Gut microbiota analysis of healthy and sacbrood virus-infected <em> Apis mellifera </em> reveals potential probiotic bacteria for honeybee health and disease resistance

Dong Van Quyen; Bui Thi Thuy Duong; Pham Thi Lanh; Ha Thi Thu

doi:10.15625/2615-9023/22384

Author affiliations

Authors

Dong Van Quyen Institute of Biology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam
Bui Thi Thuy Duong Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam
Pham Thi Lanh Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam
Ha Thi Thu Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam

DOI:

https://doi.org/10.15625/2615-9023/22384

Keywords:

Apis mellifera, gut microbiota, honeybees, metagenomics, Next-generation sequencing, Sacbrood virus

Abstract

This study aimed to determine the gut microbiota composition of adult Apis mellifera honeybees from bee farms in Bac Giang province, including both healthy colonies and those infected with Sacbrood virus (SBV). The gut microbiota of healthy and SBV-infected bees was assessed using next-generation sequencing (NGS) of the V3-V4 region in the 16S rRNA gene on the Illumina MiSeq system. As a result, NGS analysis identified 1,659 operational taxonomic units (OTUs) with a coverage of 99% and an average read length of 430 bp. The results revealed that SBV-infected bees harbored four microbial phyla: Proteobacteria (48.44%), Firmicutes (38.65%), Actinobacteria (1.57%), and Bacteria_uc (10.95%). In contrast, the healthy bee group consisted of three phyla: Proteobacteria (40.61%), Firmicutes (45.55%), and Bacteria_uc (13.37%). The species composition analysis showed that both healthy and SBV-infected bees shared common core bacterial species. However, Bifidobacterium_uc and Commensalibacter AY370188_s were more prevalent in SBV-infected bees and significantly reduced in healthy bees. Conversely, Fructobacillus fructosus and Lactobacillus kunkeei were found exclusively in healthy bees. These lactic acid bacteria (LAB) have been shown to inhibit the growth of pathogenic bacteria. Our findings provide a valuable scientific foundation for developing biological products to improve honeybee health and disease resistance.

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References

Bolger A. M., Lohse M. & Usadel B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114–2120.

Botero J., Sombolestani A. S., Cnockaert M., Peeters C., Borremans W., De Vuyst L., Vandamme P., 2023. A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont. Animal Microbiome, 5(1): 25.

Chao A., Chiu C. H., 2016. Species richness: estimation and comparison. Wiley StatsRef: statistics reference online, 1: 26.

Chen Y. P. & Siede R., 2007. Honey bee viruses. Advances in virus research, 70: 33−80.

Daisley B. A., Chmiel J. A., Pitek A. P., Thompson G. J., Reid G., 2020. Missing microbes in bees: how systematic depletion of key symbionts erodes immunity. Trends in Microbiology, 28: 1010−1021.

Dosch C., Manigk A., Streicher T., Tehel A., Paxton R. J., Tragust S., 2021. The gut microbiota can provide viral tolerance in the honey bee. Microorganisms, 9(4): 871.

Eddy S. R., 2011. Accelerated profile HMM searches. PLoS computational biology, 7(10), e1002195.

Edgar R. C., Haas B. J., Clemente J. C., Quince C., Knight R., 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16): 2194−2200.

Edgar R. C., 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19): 2460−2461.

Engel P., Kwong W. K., McFrederick Q., Anderson K. E., Barribeau S. M., Chandler J. A., Cornman R. S., Dainat J., De Miranda J. R., & Doublet V., 2016. The bee microbiome: impact on bee health and model for evolution and ecology of host–microbe interactions. MBio, 7(2): 10–1128.

Evans J. D., Lopez D. L., 2004. Bacterial probiotics induce an immune response in the honey bee (Hymenoptera: Apidae). Journal of economic entomology, 97(3): 752−756.

Fu L., Niu B., Zhu Z., Wu S., Li W., 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28(23): 3150−3152.

Hubert J., Bicianova M., Ledvinka O., Kamler M., Lester P. J., Nesvorna M., Erban T., 2017. Changes in the bacteriome of honey bees associated with the parasite Varroa destructor, and pathogens Nosema and Lotmaria passim. Microbial ecology, 73: 685−698.

Iorizzo M., Letizia F., Ganassi S., Testa B., Petrarca S., Albanese G., De Cristofaro A., 2022. Functional properties and antimicrobial activity from lactic acid bacteria as resources to improve the health and welfare of honey bees. Insects, 13(3): 308.

Kešnerová L., Mars R. A., Ellegaard K. M., Troilo M., Sauer U., Engel P., 2017. Disentangling metabolic functions of bacteria in the honey bee gut. PLoS biology, 15(12): e2003467.

Killer J., Dubná S., Sedláček I., Švec P., 2014. Lactobacillus apis sp. nov., from the stomach of honeybees (Apis mellifera), having an in vitro inhibitory effect on the causative agents of American and European foulbrood. International journal of systematic and evolutionary microbiology, 64(Pt_1): 152−157.

Kwong W. K., Medina L. A., Koch H., Sing K. W., Soh E. J. Y., Ascher J. S., Moran N. A., 2017. Dynamic microbiome evolution in social bees. Science advances, 3(3): e1600513.

Kwong W. K., Moran N. A., 2016. Gut microbial communities of social bees. Nature reviews microbiology, 14(6): 374−384.

Lanh P. T., Duong B. T., Thu H. T., Hoa N. T., Van Quyen D., 2024. Comprehensive analysis of the microbiome in Apis cerana honey highlights honey as a potential source for the isolation of beneficial bacterial strains. PeerJ, 12: e17157.

Lee B., Moon T., Yoon S., Weissman T., 2017. DUDE-Seq: fast, flexible, and robust denoising for targeted amplicon sequencing. PloS one, 12(7): e0181463.

Liu W., Zhang R., Shu R., Yu J., Li H., Long H., Wu Q., 2020. Study of the relationship between microbiome and colorectal cancer susceptibility using 16SrRNA sequencing. BioMed research international, doi: 10.1155/2020/7828392

Maes P. W., Rodrigues P. A., Oliver R., Mott B. M., Anderson K. E., 2016. Diet‐related gut bacterial dysbiosis correlates with impaired development, increased mortality and Nosema disease in the honeybee (Apis mellifera). Molecular Ecology, 25(21): 5439−5450.

Masella A. P., Bartram A. K., Truszkowski J. M., Brown D. G., Neufeld J. D., 2012. PANDAseq: paired-end assembler for illumina sequences. BMC bioinformatics, 13: 1−7.

Myers E. W., Miller W., 1988. Optimal alignments in linear space. Bioinformatics, 4(1): 11−17.

Olofsson T. C., Butler È., Markowicz P., Lindholm C., Larsson L., Vásquez A., 2016. Lactic acid bacterial symbionts in honeybees–an unknown key to honey’s antimicrobial and therapeutic activities. International Wound Journal, 13(5): 668−679.

Qian X. B., Chen T., Xu Y. P., Chen L., Sun F. X., Lu M. P., Liu Y. X., 2020. A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. Chinese Medical Journal, 133(15): 1844−1855.

Royan M. (2019). Mechanisms of probiotic action in the honeybee. Critical Reviews™ in Eukaryotic Gene Expression, 29(2).

Shehata M. G., Masry S. H., Abd El-Aziz N. M., Ridouane F. L., Mirza S. B., El-Sohaimy S. A. 2024. Probiotic potential of lactic acid bacteria isolated from honeybees stomach: Functional and technological insights. Annals of Agricultural Sciences, 69(1): 11−18.

Tlak Gajger I., Nejedli S., Cvetnić L., 2023. Influence of probiotic feed supplement on Nosema spp. infection level and the gut microbiota of adult honeybees (Apis mellifera L.). Microorganisms, 11(3): 610.

Wei R., Cao L., Feng Y., Chen Y., Chen G., Zheng H., 2022. Sacbrood virus: a growing threat to honeybees and wild pollinators. Viruses, 14(9): 1871.

Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J., 1991. 16S ribosomal DNA amplification for phylogenetic study. Journal of bacteriology, 173(2): 697−703.

Yun B. R., Truong A. T., Choi Y. S., Lee M. Y., Kim B. Y., Seo M., Cho Y. S., 2022. Comparison of the gut microbiome of sacbrood virus-resistant and-susceptible Apis cerana from South Korea. Scientific Reports, 12(1): 10010.