeguard honeybee colonies during times of food scarcity.

In beekeeping, when natural nectar or pollen sources become limited, it is crucial to provide supplemental bee feed to maintain the viability of the bee colony. This study was conducted during the autumn food shortage season, during which bees were fed with different proportions of modified bee feed. We identified an optimal bee diet by evaluating honeybee longevity, food consumption, body weight, and gut microbe distribution, with natural pollen serving as a control diet. The results indicated that bees preferred a mixture of 65% defatted soy flour, 20% corn protein powder, 13% wheat germ flour, 2% yeast powder, and a 50% sucrose solution. This bee food recipe significantly increased the longevity, feed consumption, and body weight of bees. The group fed the natural pollen diet exhibited a greater abundance of essential intestinal bacteria. The bee diets used in this study contained higher protein levels and lower concentrations of unsaturated fatty acids and vitamins than did the diets stored within the colonies. Therefore, we propose that incorporating both bee feed and natural pollen in beekeeping practices will achieve more balanced nutritional intake.

Isolation and Antimicrobial Susceptibility of Some Bacteria From The Gut of Honey Bees in Siirt Province of Türkiye

Bu çalışmada, Siirt ili ve yöresinde bulunan bal arılarının bağırsak içeriklerinden bazı aerobik bakterilerin varlığı araştırıldı. Bakteriyel etkenler konvansiyonel bakteriyolojik yöntemlerle izole edildi ve ticari identifikasyon test kiti ile identifiye edildi. İzolatların antimikrobiyal duyarlılığı disk difüzyon testi ile belirlendi. Çalışmada en yüksek oranda izole edilen etkenlerin Staphylococcus spp. ve Klebsiella spp. olduğu ve bunu sırasıyla Bacillus spp. Izolatlarının izlediği belirlendi. GSBL ve plasmidik AmpC direnci 12 adet Gram negatif etkenin 6 (%50)’sında tespit edildi. Ayrıca Enterobacteriaceae izolatlarında imipenem direncinin yüksek olduğu belirlendi. Buna karşın Staphylococcus spp. izolatlarının çalışmada kullanılan antimikrobiyal maddelerin çoğuna duyarlı olduğu görüldü. Çalışmadan elde edilen verilerin bal arıları ile ilgili yapılan çalışmalara katkı sağlayacağı düşünüldü.

GEM-based computational modeling for exploring metabolic interactions in a microbial community.

Microbial communities play fundamental roles in every complex ecosystem, such as soil, sea and the human body. The stability and diversity of the microbial community depend precisely on the composition of the microbiota. Any change in the composition of these communities affects microbial functions. An important goal of studying the interactions between species is to understand the behavior of microbes and their responses to perturbations. These interactions among species are mediated by the exchange of metabolites within microbial communities. We developed a computational model for the microbial community that has a separate compartment for exchanging metabolites. This model can predict possible metabolites that cause competition, commensalism, and mutual interactions between species within a microbial community. Our constraint-based community metabolic modeling approach provides insights to elucidate the pattern of metabolic interactions for each common metabolite between two microbes. To validate our approach, we used a toy model and a syntrophic co-culture of Desulfovibrio vulgaris and Methanococcus maripaludis, as well as another in co-culture between Geobacter sulfurreducens and Rhodoferax ferrireducens. For a more general evaluation, we applied our algorithm to the honeybee gut microbiome, composed of seven species, and the epiphyte strain Pantoea eucalypti 299R. The epiphyte strain Pe299R has been previously studied and cultured with six different phyllosphere bacteria. Our algorithm successfully predicts metabolites, which imply mutualistic, competitive, or commensal interactions. In contrast to OptCom, MRO, and MICOM algorithms, our COMMA algorithm shows that the potential for competitive interactions between an epiphytic species and Pe299R is not significant. These results are consistent with the experimental measurements of population density and reproductive success of the Pe299R strain.

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

BackgroundThe gut microbiota and their hosts profoundly affect each other’s physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria.ResultsWe established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host.ConclusionsUsing the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions.ArN8Xjm3N6Dubzus4DCSQmVideo

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA)

For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome’s role in winter survival is warranted.

Vairimorpha (Nosema) ceranae can promote Serratia development in honeybee gut: an underrated threat for bees?

The genus Serratia harbors opportunistic pathogenic species, among which Serratia marcescens is pathogenic for honeybees although little studied. Recently, virulent strains of S. marcescens colonizing the Varroa destructor mite's mouth were found vectored into the honeybee body, leading to septicemia and death. Serratia also occurs as an opportunistic pathogen in the honeybee's gut with a low absolute abundance. The Serratia population seems controlled by the host immune system, but its presence may represent a hidden threat, ready to arise when honeybees are weakened by biotic and abiotic stressors. To shed light on the Serratia pathogen, this research aims at studying Serratia's development dynamics in the honeybee body and its interactions with the co-occurring fungal pathogen Vairimorpha ceranae. Firstly, the degree of pathogenicity and the ability to permeate the gut epithelial barrier of three Serratia strains, isolated from honeybees and belonging to different species (S. marcescens, Serratia liquefaciens, and Serratia nematodiphila), were assessed by artificial inoculation of newborn honeybees with different Serratia doses (104, 106, and 108 cells/mL). The absolute abundance of Serratia in the gut and in the hemocoel was assessed in qPCR with primers targeting the luxS gene. Moreover, the absolute abundance of Serratia was assessed in the gut of honeybees infected with V. ceranae at different development stages and supplied with beneficial microorganisms and fumagillin. Our results showed that all tested Serratia strains could pass through the gut epithelial barrier and proliferate in the hemocoel, with S. marcescens being the most pathogenic. Moreover, under cage conditions, Serratia better proliferates when a V. ceranae infection is co-occurring, with a positive and significant correlation. Finally, fumagillin and some of the tested beneficial microorganisms could control both Serratia and Vairimorpha development. Our findings suggest a correlation between the two pathogens under laboratory conditions, a co-occurring infection that should be taken into consideration by researches when testing antimicrobial compounds active against V. ceranae, and the related honeybees survival rate. Moreover, our findings suggest a positive control of Serratia by the environmental microorganism Apilactobacillus kunkeei in a in vivo model, confirming the potential of this specie as beneficial bacteria for honeybees.

Antibiotic exposure alters the honeybee gut microbiota and may interfere with the honeybee behavioral caste transition.

Behavioral division is essential for the sustainability and reproduction of honeybee populations. While accumulating evidence has documented that antibiotic exposure interferes with bee behavioral divisions, how the gut microbiome, host physiology, and genetic regulation are implicated in this process remains understudied. Here, by constructing single-cohort colonies, we validated that the gut microbiota varied in composition between age-matched nurse and forager bees. Perturbing the gut microbiota with a low dose of antibiotic retained the gut bacterial size, but the structure of the microbial community continuously diverged from the control group after antibiotic treatment. Fewer foragers were observed in the antibiotic groups in the field experiment. A combinatorial effect of decreased gut metabolic gene repertoires, reduced brain neurotransmitter titers, and downregulated brain immune genes could potentially be related to behavioral tasks transition delay. This work indicates that the disturbance to both the gut microbiome and host physiologies after antibiotic exposure may have implications on social behavior development, highlighting the need for further research focusing on antibiotic pollution threatening the honeybee population's health.

Bifidobacterium apis sp. nov., isolated from the gut of honeybee (Apis mellifera).

A novel bifidobacterium (designated F753-1T) was isolated from the gut of honeybee (Apis mellifera). Strain F753-1T was characterized using a polyphasic taxonomic approach. Strain F753-1T was phylogenetically related to the type strains of Bifidobacterium mizhiensis, Bifidobacterium asteroides, Bifidobacterium choladohabitans, Bifidobacterium mellis, Bifidobacterium apousia and Bifidobacterium polysaccharolyticum, having 98.4-99.8 % 16S rRNA gene sequence similarities. The phylogenomic tree indicated that strain F753-1T was most closely related to the type strains of B. mellis and B. choladohabitans. Strain F753-1T had the highest average nucleotide identity (94.1-94.5 %) and digital DNA-DNA hybridization (56.3 %) values with B. mellis Bin7NT. Acid production from amygdalin, d-fructose, gentiobiose, d-mannose, maltose, sucrose and d-xylose, activity of α-galactosidase, pyruvate utilization and hydrolysis of hippurate could differentiate strain F753-1T from B. mellis CCUG 66113T and B. choladohabitans JCM 34586T. Based upon the data obtained in the present study, a novel species, Bifidobacterium apis sp. nov., is proposed, and the type strain is F753-1T (=CCTCC AB 2023227T=JCM 36562T=LMG 33388T).