Metagenomic Analysis of Bacterial Communities in Bee Bread in Türkiye

Yıl 2024, Cilt: 11 Sayı: 4, 904 - 914, 12.10.2024

Esengül Erdem

https://doi.org/10.30910/turkjans.1455870

Öz

This study aims to investigate the bacterial community structure in bee bread samples collected from 10 provinces of Türkiye using next-generation sequencing (NGS) and metagenomic analysis. Bacterial genomic DNA was extracted and sequenced using Illumina MiSeq. Bioinformatic analysis involved quality assessment, OTU classification, principal coordinate analysis (PCoA), and diversity index calculations. Heatmap and PCoA were utilized to explore the impact of locality and ecological zones on microbial diversity. Metagenomic analysis of 12 bee bread samples revealed 276,583 high-quality sequencing reads. The dominant bacterial phyla identified were Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. At the genus level, Streptomyces, Streptococcus, Bacillus, and Synechococcus were the most abundant, with Streptomyces and Bacillus playing key roles in the fermentation process of bee bread. The Shannon diversity index (ranging from 2.92 to 4.26) and Simpson's index (0.83 to 0.95) indicated high species diversity and relative abundance in bee bread. The study underscores the need for locality-specific approaches in beekeeping management and highlights the potential significance of beneficial bacterial taxa, particularly those involved in fermentation, in contributing to the nutritional and health properties of bee bread. These findings provide a foundation for further research on the microbial dynamics that support bee colony health.

Anahtar Kelimeler

Bee bread, bacterial community structure, metagenomic analysis, microbial diversity, Türkiye

Türkiye'de Arı Ekmeğinde Bulunan Bakteriyel Toplulukların Metagenomik Analizi

Öz

Bu çalışma, Türkiye'nin 10 ilinden toplanan 12 adet arı ekmeği örneğindeki bakteriyel topluluk yapısını next-generation sequencing (NGS) ve metagenomik analiz kullanarak araştırmayı amaçlamaktadır. Bakteriyel genomik DNA, Illumina MiSeq kullanılarak ekstrakte edilmiş ve dizilenmiştir. Biyoinformatik analiz, kalite değerlendirmesi, OTU sınıflandırması, principal coordinate analysis (PCoA) ve çeşitlilik indeksi hesaplamalarını içermektedir. Isı haritası ve PCoA, lokasyon ve ekolojik bölgelerin mikrobiyal çeşitlilik üzerindeki etkisini belirlemek amacı ile kullanılmıştır. 12 arı ekmeği örneği analiz edilerek 276,583 yüksek kaliteli DNA dizilimi elde edilmiştir. En baskın bakteri şubeleri Proteobacteria, Actinobacteria, Cyanobacteria ve Firmicutes olarak belirlenmiştir. Streptomyces, Streptococcus, Bacillus ve Synechococcus en bol bulunan cinsler olarak belirlenmiştir. Streptomyces ve Bacillus, arı ekmeğinin fermantasyon sürecinde kilit rol oynamaktadır. Shannon çeşitlilik indeksi (2.92 ile 4.26 arasında değişmekte) ve Simpson indeksi (0.83 ile 0.95 arasında değişmekte) arı ekmeğinde yüksek tür çeşitliliği ve göreceli bolluğu göstermiştir. Çalışma, arıcılıkta lokasyona özgü yaklaşımların gerekliliğini vurgulamakta ve özellikle fermantasyon sürecine katılan faydalı bakteriyel taksonların arı ekmeğinin besin ve sağlık özelliklerine katkıda bulunmadaki potansiyel önemine dikkat çekmektedir. Bu bulgular, koloni sağlığını destekleyen mikrobiyal dinamikler üzerine gelecekte yapılacak araştırmalar için bir temel sağlamaktadır.

Anahtar Kelimeler

Arı ekmeği, bakteri topluluk yapısı, metagenomik analiz mikrobiyal çeşitlilik, Türkiye

Kaynakça

• Abou-Shaara, H.F., A.A. Owayss, Y.Y. Ibrahim & N.K. Basuny, 2017. A review of impacts of temperature and relative humidity on various activities of honey bees. Insects Soc., (64):455–463.
• Anderson, K.E., M.J. Carroll, T. Sheehan, B.M. Mott & P. Maes, 2014. Corby-Harris, V. Hive-stored pollen of honey bees: Many lines of evidence are consistent with pollen preservation, not nutrient conversion. Mol. Ecol., (23): 5904–5917.
• Anderson, K.E., T.H. Sheehan, B.M. Mott, P. Maes, L. Snyder, M.R. Schwan, A. Walton, B.M. Jones & Corby- V. Harris, 2013. Microbial ecology of the hive and pollination landscape: Bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera). PLoS ONE 8: e83125.
• Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data.
• Arserim Uçar, D.K., M.N.Z. Yurt, B.B. Taşbaşı, E.E. Acar, Z. Yeğin, V.C. Özalp & M. Sudağıdan, 2022. Identification of Bacterial Diversity of Bee Collected Pollen and Bee Bread Microbiota by Metagenomic Analysis. Acta Veterinaria Eurasia, 48(3).
• Asama, T., T.H. Arima, T. Gomi, T. Keishi, H. Tani & Y. Kimura. 2015. Lactobacillus kunkeei YB38 from honeybee products enhances IgA production in healthy adults. Journal of Applied Microbiol.,119 (3): 818.
• Bolger, A.M., M. Lohse & B. Usadel, 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114-2120.
• Crone, M. K., D.J. Biddinger & C.M. Grozinger, 2022. Wild bee nutritional ecology: Integrative strategies to assess foraging preferences and nutritional requirements. Frontiers in Sustainable Food Systems, 6: 847003.
• Danner, N., A. Keller, S. Härtel & I. Steffan-Dewenter, 2017. Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. PloS one, 12(8): e0183716.
• Davis, P.H. (ed), 1965-1985. Flora of Türkiye and the East Aegean Islands. Vols. 1-9. Edinburgh: Edinburgh University Press.
• Davis, P.H., R.R. Mill & K. Tan (eds). 1988. Flora of Türkiye and the East Aegean Islands (supplement). Vol. 10. Edinburgh: Edinburgh University Press.
• De Palma, A., S. Abrahamczyk, M.A. Aizen, M. Albrecht, Y. Basset, A. Bates… & A. Purvis, 2016. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases. Scientific Reports, 6(1): 31153.
• Disayathanoowat, T., H. Li, N. Supapimon, N. Suwannarach, S. Lumyong, P. Chantawannakul & J. Guo, 2020. Different dynamics of bacterial and fungal communities in hive-stored bee bread and their possible roles: a case study from two commercial honey bees in China. Microorganisms, 8(2): 264.
• Donkersley, P., G. Rhodes, R.W. Pickup, K.C. & K. Jones, 2018. Wilson, Bacterial communities associated with honeybee food stores are correlated with land use. Ecol. Evol., 8: 4743–4756.
• Erlacher, A., T. Cernava, M. Cardinale, J. Soh, C.W. Sensen, M. Grube & G. Berg, 2015. Rhizobiales as functional and endosymbiotic member in the lichen symbiosis of Lobaria pulmonaria L. Front. Microbiol., 6: 53.
• Anonymous, 2022. Food and Agriculture Organization of the United Nations, https://www.fao.org/faostat/en/ (Accession date: 06/08/2028)
• Garrity, G.M., J.A. Bell, T. Lilburn & I. Class, 2005. Alphaproteobacteria class. nov. In Bergey’s Manual of Systematic Bacteriology; Garrity, G.M., Brenner, D.J., Krieg, N.R., Staley, J.T., Eds.; Springer: New York, NY, USA, Volume 2.
• Ghosh, S. & C. Jung, 2022. Temporal changes of nutrient composition from pollen patty to bee bread with special emphasis on amino and fatty acids composition. Journal of Asia-Pacific Entomology, 25(1): 101873.
• Ghosh, S., S.M. Namin & C. Jung, 2021. Metagenomics of pollen-borne microbes and gut microbiota of the honey bee. In Metagenomics and Microbial Ecology; (Eds. De Mandal, S., A.K. Panda, N.S. Kumar, S.S. Bisht, F. Jin), CRC Press: New York, NY, USA.
• Güner, A., N. Özhatay, T. Ekim & K.H.C. Bafler, 2000. Flora of Türkiye and the East Aegean Islands. Vol. 11. Edinburgh: Edinburgh University Press, 656 pp.
• Güner, A., S. Aslan, T. Ekim M. Vural & M.T. Babaç, 2012. Türkiye Bitkileri Listesi (Damarlı Bitkiler) [List of Türkiye Plants]. Nezahat Gökyiğit Botanic Garden and Flora Research Society Publishing, Istanbul, 610 pp.
• Jones, J.C., C.Fruciano, J. Marchant, F.Hildebrand, S. Forslund, P. Bork, P. Engel & W.O.H. Hughes, 2018. The gut microbiome is associated with behavioural task in honey bees. Insectes sociaux, 65: 419-429.
• Kieliszek, M., K. Piwowarek, A.M. Kot, S. Błażejak, A. Chlebowska-Śmigiel & I. Wolska, 2018. Pollen and bee bread as new health-oriented products: A review. Trends in Food Science & Technology, 71: 170-180.
• Kleinhenz, M., B. Bujok, S. Fuchs & J. Tautz, 2003. Hot bees in empty broodnest cells: Heating from within. J. Exp. Biol., 205: 4217–4231.
• Kösoğlu, M., E. Topal, N. Özsoy, Ü. Karaca, Ç. Takma & A. Özkırım, 2019. Perspective of Izmir Province Beekeepers on Bee Diseases and Pests. Ege Univ. Ziraat Fak. Derg., 56 (2):187-193.
• Kwong, W.K. & N.A. Moran, 2016. Gut microbial communities of social bees. Nature reviews microbiology,14(6): 374-384.
• Lozo, J., T. Beric, A. Terzic -Vidojevic, S. Stankovic , D. Fira & L. Stanisavljevic, 2015. Microbiota associated with pollen, bee bread, larvae and adults of solitary bee Osmia cornuta (Hymenoptera: Megachilidae). Bull. Entomol. Res., 105: 470–476.
• Martinson, V.G., J. Moy, & N.A. Moran, 2012. Establishment of characteristic gut bacteria during development of the honeybee worker. Applied and environmental microbiology, 78(8): 2830-2840.
• Moran, N.A. 2015. Genomics of the honey bee microbiome. Current opinion in insect science, 10: 22-28.
• Muñoz-Colmenero, M., I. Baroja-Careaga, M. Kovacic, J. Filipi, Z. Puškadija, N. Kezic, A. Estonaba, R. Büchler & I. Zarraonaindia, 2020. Differences in honey bee bacterial diversity and composition in agricultural and pristine environments. Apidologie, 51:1018–1037.
• Pang, S., Z. Lin, W. Zhang, S. Mishra, P. Bhatt & S. Chen, 2020. Insights into the microbial degradation and biochemical mechanisms of neonicotinoids. Front. Microbiol., 11: 868.
• Papp M, L. Békési, R. Farkas, L. Makrai, M.F. Judge, G.Maróti, et al., 2022. Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states. PLoS ONE, 17(9): e0273844.
• Saraiva, M.A., A.P.P. Zemolin, J.L. Franco, J.T. Boldo, V.M. Stefenon, E W. Triplett,... & L.F.W. Roesch, 2015. Relationship between honeybee nutrition and their microbial communities. Antonie Van Leeuwenhoek, 107: 921-933.
• Stabler, D., P. P. Paoli, S. W. Nicolson & G. A. Wright, 2015. Nutrient balancing of the adult worker bumblebee (Bombus terrestris) depends on the dietary source of essential amino acids. J. Exp. Biol., 218: 793–802.
• Vásquez, A. & T.C. Olofsson, 2009. The lactic acid bacteria involved in the production of bee pollen and bee bread. Journal of apicultural research, 48(3): 189-195.
• Vaudo, A.D., J.F. Tooker, H.M. Patch, D. J. Biddinger, M. Coccia, M.K. Crone, M. Fiely et al., 2020. Pollen protein: lipid macronutrient ratios may guide broad patterns of bee species floral preferences. Insects, 11(2): 132.
• Wood, D.E. & S.L. Salzberg, 2014. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biology, 15: R46.
• Yun, J.H., M.J. Jung, P.S. Kim & J.W. Bae, 2018. "Social status shapes the bacterial and fungal gut communities of the honey bee. Scientific reports, 8(1): 2019.