Computational Molecular Biology 2025, Vol.15, No.6, 299-306 http://bioscipublisher.com/index.php/cmb 305 closely related to soil conditions, plant health, and the operation of ecosystems. The gene flow map outlined through computational tools also enables researchers to more easily understand the interaction patterns among different bacterial communities, thereby providing more practical basis for ecological models. When studying horizontal gene transfer in soil, computational analysis has almost become an unavoidable step. A process like MetaCHIP is to infer which genes might "come from elsewhere" by leveraging phylogenetic relationships and best-matching information without a reference genome. This method can not only capture recent gene exchanges but also reveal some earlier traces, thereby providing a clearer understanding of the role of HGT in resistance, metabolism and environmental adaptation. However, the reality is often not as smooth as the flowchart. Incomplete metagenomic assembly and overly similar strains often cause interference to the analysis, and this is basically inevitable in actual operation. Acknowledgments We thank the anonymous reviewers for their insightful comments and suggestions that greatly improved the manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Arnold B., Huang I., and Hanage W., 2021, Horizontal gene transfer and adaptive evolution in bacteria, Nature Reviews Microbiology, 20(4): 206-218. https://doi.org/10.1038/s41579-021-00650-4 Brito I., 2021, Examining horizontal gene transfer in microbial communities, Nature Reviews Microbiology, 19(7): 442-453. https://doi.org/10.1038/s41579-021-00534-7 Carpanzano S., Santorsola M., nf-core community, and Lescai F., 2022, hgtseq: a standard pipeline to study horizontal gene transfer, International Journal of Molecular Sciences, 23(23): 14512. https://doi.org/10.3390/ijms232314512 Coyte K., Stevenson C., Knight C., Harrison E., Hall J., and Brockhurst M., 2022a, Horizontal gene transfer and ecological interactions jointly control microbiome stability, PLOS Biology, 20(11): e3001847. https://doi.org/10.1371/journal.pbio.3001847 Coyte K., Stevenson C., Knight C., Harrison E., Hall J., and Brockhurst M., 2022b, Horizontal gene transfer increases microbiome stability, bioRxiv, 25: 481914. https://doi.org/10.1101/2022.02.25.481914 De Sousa J., Lourenço M., and Gordo I., 2023, Horizontal gene transfer among host-associated microbes, Cell Host & Microbe, 31(4): 513-527. https://doi.org/10.1016/j.chom.2023.03.017 Hong Y.D., and Huang H.Y., 2024, The role of soil microbiota in rice cultivation and its implications for agricultural sustainability, Molecular Soil Biology, 15(2): 87-98. https://doi.org/10.5376/msb.2024.15.0010 Islam M., Summers A., and Arpinar I., 2025, Knowledge graph-based framework for detecting horizontal gene transfer events driving antimicrobial resistance, bioRxiv, 9: 658534. https://doi.org/10.1101/2025.06.09.658534 Macedo G., Olesen A., Maccario L., Leal H., Maas P., Heederik D., Mevius D., Sørensen S., and Schmitt H., 2022, Horizontal gene transfer of an IncP1 plasmid to soil bacterial community introduced by Escherichia coli through manure amendment in soil microcosms, Environmental Science & Technology, 56(16): 11398-11408. https://doi.org/10.1021/acs.est.2c02686 Maheshwari M., Abulreesh H., Khan M., Ahmad I., and Pichtel J., 2017, Horizontal gene transfer in soil and the rhizosphere: impact on ecological fitness of bacteria, In: Agriculturally Important Microbes for Sustainable Agriculture: Volume I: Plant-Soil-Microbe Nexus, Singapore: Springer Singapore, pp.111-130. https://doi.org/10.1007/978-981-10-5589-8_6 Nielsen K., and Van Elsas J., 2019, Horizontal gene transfer and microevolution in soil, In: Modern Soil Microbiology, Third Edition, CRC press, pp.105-123. https://doi.org/10.1201/9780429059186-7 Ravenhall M., Skunca N., Lassalle F., and Dessimoz C., 2015, Inferring horizontal gene transfer, PLoS Computational Biology, 11(5): e1004095. https://doi.org/10.1371/journal.pcbi.1004095 Ren Z., Zhao Y., Han S., and Li X., 2022, Regulatory strategies for inhibiting horizontal gene transfer of ARGs in paddy and dryland soil through computer-based methods, Science of the Total Environment, 856: 159096. https://doi.org/10.1016/j.scitotenv.2022.159096 Sevillya G., Adato O., and Snir S., 2020, Detecting horizontal gene transfer: a probabilistic approach, BMC Genomics, 21(Suppl 1): 106. https://doi.org/10.1186/s12864-019-6395-5
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