Amplicon-based gut microbial profiling and their predicted functional potential in Apis dorsata across two ecological regions of Pakistan
-
Iram Asad
,
Mubashar Hussain
,
Sheeza Sakhawat
,
Arooj Fatima
,
Aqsa Noreen
,
Aniza Iftikhar
,
Suleman Hussain Shah
,
Saira Bashir
,
Samia Arif
,
Iqra Rafiq
,
Haseeb Raza
,
Yasal Cheema
,
Iqra Nawaz
,
Muhammad Sikander
Abstract
Background and Objectives: Apis dorsata (A. dorsata), the giant honeybee, is an important pollinator of Asia. Gut-microbial assemblages contribute to nutrient utilization and metabolism, yet their diversity in the gut of A. dorsata remains underexplored. The main objective of the current study was to explore the impact of local geographical conditions on the gut microbial diversity and the functional potential of A. dorsata gut-associated bacteria.
Materials and Methods: Bacterial community profiling and characterization were performed using high-throughput sequencing on the DNA Nanoball Sequencing (DNBseq) platform.
Results: Fifty-four bacterial species were detected from the gut of A. dorsata, expanding the known microbial diversity of this host species. The comprehensive analysis of pooled samples from two regions revealed that higher microbial diversity in district Bhimber than in Jhelum. Nevertheless, site-specific putative differences were observed in the pathways related to carbohydrate metabolism, amino acid synthesis, and other cellular activities.
Conclusion: This exploratory pilot investigation revealed site-wise preliminary differences in taxonomy and putative metabolic functions of bacterial species. These results provide a baseline for future studies on the diversity and dynamics of functioning of gut-associated microbial communities of A. dorsata.
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25. Su Q, Tang M, Hu J, Tang J, Zhang X, Li X, et al. Significant compositional and functional variation reveals the patterns of gut microbiota evolution among the widespread Asian honeybee populations. Front Microbiol 2022; 13: 934459.
26. Liao HY, Ren YS, Li J, Huang HT, Li ZL, Zeng Y, et al. Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors. Front Microbiol 2026; 17: 1752887.
27. Khan KA, Ansari MJ, Al-Ghamdi A, Nuru A, Harakeh S, Iqbal J. Investigation of gut microbial communities associated with indigenous honey bee (Apis mellifera jemenitica) from two different eco-regions of Saudi Arabia. Saudi J Biol Sci 2017; 24: 1061-1068.
28. Zheng H, Perreau J, Powell JE, Han B, Zhang Z, Kwong WK, et al. Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 2019; 116: 25909-25916.
29. Prasad A, Pallujam AD, Siddaganga R, Suryanarayanan A, Mazel F, Brockmann A, et al. Evolution of gut microbiota across honeybee species revealed by comparative metagenomics. Nat Commun 2025; 16: 9069.
30. Segers FH, Kešnerová L, Kosoy M, Engel P. Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. ISME J 2017; 11: 1232-1244.
31. Engel P, Martinson VG, Moran NA. Functional diversity within the simple gut microbiota of the honey bee. Proc Natl Acad Sci U S A 2012; 109: 11002-11007.
32. Powell JE, Leonard SP, Kwong WK, Engel P, Moran NA. Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont. Proc Natl Acad Sci 2016; 113: 13887-13892.
33. Kwong WK, Moran NA. Gut microbial communities of social bees. Nat Rev Microbiol 2016; 14: 374-384.
34. Budge GE, Adams I, Thwaites R, Pietravalle S, Drew GC, Hurst GD, et al. Identifying bacterial predictors of honey bee health. J Invertebr Pathol 2016; 141: 41-44.
35. Yin Y, Wang S, Li Y, Yao D, Zhang K, Kong X, et al. Antagonistic effect of the beneficial bacterium Enterobacter hormaechei against the heavy metal Cu2+ in housefly larvae. Ecotoxicol Environ Saf 2024; 272: 116077.
36. Ying JP, Zou YF, Jiang T, Chang JL. Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes. PloS One 2026; 21(1): e339926.
2. Ali H, Iqbal J, Raweh HS, Alqarni AS. Proboscis behavioral response of four honey bee Apis species towards different concentrations of sucrose, glucose, and fructose. Saudi J Biol Sci 2021; 28: 3275-3283.
3. Otis GW, Huang MJ, Kitnya N, Sheikh UAA, Faiz AuH, Phung CH, et al. The distribution of Apis laboriosa revisited: Range extensions, biogeographic affinities, and species distribution modelling. Front Bee Sci 2024; 2: 1374852.
4. Cao L, Dai Z, Tan H, Zheng H, Wang Y, Chen J, et al. Population structure, demographic history, and adaptation of giant honeybees in China revealed by population genomic data. Genome Biol Evol 2023; 15(3): evad025.
5. Soares KO, Da Rocha TF, Hale VL, Vasconcelos PC, do Nascimento LJ, da Silva NMV, et al. Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes. Sci Rep 2025; 15: 5293.
6. Xu K, Niu Q, Zhao H, Du Y, Jiang Y. Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana). PLoS One 2017; 12(8): e0184468.
7. Horak RD, Leonard SP, Moran NA. Symbionts shape host innate immunity in honeybees. Proc Biol Sci 2020; 287: 20201184.
8. Tang J, Zuo W, Guo L, Han Z, Yang C, Han B, et al. Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 2024; 15: 6937.
9. Ge Y, Jing Z, Diao Q, He JZ, Liu YJ. Host species and geography differentiate honeybee gut bacterial communities by changing the relative contribution of community assembly processes. mBio 2021; 12(3): e0075121.
10. Moharrami M, Mojgani N, Bagheri M, Toutiaee S. Role of honey bee gut microbiota in the control of American foulbrood and European foulbrood diseases. Arch Razi Inst 2022; 77: 1331-1339.
11. Nguyen PN, Rehan SM. The effects of urban land use gradients on wild bee microbiomes. Front Microbiol 2022; 13: 992660.
12. Shafique M, Ali W, Bukhari SM, Mehmood S. Comparative analysis of gut microbiota in Bombyx mori fed on M. alba and M. nigra using 16S rRNA amplicon sequencing. Open Vet J 2026; 16: 275-286.
13. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15(3): R46.
14. Hussain M, Ali W, Meyer C, Javid A, Imran M. Characterization and metagenomics analysis of the oral microbiome of Pteropus medius: Insights from next-generation sequencing. Regul Mech Biosyst 2025; 16(1): e25016.
15. Bukhari SM, Andleeb S, Alghamdi HA, Rehman Ku, Javid A, Ali W, et al. Exploration of gut microbial diversity of pheasants through pyrosequencing of 16S rRNA gene. J Exp Zool A Ecol Integr Physiol 2024; 341: 950-959.
16. Evans EC, Spivak M. Effects of honey bee (Hymenoptera: Apidae) and bumble bee (Hymenoptera: Apidae) presence on cranberry (Ericales: Ericaceae) pollination. J Econ Entomol 2006; 99: 614-620.
17. Kešnerová L, Moritz R, Engel P. Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria. Int J Syst Evol Microbiol 2016; 66: 414-421.
18. Emery O, Schmidt K, Engel P. Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera). Mol Ecol 2017; 26: 2576-2590.
19. Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: update on taxonomy, clinical aspects, and emerging antimicrobial resistance. Clin Microbiol Rev 2019; 32(4): e00002-19.
20. Joseph S, Sonbol H, Hariri S, Desai P, McClelland M, Forsythe SJ. Diversity of the Cronobacter genus as revealed by multilocus sequence typing. J Clin Microbiol 2012; 50: 3031-3039.
21. Ganeshprasad D, Lone JK, Jani K, Shouche YS, Khan KA, Sayed S, et al. Gut bacterial flora of open-nested honeybee, Apis florea. Front Ecol Evol 2022; 10: 837381.
22. Lazarova S, Lozanova L, Neov B, Shumkova R, Balkanska R, Palova N, et al. Composition and diversity of bacterial communities associated with honey bee foragers from two contrasting environments. Bull Entomol Res 2023; 113: 693-702.
23. Kešnerová L, Mars RAT, Ellegaard KM, Troilo M, Sauer U, Engel P. Disentangling metabolic functions of bacteria in the honey bee gut. PLoS Biol 2017; 15(12): e2003467.
24. Tola YH, Waweru JW, Hurst GD, Slippers B, Paredes JC. Characterization of the Kenyan honey bee (Apis mellifera) gut microbiota: A first look at tropical and Sub-Saharan African bee associated microbiomes. Microorganisms 2020; 8: 1721.
25. Su Q, Tang M, Hu J, Tang J, Zhang X, Li X, et al. Significant compositional and functional variation reveals the patterns of gut microbiota evolution among the widespread Asian honeybee populations. Front Microbiol 2022; 13: 934459.
26. Liao HY, Ren YS, Li J, Huang HT, Li ZL, Zeng Y, et al. Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors. Front Microbiol 2026; 17: 1752887.
27. Khan KA, Ansari MJ, Al-Ghamdi A, Nuru A, Harakeh S, Iqbal J. Investigation of gut microbial communities associated with indigenous honey bee (Apis mellifera jemenitica) from two different eco-regions of Saudi Arabia. Saudi J Biol Sci 2017; 24: 1061-1068.
28. Zheng H, Perreau J, Powell JE, Han B, Zhang Z, Kwong WK, et al. Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 2019; 116: 25909-25916.
29. Prasad A, Pallujam AD, Siddaganga R, Suryanarayanan A, Mazel F, Brockmann A, et al. Evolution of gut microbiota across honeybee species revealed by comparative metagenomics. Nat Commun 2025; 16: 9069.
30. Segers FH, Kešnerová L, Kosoy M, Engel P. Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. ISME J 2017; 11: 1232-1244.
31. Engel P, Martinson VG, Moran NA. Functional diversity within the simple gut microbiota of the honey bee. Proc Natl Acad Sci U S A 2012; 109: 11002-11007.
32. Powell JE, Leonard SP, Kwong WK, Engel P, Moran NA. Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont. Proc Natl Acad Sci 2016; 113: 13887-13892.
33. Kwong WK, Moran NA. Gut microbial communities of social bees. Nat Rev Microbiol 2016; 14: 374-384.
34. Budge GE, Adams I, Thwaites R, Pietravalle S, Drew GC, Hurst GD, et al. Identifying bacterial predictors of honey bee health. J Invertebr Pathol 2016; 141: 41-44.
35. Yin Y, Wang S, Li Y, Yao D, Zhang K, Kong X, et al. Antagonistic effect of the beneficial bacterium Enterobacter hormaechei against the heavy metal Cu2+ in housefly larvae. Ecotoxicol Environ Saf 2024; 272: 116077.
36. Ying JP, Zou YF, Jiang T, Chang JL. Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes. PloS One 2026; 21(1): e339926.
| Files | ||
| Issue | Vol 18 No 5 (2026) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v18i5.22869 | |
| Keywords | ||
| Apis dorsata 16S rRNA Next-generation sequencing Microbiota Predicted function annotation | ||
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How to Cite
1.
Asad I, Hussain M, Sakhawat S, Fatima A, Noreen A, Iftikhar A, Shah SH, Bashir S, Arif S, Rafiq I, Raza H, Cheema Y, Nawaz I, Sikander M. Amplicon-based gut microbial profiling and their predicted functional potential in Apis dorsata across two ecological regions of Pakistan. Iran J Microbiol. 2026;18(5):787-798.
