Horizontal Gene Transfer and the Collapse of Bacterial Diversity under Antibiotic Stress
DOI:
https://doi.org/10.24237/04.02.816Keywords:
HGT, Bacteria, ABR, Bacterial Diversity, BiofilmAbstract
Horizontal gene transfer (HGT) is a biological process that enables bacteria to exchange genetic material independently of cell division and plays a key role in the spread of antibiotic resistance (ABR). This review provides an overview of how antibiotic stress, particularly misuse and low-dose exposure, can enhance HGT and alter bacterial community diversity. Based on evidence from environmental, clinical, and agriculture studies, we highlight that antibiotic pressure can facilitate HGT through several mechanisms, including increased cell-to-cell contact, activation of stress response pathways, and the formation of biofilms that act as hotspots for genetic exchange. As HGT promotes the spread of resistance genes and improves bacterial survival under antibiotic pressure, gradually, resistant strains may become dominant within microbial communities, leading to a decline in bacterial diversity. Such loss of diversity may result in significant ecological consequences, including reduced efficiency of pollutant degradation and disruption of nitrogen cycling processes. Furthermore, emerging strategies aimed at limiting HGT under antibiotic pressure are discussed; particularly those that may help preserve microbial diversity, support ecosystem stability, and contribute to improved public health outcomes.
Downloads
References
References
[1] E. W. Meressa and B. A. Tseha, “Horizontal gene transfer: The hidden hazards of genetic engineering,” J. Life Sci. Biomed., vol. 14, no. 4, pp. 99–108, 2024, doi:10.54203/jlsb.2024.10.
[2] S. J. Sørensen, M. Bailey, L. H. Hansen, N. Kroer, and S. Wuertz, “Studying plasmid horizontal transfer in situ: A critical review,” Nat. Rev. Microbiol., vol. 3, no. 9, pp. 700–710, 2005, doi:10.1038/nrmicro1232.
[3] N. A. Lerminiaux and A. D. S. Cameron, “Horizontal transfer of antibiotic resistance genes in clinical environments,” Can. J. Microbiol., vol. 65, no. 1, pp. 34–44, 2019, doi:10.1139/cjm-2018-0275.
[4] M. Arnold, A. Bressin, O. Jasnovidova, D. Meierhofer, and A. Mayer, “A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination,” Mol. Cell., vol. 81, no. 17, pp. 3589–3603.e13, 2021, doi:10.1016/j.molcel.2021.06.026.
[5] C. Verraes et al., “Antimicrobial resistance in the food chain: A review,” Int. J. Environ. Res. Public Health, vol. 10, no. 7, pp. 2643–2669, 2013, doi:10.3390/ijerph10072643.
[6] C. J. H. von Wintersdorff et al., “Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer,” Front. Microbiol., vol. 7, p. 173, 2016, doi:10.3389/fmicb.2016.00173.
[7] K. A. Glen and I. L. Lamont, “β-lactam resistance in Pseudomonas aeruginosa: Current status and future prospects,” Pathogens, vol. 10, p. 1638, 2021, doi:10.3390/pathogens10121638.
[8] E. Marti, E. Variatza, and J. L. Balcazar, “The role of aquatic ecosystems as reservoirs of antibiotic resistance,” Trends Microbiol., vol. 22, pp. 36–41, 2014, doi:10.1016/j.tim.2013.11.001.
[9] D. Wang et al., “Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm,” Appl. Environ. Microbiol., vol. 81, pp. 890–899, 2015, doi:10.1128/AEM.02617-14.
[10] Y. Chen et al., “Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environments,” Water Res., vol. 162, pp. 127–138, 2019, doi:10.1016/j.watres.2019.06.047.
[11] M. Haudiquet, J. M. de Sousa, M. Touchon, and E. P. C. Rocha, “Selfish, promiscuous and sometimes useful: How mobile genetic elements drive horizontal gene transfer in microbial populations,” Philos. Trans. R. Soc. B Biol. Sci., vol. 377, p. 20210234, 2022, doi:10.1098/rstb.2021.0234.
[12] K. Abe, N. Nomura, and S. Suzuki, “Biofilms: Hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism,” FEMS Microbiol. Ecol., vol. 96, p. fiaa031, 2020, doi:10.1093/femsec/fiaa031.
[13] L. Ma, M. E. Konkel, and X. Lu, “Antimicrobial resistance gene transfer from Campylobacter jejuni in mono- and dual-species biofilms,” Appl. Environ. Microbiol., vol. 87, p. e00659-21, 2021, doi:10.1128/AEM.00659-21.
[14] L. He et al., “Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization,” Cell, vol. 188, no. 23, pp. 6636–6653.e17, 2025, doi:10.1016/j.cell.2025.08.019.
[15] R. Kogay and O. Zhaxybayeva, “Selection for translational efficiency in genes associated with Alphaproteobacterial gene transfer agents,” mSystems, vol. 7, no. 6, p. e00892-22, 2022, doi:10.1128/msystems.00892-22.
[16] A. A. Vetrova et al., “Antibiotic resistance as a functional characteristic of urban dust particles’ microbial communities,” Biology, vol. 13, no. 12, p. 1022, 2024, doi:10.3390/biology13121022.
[17] A. Tello, B. Austin, and T. C. Telfer, “Selective pressure of antibiotic pollution on bacteria of importance to public health,” Environ. Health Perspect., vol. 120, no. 8, pp. 1100–1106, 2012, doi:10.1289/ehp.1104650.
[18] G. Muteeb, M. T. Rehman, M. Shahwan, and M. Aatif, “Origin of antibiotics and antibiotic resistance, and their impacts on drug development: A narrative review,” Pharmaceuticals, vol. 16, no. 11, p. 1615, 2023, doi:10.3390/ph16111615.
[19] C. Manyi-Loh et al., “Antibiotic use in agriculture and its consequential resistance in environmental sources: Potential public health implications,” Molecules, vol. 23, no. 4, p. 795, 2018, doi:10.3390/molecules23040795.
[20] S. Pandey et al., “Antibiotic resistance in livestock, environment and humans: One Health perspective,” J. Anim. Sci. Technol., 2024, doi:10.5187/jast.2023.e129.
[21] S. A. Kraemer, A. Ramachandran, and G. G. Perron, “Antibiotic pollution in the environment: From microbial ecology to public policy,” Microorganisms, vol. 7, no. 6, p. 180, 2019, doi:10.3390/microorganisms7060180.
[22] J. A. Thibodeau, M. Barret, F. Mouchet, V. X. Nguyen, and E. Pinelli, “The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review,” Environ. Pollut., vol. 350, p. 123894, 2024, doi:10.1016/j.envpol.2024.123894.
[23] R. Thakur et al., “Global perspectives on residual antibiotics: Environmental challenges and trends,” Discov. Sustain., vol. 6, p. 232, 2025, doi:10.1007/s43621-025-01048-5.
[24] L. M. O’Connell et al., “Natural transformation in Gram-positive bacteria and its biotechnological relevance to lactic acid bacteria,” Annu. Rev. Food Sci. Technol., vol. 13, pp. 409–431, 2022, doi:10.1146/annurev-food-052720-011445.
[25] J. C. Mell and R. J. Redfield, “Natural competence and the evolution of DNA uptake specificity,” J. Bacteriol., vol. 196, no. 8, pp. 1471–1483, 2014, doi:10.1128/JB.01293-13.
[26] J. P. Gogarten and J. P. Townsend, “Horizontal gene transfer, genome innovation and evolution,” Nat. Rev. Microbiol., vol. 3, no. 9, pp. 679–687, 2005, doi:10.1038/nrmicro1204.
[27] P. Corvaglia et al., “A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains,” Proc. Natl. Acad. Sci. U.S.A., vol. 107, no. 26, pp. 11954–11958, 2010, doi:10.1073/pnas.1000489107.
[28] J. G. Lawrence, “The dynamics of genome evolution in bacteria,” Annu. Rev. Genet., vol. 29, pp. 487–524, 1995, doi:10.1146/annurev.ge.29.120195.002415.
[29] R. Popa and R. Dagan, “Trends and barriers to lateral gene transfer in prokaryotes,” Curr. Opin. Microbiol., vol. 14, no. 5, pp. 615–623, 2011, doi:10.1016/j.mib.2011.07.027.
[30] A. L. Mell, C. Shumilina, T. Borner, and T. Bock, “Evidence for the recent horizontal transfer of a bacterial gene to the plastid genome of land plants,” Plant Cell Physiol., vol. 53, no. 8, pp. 1241–1252, 2012, doi:10.1093/pcp/pcs070.
[31] J. Rankin, E. P. C. Rocha, and S. Brown, “What traits are carried on mobile genetic elements, and why?” Heredity, vol. 106, no. 1, pp. 1–10, 2011, doi:10.1038/hdy.2010.24.
[32] C. Smillie, J. Garcillán-Barcia, M. Francia, E. Rocha, and F. de la Cruz, “Mobility of plasmids,” Microbiol. Mol. Biol. Rev., vol. 74, no. 3, pp. 434–452, 2010, doi:10.1128/MMBR.00020-10.
[33] C. M. Thomas and K. M. Nielsen, “Mechanisms of, and barriers to, horizontal gene transfer between bacteria,” Nat. Rev. Microbiol., vol. 3, no. 9, pp. 711–721, 2005, doi:10.1038/nrmicro1234.
[34] M. Vos, A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk, “Micro-scale determinants of bacterial diversity in soil,” FEMS Microbiol. Rev., vol. 37, no. 6, pp. 936–954, 2013, doi:10.1111/1574-6976.12023.
[35] R. Aminov, “The role of antibiotics and antibiotic resistance in nature,” Environ. Microbiol., vol. 11, no. 12, pp. 2970–2988, 2009, doi:10.1111/j.1462-2920.2009.01972.x.
[36] C. A. Fuchsman, R. E. Collins, G. Rocap, and W. J. Brazelton, “Effect of environmental variation on the fitness impact of horizontally transferred genes,” ISME J., vol. 11, no. 12, pp. 2877–2887, 2017, doi:10.1038/ismej.2017.133.
[37] M. Ochman, J. G. Lawrence, and E. A. Groisman, “Lateral gene transfer and the nature of bacterial innovation,” Nature, vol. 405, no. 6784, pp. 299–304, 2000, doi:10.1038/35012500.
[38] S. E. Atta, L. A. Ghannawi, K. Gharab, O. Y. Shakir, A. H. Khleef, and S. B. Ismael, “Analysis of mecA gene in methicillin-resistant Staphylococcus aureus isolated from diverse clinical sources,” East. Ukr. Med. J., vol. 13, no. 3, pp. 834–847, 2025, doi:10.21272/eumj.2025;13(3):834-847.
[39] C. Boto, “Horizontal gene transfer in evolution: Facts and challenges,” Proc. R. Soc. B, vol. 277, no. 1683, pp. 819–827, 2010, doi:10.1098/rspb.2009.1679.
[40] R. Frost, E. Leplae, A. Summers, and A. Toussaint, “Mobile genetic elements: The agents of open source evolution,” Nat. Rev. Microbiol., vol. 3, no. 9, pp. 722–732, 2005, doi:10.1038/nrmicro1235.
[41] P. Soucy, J. Huang, and J. P. Gogarten, “Horizontal gene transfer: Building the web of life,” Nat. Rev. Genet., vol. 16, no. 8, pp. 472–482, 2015, doi:10.1038/nrg3962.
[42] S. E. Atta, L. Ghannawi, O. Y. Shakir, and K. M. Gharab, “Molecular investigation of gyrA mutations in clinical isolates of methicillin-resistant Staphylococcus aureus derived from diverse sources,” Al-Rafidain J. Med. Sci., vol. 5, no. 1S, pp. S64–S70, 2023, doi:10.54133/ajms.v5i1S.282.
[43] M. Jain, H. Olsen, and T. Polz, “Horizontal gene transfer among microbial genomes: The driving force of ecological and evolutionary innovation,” Nat. Rev. Microbiol., vol. 20, no. 3, pp. 142–156, 2022, doi:10.1038/s41579-021-00642-9.
[44] S. Shintani, A. Sanchez, and M. Kimbara, “Genetic factors involved in conjugative transfer of plasmids,” Front. Microbiol., vol. 6, p. 242, 2015, doi:10.3389/fmicb.2015.00242.
[45] C. Gillings, “Evolutionary consequences of antibiotic use for the resistome, mobilome, and microbial pangenome,” Front. Microbiol., vol. 4, p. 4, 2013, doi:10.3389/fmicb.2013.00004.
[46] C. Berendonk et al., “Tackling antibiotic resistance: The environmental framework,” Nat. Rev. Microbiol., vol. 13, no. 5, pp. 310–317, 2015, doi:10.1038/nrmicro3439.
[47] L. Lan, Y. Wang, Y. Chen, T. Wang, and J. Zhang, “A review on the prevalence and treatment of antibiotic resistance genes in hospital wastewater,” Toxics, vol. 13, no. 4, p. 263, 2025, doi:10.3390/toxics13040263.
[48] X. Shi, Y. Xia, W. Wei, and B. J. Ni, “Accelerated spread of antibiotic resistance genes induced by non-antibiotic conditions: Roles and mechanisms,” Water Res., vol. 224, p. 119060, 2022, doi:10.1016/j.watres.2022.119060.
[49] M. P. Garcillán-Barcia et al., “Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies,” Mol. Microbiol., vol. 63, no. 2, pp. 404–416, 2007, doi:10.1111/j.1365-2958.2006.05523.x.
[50] Q. Li, P. Zhao, L. Li, H. Zhao, L. Shi, and P. Tian, “Engineering a CRISPR interference system to repress a class 1 integron in Escherichia coli,” Antimicrob. Agents Chemother., vol. 64, no. 3, p. e01789-19, 2020, doi:10.1128/AAC.01789-19.
[51] L. Zhang et al., “Fast evolution of SOS-independent multidrug resistance in bacteria,” eLife, vol. 13, p. RP95058, 2025, doi:10.7554/eLife.95058.
[52] B. S. I. Supina and J. J. Dennis, “The current landscape of phage–antibiotic synergistic (PAS) interactions,” Antibiotics, vol. 14, no. 6, p. 545, 2025, doi:10.3390/antibiotics14060545.
[53] Y. Xie, H. Liu, Z. Teng, J. Ma, and G. Liu, “Nanomaterial-enabled anti-biofilm strategies: New opportunities for treatment of bacterial infections,” Nanoscale, vol. 17, pp. 5605–5628, 2025, doi:10.1039/D4NR04774E.
[54] Y. Luo, Q. Yang, D. Zhang, and W. Yan, “Mechanisms and control strategies of antibiotic resistance in pathological biofilms,” J. Microbiol. Biotechnol., vol. 31, no. 1, pp. 1–7, 2021, doi:10.4014/jmb.2010.10021.
[55] A. Iaconis, L. M. De Plano, A. Caccamo, D. Franco, and S. Conoci, “Anti-biofilm strategies: A focused review on innovative approaches,” Microorganisms, vol. 12, no. 4, p. 639, 2024, doi:10.3390/microorganisms12040639.
[56] H. Kadkhoda et al., “Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance,” Heliyon, vol. 10, no. 14, p. e34692, 2024, doi:10.1016/j.heliyon.2024.e34692.
[57] A. Mayorga-Ramos et al., “CRISPR-Cas-based antimicrobials: Design, challenges, and bacterial mechanisms of resistance,” ACS Infect. Dis., vol. 9, no. 7, pp. 1283–1302, 2023, doi:10.1021/acsinfecdis.2c00649.
[58] S. Tao, H. Chen, N. Li, T. Wang, and W. Liang, “The spread of antibiotic resistance genes in vivo model,” Can. J. Infect. Dis. Med. Microbiol., p. 3348695, 2022, doi:10.1155/2022/3348695.
[59] H. Endale, M. Mathewos, and D. Abdeta, “Potential causes of spread of antimicrobial resistance and preventive measures in One Health perspective: A review,” Infect. Drug Resist., vol. 16, pp. 7515–7545, 2023, doi:10.2147/IDR.S428837.
[60] D. Ding et al., “The spread of antibiotic resistance to humans and potential protection strategies,” Ecotoxicol. Environ. Saf., vol. 254, p. 114734, 2023, doi:10.1016/j.ecoenv.2023.114734.
[61] S. Zhu, J. Hong, and T. Wang, “Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species,” Nat. Commun., vol. 15, p. 800, 2024, doi:10.1038/s41467-024-45154-w.
[62] Y. Yang et al., “Response of soil general and specific functions following loss of microbial diversity: A review,” Soil Secur., vol. 15, p. 100151, 2024, doi:10.1016/j.soisec.2024.100151.
[63] I. P. A. Lee, O. T. Eldakar, J. P. Gogarten, and C. P. Andam, “Bacterial cooperation through horizontal gene transfer,” Trends Ecol. Evol., vol. 37, no. 3, pp. 223–232, 2022, doi:10.1016/j.tree.2021.11.006.
[64] A. San Millan et al., “Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1,” ISME J., vol. 12, pp. 3014–3024, 2018, doi:10.1038/s41396-018-0224-8.
[65] S. Donati, T. Sander, and H. Link, “Crosstalk between transcription and metabolism: How much enzyme is enough for a cell?” Wiley Interdiscip. Rev. Syst. Biol. Med., vol. 10, p. e1396, 2018, doi:10.1002/wsbm.1396.
[66] G. A. C. Bell, “Experimental evolution in Chlamydomonas. I. Short-term selection in uniform and diverse environments,” Heredity, vol. 78, pp. 490–497, 1997.
[67] B. Segerman, “The genetic integrity of bacterial species: The core genome and the accessory genome, two different stories,” Front. Cell. Infect. Microbiol., vol. 2, p. 116, 2012, doi:10.3389/fcimb.2012.00116.
[68] S. S. Dhaif, D. B. Mahmood, G. S. Jawad, L. A. Ghannawi, and H. F. Al-Rubaye, “Synergism effect of silver nanoparticles and cefotaxime to treat biofilm formation of Staphylococcus aureus clinical isolates,” Stud. Biol., vol. 19, no. 2, 2025, doi:10.30970/sbi.1902.833.
[69] D. O. Hessen, “Biotic deterioration and homogenization: Why it matters,” Int. J. Polit. Cult. Soc., 2024, doi:10.1007/s10767-024-09498-x.
[70] D. K. Sharma and Y. S. Rajpurohit, “Multitasking functions of bacterial extracellular DNA in biofilms,” J. Bacteriol., vol. 206, no. 4, p. e00006-24, 2024, doi:10.1128/jb.00006-24.
[71] M. Bustamante et al., “An eco-evolutionary perspective on antimicrobial resistance in the context of One Health,” iScience, vol. 28, no. 1, p. 111534, 2024, doi:10.1016/j.isci.2024.111534.
[72] J. Sanjuan et al., “Horizontal gene transfer in rhizobia: Ecological implications,” in Nitrogen Fixation: From Molecules to Crop Productivity, Dordrecht, Netherlands: Springer, 2000, p. 336, doi:10.1007/0-306-47615-0_336.
[73] P. M. de Lajudie et al., “Minimal standards for the description of new genera and species of rhizobia and agrobacteria,” Int. J. Syst. Evol. Microbiol., vol. 69, pp. 1852–1863, 2019, doi:10.1099/ijsem.0.003426.
[74] S. Liu, J. Jiao, and C. F. Tian, “Adaptive evolution of rhizobial symbiosis beyond horizontal gene transfer: From genome innovation to regulation reconstruction,” Genes, vol. 14, no. 2, p. 274, 2023, doi:10.3390/genes14020274.
[75] F. Keesing et al., “Impacts of biodiversity on the emergence and transmission of infectious diseases,” Nature, vol. 468, no. 7324, pp. 647–652, 2010, doi:10.1038/nature09575.
[76] M. J. Johnson-Chappell and L. Lavalle, “Food security and biodiversity: Can we have both? An agroecological analysis,” Agric. Hum. Values, vol. 28, pp. 3–26, 2011, doi:10.1007/s10460-009-9251-4.
[77] D. R. Ha, N. M. Haste, and D. P. Gluckstein, “The role of antibiotic stewardship in promoting appropriate antibiotic use,” Am. J. Lifestyle Med., vol. 13, no. 4, pp. 376–383, 2017, doi:10.1177/1559827617700824.
[78] M. Hazra et al., “An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants,” Sci. Total Environ., vol. 917, p. 170433, 2024, doi:10.1016/j.scitotenv.2024.170433.
[79] M. Łobocka, K. Dąbrowska, and A. Górski, “Engineered bacteriophage therapeutics: Rationale, challenges and future,” BioDrugs, vol. 35, no. 3, pp. 255–280, 2021, doi:10.1007/s40259-021-00480-z.
[80] A. Vashistha et al., “Quorum sensing inhibitors as therapeutics: Bacterial biofilm inhibition,” Bioorg. Chem., vol. 136, p. 106551, 2023, doi:10.1016/j.bioorg.2023.106551.
[81] C. Palencia-Gándara et al., “Conjugation inhibitors effectively prevent plasmid transmission in natural environments,” mBio, vol. 12, no. 4, p. e01277-21, 2021, doi:10.1128/mBio.01277-21.
[82] R. H. Lathakumari et al., “Antibiotics and the gut microbiome: Understanding the impact on human health,” Med. Microecol., vol. 20, p. 100106, 2024, doi:10.1016/j.medmic.2024.100106.
Downloads
Published
Issue
Section
License
Copyright (c) 2026 CC BY 4.0
This work is licensed under a Creative Commons Attribution 4.0 International License.
