[1]

Jiang G, Liu C, Xiong W, Shen Q, Wei, Z. 2024. Protist predation selects for the soil resistome. The ISME Journal 18(1):wrad007

doi: 10.1093/ismejo/wrad007
[2]

Cytryn E. 2013. The soil resistome: the anthropogenic, the native, and the unknown. Soil Biology and Biochemistry 63:18−23

doi: 10.1016/j.soilbio.2013.03.017
[3]

Yang H, Liu R, Liu H, Wang C, Yin X, et al. 2021. Evidence for long-term anthropogenic pollution: the hadal trench as a depository and indicator for dissemination of antibiotic resistance genes. Environmental Science & Technology 55(22):15136−15148

doi: 10.1021/acs.est.1c03444
[4]

Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J. 2009. Functional metagenomics reveals diverse β-lactamases in a remote alaskan soil. The ISME Journal 3(2):243−251

doi: 10.1038/ismej.2008.86
[5]

Lang KS, Anderson JM, Schwarz S, Williamson L, Handelsman J, et al. 2010. Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Applied and Environmental Microbiology 76(15):5321−5326

doi: 10.1128/AEM.00323-10
[6]

Zhao Y, Li L, Huang Y, Xu X, Liu Z, et al. 2025. Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome. Nature Communications 16(1):7141

doi: 10.1038/s41467-025-61606-3
[7]

Bhullar K, Waglechner N, Pawlowski A, Koteva K, Banks ED, et al. 2012. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS One 7(4):e34953

doi: 10.1371/journal.pone.0034953
[8]

D'Costa VM, King CE, Kalan L, Morar M, Sung WWL, et al. 2011. Antibiotic resistance is ancient. Nature 477(7365):457−461

doi: 10.1038/nature10388
[9]

Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, et al. 2010. Call of the wild: antibiotic resistance genes in natural environments. Nature Reviews Microbiology 8(4):251−259

doi: 10.1038/nrmicro2312
[10]

Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews 74(3):417−433

doi: 10.1128/MMBR.00016-10
[11]

Martinez JL. 2009. The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proceedings of the Royal Society B: Biological Sciences 276(1667):2521−2530

doi: 10.1098/rspb.2009.0320
[12]

World Health Organization (WHO). 2020. Technical brief on water, sanitation, hygiene (WASH) and wastewater management to prevent infections and reduce the spread of antimicrobial resistance (AMR). WHO, Geneva, Switzerland. https://iris.who.int/server/api/core/bitstreams/b3b1a541-91ac-474d-8a49-10660e3ef6d2/content

[13]

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America 108(Suppl 1):4516−4522

doi: 10.1073/pnas.1000080107
[14]

Mitchell AM, Silhavy TJ. 2019. Envelope Stress responses: balancing damage repair and toxicity. Nature Reviews Microbiology 17(7):417−428

doi: 10.1038/s41579-019-0199-0
[15]

Liu Z, Yao X, Chen C, Zhao Y, Dong C, et al. 2025. Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits. Microbiome 13(1):8

doi: 10.1186/s40168-024-02005-6
[16]

Access to Medicine Foundation. 2020. 2020 Antimicrobial resistance benchmark. Report. Access to Medicine Foundation, Amsterdam, The Netherlands. https://accesstomedicinefoundation.org/resource/2020-antimicrobial-resistance-benchmark

[17]

European Parliament. 2020. Strategic approach to pharmaceuticals in the environment. Resolution 2019/2816(RSP). European Parliament, Brussels, Belgium. https://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:52020IP0226

[18]

Review on Antimicrobial Resistance. 2015. Antimicrobials in agriculture and the environment: reducing unnecessary waste. Review on Antimicrobial Resistance, London, UK. https://static-cdn.publive.online/english-betterindia/media/pdf_files/sites/default/filesAntimicrobials%20in%20agriculture%20and%20the%20environment%20-%20Reducing%20unnecessary%20use%20and%20waste.pdf

[19]

United Nations Environment Programme. 2017. Frontiers 2017: emerging issues of environmental concern. Report. United Nations Environment Programme, Nairobi, Kenya. www.unep.org/resources/frontiers-2017-emerging-issues-environmental-concern

[20]

Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, et al. 2020. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiology Reviews 44(2):171−188

doi: 10.1093/femsre/fuaa001
[21]

Bengtsson-Palme J, Kristiansson E, Larsson DGJ. 2018. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews 42(1):fux053

doi: 10.1093/femsre/fux053
[22]

Berendonk TU, Manaia CM, Merlin C, Fatta-Kassinos D, Cytryn E, et al. 2015. Tackling antibiotic resistance: the environmental framework. Nature Reviews Microbiology 13(5):310−317

doi: 10.1038/nrmicro3439
[23]

Chow LKM, Ghaly TM, Gillings MR. 2021. A survey of sub-inhibitory concentrations of antibiotics in the environment. Journal of Environmental Sciences 99:21−27

doi: 10.1016/j.jes.2020.05.030
[24]

Graham DW, Bergeron G, Bourassa MW, Dickson J, Gomes F, et al. 2019. Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems. Annals of the New York Academy of Sciences 1441(1):17−30

doi: 10.1111/nyas.14036
[25]

Singer AC, Shaw H, Rhodes V, Hart A. 2016. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Frontiers in Microbiology 7:1728

doi: 10.3389/fmicb.2016.01728
[26]

Smalla K, Cook K, Djordjevic SP, Klümper U, Gillings M. 2018. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiology Ecology 94(12):fiy195

doi: 10.1093/femsec/fiy195
[27]

Wellington EMH, Boxall AB, Cross P, Feil EJ, Gaze WH, et al. 2013. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. The Lancet Infectious Diseases 13(2):155−165

doi: 10.1016/S1473-3099(12)70317-1
[28]

Inda-Díaz JS, Lund D, Parras-Moltó M, Johnning A, Bengtsson-Palme J, et al. 2023. Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. Microbiome 11(1):44

doi: 10.1186/s40168-023-01479-0
[29]

Lund D, Coertze RD, Parras-Moltó M, Berglund F, Flach CF, et al. 2023. Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens. Communications Biology 6(1):812

doi: 10.1038/s42003-023-05174-6
[30]

Lund D, Kieffer N, Parras-Moltó M, Ebmeyer S, Berglund F, et al. 2022. Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes. Microbial Genomics 8(1):000770

doi: 10.1099/mgen.0.000770
[31]

Graham DW, Knapp CW, Christensen BT, McCluskey S, Dolfing J. 2016. Appearance of β-lactam resistance genes in agricultural soils and clinical isolates over the 20th century. Scientific Reports 6:21550

doi: 10.1038/srep21550
[32]

Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, et al. 2016. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. The Lancet Infectious Diseases 16(2):161−168

doi: 10.1016/S1473-3099(15)00424-7
[33]

Baquero F, Coque TM, Martínez JL, Aracil-Gisbert S, Lanza VF. 2019. Gene transmission in the One Health microbiosphere and the channels of antimicrobial resistance. Frontiers in Microbiology 10:2892

doi: 10.3389/fmicb.2019.02892
[34]

Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, et al. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480(7376):241−244

doi: 10.1038/nature10571
[35]

Akob DM, Oates AE, Girguis PR, Badgley BD, Cooper VS, et al. 2024. Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology. mSphere 9(11):e00307-24

doi: 10.1128/msphere.00307-24
[36]

Berglund F, Ebmeyer S, Kristiansson E, Joakim Larsson DG. 2023. Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge. Communications Biology 6(1):321

doi: 10.1038/s42003-023-04676-7
[37]

Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. 2023. Antimicrobial resistance in the global health network: known unknowns and challenges for efficient responses in the 21st century. Microorganisms 11(4):1050

doi: 10.3390/microorganisms11041050
[38]

Andersson DI, Jerlström-Hultqvist J, Näsvall J. 2015. Evolution of new functions de novo and from preexisting genes. Cold Spring Harbor Perspectives in Biology 7(6):a017996

doi: 10.1101/cshperspect.a017996
[39]

Morar M, Wright GD. 2010. The genomic enzymology of antibiotic resistance. Annual Review of Genetics 44:25−51

doi: 10.1146/annurev-genet-102209-163517
[40]

Wood JL, Malik AA, Greening C, Green PT, McGeoch M, et al. 2023. Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits. The ISME Journal 17(11):1793−1797

doi: 10.1038/s41396-023-01486-x
[41]

Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, et al. 2021. Physiological functions of bacterial 'multidrug' efflux pumps. Chemical Reviews 121(9):5417−5478

doi: 10.1021/acs.chemrev.0c01226
[42]

Saier MH Jr, Paulsen IT. 2001. Phylogeny of multidrug transporters. Seminars in Cell & Developmental Biology 12(3):205−213

doi: 10.1006/scdb.2000.0246
[43]

Elbourne LDH, Tetu SG, Hassan KA, Paulsen IT. 2017. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Research 45(D1):D320−D324

doi: 10.1093/nar/gkw1068
[44]

Neyfakh AA. 2002. Mystery of multidrug transporters: the answer can be simple. Molecular Microbiology 44(5):1123−1130

doi: 10.1046/j.1365-2958.2002.02965.x
[45]

Neyfakh AA. 1997. Natural functions of bacterial multidrug transporters. Trends in Microbiology 5(8):309−313

doi: 10.1016/S0966-842X(97)01064-0
[46]

Paulsen IT, Brown MH, Skurray RA. 1996. Proton-dependent multidrug efflux systems. Microbiological Reviews 60(4):575−608

doi: 10.1128/MMBR.60.4.575-608.1996
[47]

Piddock LJV. 2006. Multidrug-resistance efflux pumps? Not just for resistance. Nature Reviews Microbiology 4(8):629−636

doi: 10.1038/nrmicro1464
[48]

Teelucksingh T, Thompson LK, Cox G. 2020. The evolutionary conservation of Escherichia coli drug efflux pumps supports physiological functions. Journal of Bacteriology 202(22):10.1128/JB.00367-20

doi: 10.1128/JB.00367-20
[49]

Du D, Xuan WK, Neuberger A, van Veen HW, Pos KM, et al. 2018. Multidrug efflux pumps: structure, function and regulation. Nature Reviews Microbiology 16(9):523−539

doi: 10.1038/s41579-018-0048-6
[50]

Saier MH Jr, Beatty JT, Goffeau A, Harley KT, Heijne WH, et al. 1999. The major facilitator superfamily. Journal of Molecular Microbiology and Biotechnology 1(2):257−279

[51]

Tseng TT, Gratwick KS, Kollman J, Park D, Nies DH, et al. 1999. The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. Journal of Molecular Microbiology and Biotechnology 1(1):107−125

[52]

Rodríguez-Beltrán J, DelaFuente J, León-Sampedro R, MacLean RC, San Millán Á. 2021. Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nature Reviews Microbiology 19(6):347−359

doi: 10.1038/s41579-020-00497-1
[53]

Dagan T, Artzy-Randrup Y, Martin W. 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proceedings of the National Academy of Sciences of the United States of America 105(29):10039−10044

doi: 10.1073/pnas.0800679105
[54]

Jain R, Rivera MC, Moore JE, Lake JA. 2003. Horizontal gene transfer accelerates genome innovation and evolution. Molecular Biology and Evolution 20(10):1598−1602

doi: 10.1093/molbev/msg154
[55]

Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299−304

doi: 10.1038/35012500
[56]

Carattoli A. 2009. Resistance plasmid families in Enterobacteriaceae. Antimicrobial Agents and Chemotherapy 53(6):2227−2238

doi: 10.1128/AAC.01707-08
[57]

Pilla G, Tang CM. 2018. Going around in circles: virulence plasmids in enteric pathogens. Nature Reviews Microbiology 16(8):484−495

doi: 10.1038/s41579-018-0031-2
[58]

San Millan A, Toll-Riera M, Qi Q, Betts A, Hopkinson RJ, et al. 2018. Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1. The ISME Journal 12(12):3014−3024

doi: 10.1038/s41396-018-0224-8
[59]

Park C, Zhang J. 2012. High expression hampers horizontal gene transfer. Genome Biology and Evolution 4(4):523−532

doi: 10.1093/gbe/evs030
[60]

Couce A, Rodríguez-Rojas A, Blázquez J. 2015. Bypass of genetic constraints during mutator evolution to antibiotic resistance. Proceedings of the Royal Society B: Biological Sciences 282(1804):20142698

doi: 10.1098/rspb.2014.2698
[61]

San Millan A, Escudero JA, Gifford DR, Mazel D, MacLean RC. 2016. Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria. Nature Ecology & Evolution 1(1):10

doi: 10.1038/s41559-016-0010
[62]

Anda M, Ohtsubo Y, Okubo T, Sugawara M, Nagata Y, et al. 2015. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome. Proceedings of the National Academy of Sciences of the United States of America 112(46):14343−14347

doi: 10.1073/pnas.1514326112
[63]

Ikeda S, Okubo T, Kaneko T, Inaba S, Maekawa T, et al. 2010. Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels. The ISME Journal 4(3):315−326

doi: 10.1038/ismej.2009.119
[64]

Barlow M, Fatollahi J, Salverda M. 2009. Evidence for recombination among the alleles encoding TEM and SHV β-lactamases. Journal of Antimicrobial Chemotherapy 63(2):256−259

doi: 10.1093/jac/dkn475
[65]

Mroczkowska JE, Barlow M. 2008. Recombination and selection can remove blaTEM alleles from bacterial populations. Antimicrobial Agents and Chemotherapy 52(9):3408−3410

doi: 10.1128/AAC.00501-08
[66]

Baquirin MHC, Barlow M. 2008. Evolution and recombination of the plasmidic qnr alleles. Journal of Molecular Evolution 67(1):103−110

doi: 10.1007/s00239-008-9131-3
[67]

Weisberg AJ, Davis EW 2nd, Tabima J, Belcher MS, Miller M, et al. 2020. Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368(6495):eaba5256

doi: 10.1126/science.aba5256
[68]

Hernández-Arriaga AM, Chan WT, Espinosa M, Díaz-Orejas R. 2014. Conditional activation of toxin-antitoxin systems: postsegregational killing and beyond. Microbiology Spectrum 2(5):10.1128/microbiolspec.plas-0009-2013

doi: 10.1128/microbiolspec.plas-0009-2013
[69]

Rankin DJ, Rocha EPC, Brown SP. 2011. What traits are carried on mobile genetic elements, and why? Heredity 106(1):1−10

doi: 10.1038/hdy.2010.24
[70]

Werren JH. 2011. Selfish genetic elements, genetic conflict, and evolutionary innovation. Proceedings of the National Academy of Sciences of the United States of America 108(Suppl 2):10863−10870

doi: 10.1073/pnas.1102343108
[71]

Ares-Arroyo M, Bernabe-Balas C, Santos-Lopez A, Baquero MR, Prasad KN, et al. 2018. PCR-based analysis of ColE1 plasmids in clinical isolates and metagenomic samples reveals their importance as gene capture platforms. Frontiers in Microbiology 9:469

doi: 10.3389/fmicb.2018.00469
[72]

Attéré SA, Vincent AT, Paccaud M, Frenette M, Charette SJ. 2017. The role for the small cryptic plasmids as moldable vectors for genetic innovation in Aeromonas salmonicida subsp. salmonicida. Frontiers in Genetics 8:211

doi: 10.3389/fgene.2017.00211
[73]

Szpirer C, Top E, Couturier M, Mergeay M. 1999. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology 145(12):3321−3329

doi: 10.1099/00221287-145-12-3321
[74]

Tock MR, Dryden DT. 2005. The biology of restriction and anti-restriction. Current Opinion in Microbiology 8(4):466−472

doi: 10.1016/j.mib.2005.06.003
[75]

Knapp CW, Dolfing J, Ehlert PAI, Graham DW. 2010. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environmental Science & Technology 44(2):580−587

doi: 10.1021/es901221x
[76]

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. 2017. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology 35(9):833−844

doi: 10.1038/nbt.3935
[77]

Wu J, Wang J, Li Z, Guo S, Li K, et al. 2023. Antibiotics and antibiotic resistance genes in agricultural soils: a systematic analysis. Critical Reviews in Environmental Science and Technology 53(7):847−864

doi: 10.1080/10643389.2022.2094693
[78]

Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, et al. 2021. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184(13):3376−3393.e17

doi: 10.1016/j.cell.2021.05.002
[79]

Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, et al. 2023. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nature Communications 14(1):1706

doi: 10.1038/s41467-023-37428-6
[80]

Stokes HW, Gillings MR. 2011. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into gram-negative pathogens. FEMS Microbiology Reviews 35(5):790−819

doi: 10.1111/j.1574-6976.2011.00273.x
[81]

Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, et al. 2014. Bacterial phylogeny structures soil resistomes across habitats. Nature 509(7502):612−616

doi: 10.1038/nature13377
[82]

Peng Z, Qian X, Liu Y, Li X, Gao H, et al. 2024. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nature Communications 15(1):3624

doi: 10.1038/s41467-024-47348-8
[83]

Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MOA, et al. 2012. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337(6098):1107−1111

doi: 10.1126/science.1220761
[84]

Wright GD. 2010. Antibiotic resistance in the environment: a link to the clinic? Current Opinion in Microbiology 13(5):589−594

doi: 10.1016/j.mib.2010.08.005
[85]

Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. 2006. The role of root exudates in rhizosphere interactions with plants and other organisms. Annual Review of Plant Biology 57:233−266

doi: 10.1146/annurev.arplant.57.032905.105159
[86]

Bremer H, Dennis PP. 2008. Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus 3(1):10.1128/ecosal.5.2.3

doi: 10.1128/ecosal.5.2.3
[87]

Dai X, Zhu M. 2020. Coupling of ribosome synthesis and translational capacity with cell growth. Trends in Biochemical Sciences 45(8):681−692

doi: 10.1016/j.tibs.2020.04.010
[88]

Jørgensen BB, Boetius A. 2007. Feast and famine − microbial life in the deep-sea bed. Nature Reviews Microbiology 5(10):770−781

doi: 10.1038/nrmicro1745
[89]

Reyes-Lamothe R, Sherratt DJ. 2019. The bacterial cell cycle, chromosome inheritance and cell growth. Nature Reviews Microbiology 17(8):467−478

doi: 10.1038/s41579-019-0212-7
[90]

Guruge SK, Han Z, Dai S, Islam A, Ben W, et al. 2025. Seasonal variation of antibiotic resistance genes in activated sludge of a full-scale municipal wastewater treatment plant: contribution of activated sludge functional taxa and clinically relevant taxa. Water Research 268:122598

doi: 10.1016/j.watres.2024.122598
[91]

Bruggeman FJ, Planqué R, Molenaar D, Teusink B. 2020. Searching for principles of microbial physiology. FEMS Microbiology Reviews 44(6):821−844

doi: 10.1093/femsre/fuaa034
[92]

Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, et al. 2013. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342(6158):621−624

doi: 10.1126/science.1243768
[93]

Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, et al. 2012. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal 6(5):1007−1017

doi: 10.1038/ismej.2011.159
[94]

Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America 109(52):21390−21395

doi: 10.1073/pnas.1215210110
[95]

Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 91(12):3463−3470

doi: 10.1890/10-0426.1
[96]

Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, et al. 2017. Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. Microbiome 5(1):5

doi: 10.1186/s40168-016-0221-y
[97]

Larsson DGJ, Flach CF. 2022. Antibiotic resistance in the environment. Nature Reviews Microbiology 20(5):257−269

doi: 10.1038/s41579-021-00649-x
[98]

Wiedenbeck J, Cohan FM. 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiology Reviews 35(5):957−976

doi: 10.1111/j.1574-6976.2011.00292.x
[99]

Alekshun MN, Levy SB. 2007. Molecular mechanisms of antibacterial multidrug resistance. Cell 128(6):1037−1050

doi: 10.1016/j.cell.2007.03.004
[100]

Blake KS, Choi J, Dantas G. 2021. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cellular and Molecular Life Sciences 78(6):2585−2606

doi: 10.1007/s00018-020-03717-2
[101]

Lund D, Parras-Moltó M, Inda-Díaz JS, Ebmeyer S, Joakim Larsson DG, et al. 2025. Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes. Nature Communications 16(1):2595

doi: 10.1038/s41467-025-57825-3
[102]

Shaferman M, Gencel M, Alon N, Alasad K, Rotblat B, et al. 2023. The fitness effects of codon composition of the horizontally transferred antibiotic resistance genes intensify at sub-lethal antibiotic levels. Molecular Biology and Evolution 40(6):msad123

doi: 10.1093/molbev/msad123
[103]

Grossman TH. 2016. Tetracycline antibiotics and resistance. Cold Spring Harbor Perspectives in Medicine 6(4):a025387

doi: 10.1101/cshperspect.a025387
[104]

Porse A, Schou TS, Munck C, Ellabaan MMH, Sommer MOA. 2018. Biochemical mechanisms determine the functional compatibility of heterologous genes. Nature Communications 9(1):522

doi: 10.1038/s41467-018-02944-3
[105]

Rodríguez-Beltrán J, León-Sampedro R, Ramiro-Martínez P, de la Vega C, Baquero F, et al. 2022. Translational demand is not a major source of plasmid-associated fitness costs. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 377(1842):20200463

doi: 10.1098/rstb.2020.0463
[106]

Xie X, Cheng W, Li Z, He R, Yuan K, et al. 2025. Functional metagenomics reveals novel antibiotic resistomes in polar soils. iMeta 4(4):e70069

doi: 10.1002/imt2.70069
[107]

Chen B, Yuan K, Chen X, Yang Y, Zhang T, et al. 2016. Metagenomic analysis revealing antibiotic resistance genes (ARGs) and their genetic compartments in the Tibetan environment. Environmental Science & Technology 50(13):6670−6679

doi: 10.1021/acs.est.6b00619
[108]

Koskiniemi S, Sun S, Berg OG, Andersson DI. 2012. Selection-driven gene loss in bacteria. PLoS Genetics 8(6):e1002787

doi: 10.1371/journal.pgen.1002787
[109]

Aminov RI, Mackie RI. 2007. Evolution and ecology of antibiotic resistance genes. FEMS Microbiology Letters 271(2):147−161

doi: 10.1111/j.1574-6968.2007.00757.x
[110]

Jacoby GA, Munoz-Price LS. 2005. The new β-lactamases. The New England Journal of Medicine 352(4):380−391

doi: 10.1056/NEJMra041359
[111]

Medeiros AA. 1997. Evolution and dissemination of β-lactamases accelerated by generations of β-lactam antibiotics. Clinical Infectious Diseases 24(Suppl 1):S19−S45

doi: 10.1093/clinids/24.Supplement_1.S19
[112]

The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207−214

doi: 10.1038/nature11234
[113]

Numberger D, Ganzert L, Zoccarato L, Mühldorfer K, Sauer S, et al. 2019. Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing. Scientific Reports 9(1):9673

doi: 10.1038/s41598-019-46015-z
[114]

Ebmeyer S, Kristiansson E, Larsson DGJ. 2021. A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology 4(1):8

doi: 10.1038/s42003-020-01545-5
[115]

Xie X, Chen B, Zhu S, Yang R, Yuan K, et al. 2024. Comparative analysis of characteristics of antibiotic resistomes between arctic soils and representative contaminated samples using metagenomic approaches. Journal of Hazardous Materials 469:133943

doi: 10.1016/j.jhazmat.2024.133943
[116]

Yuan K, Yu K, Yang R, Zhang Q, Yang Y, et al. 2019. Metagenomic characterization of antibiotic resistance genes in antarctic soils. Ecotoxicology and Environmental Safety 176:300−308

doi: 10.1016/j.ecoenv.2019.03.099
[117]

Zhang AN, Gaston JM, Dai CL, Zhao S, Poyet M, et al. 2021. An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature Communications 12(1):4765

doi: 10.1038/s41467-021-25096-3
[118]

McGrath D, Poole DBR, Fleming GA, Sinnott J. 1982. Soil ingestion by grazing sheep. Irish Journal of Agricultural Research 21(2/3):135−145

[119]

Fries GF, Marrow GS, Snow PA. 1982. Soil Ingestion by dairy cattle. Journal of Dairy Science 65(4):611−618

doi: 10.3168/jds.S0022-0302(82)82238-8
[120]

Zhang Z, Zhang Q, Wang T, Xu N, Lu T, et al. 2022. Assessment of global health risk of antibiotic resistance genes. Nature Communications 13(1):1553

doi: 10.1038/s41467-022-29283-8
[121]

Zheng F, Zhou GW, Zhu D, Neilson R, Zhu YG, et al. 2022. Does plant identity affect the dispersal of resistomes above and below ground? Environmental Science & Technology 56(21):14904−14912

doi: 10.1021/acs.est.1c08733
[122]

Browne AJ, Chipeta MG, Haines-Woodhouse G, Kumaran EPA, Hamadani BHK, et al. 2021. Global antibiotic consumption and usage in humans, 2000–18: a spatial modelling study. The Lancet Planetary Health 5(12):e893−e904

doi: 10.1016/S2542-5196(21)00280-1
[123]

Yang L, Shen Y, Jiang J, Wang X, Shao D, et al. 2022. Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature Food 3(3):197−205

doi: 10.1038/s43016-022-00470-6
[124]

Pehrsson EC, Tsukayama P, Patel S, Mejía-Bautista M, Sosa-Soto G, et al. 2016. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533(7602):212−216

doi: 10.1038/nature17672
[125]

Sieber RN, Skov RL, Nielsen J, Schulz J, Price LB, et al. 2018. Drivers and dynamics of methicillin-resistant livestock-associated Staphylococcus aureus CC398 in pigs and humans in Denmark. mBio 9(6):10.1128/mbio.02142-18

doi: 10.1128/mBio.02142-18
[126]

Martínez JL, Coque TM, Baquero F. 2015. What is a resistance gene? Ranking risk in resistomes. Nature Reviews Microbiology 13(2):116−123

doi: 10.1038/nrmicro3399
[127]

Sommer MOA, Dantas G, Church GM. 2009. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325(5944):1128−1131

doi: 10.1126/science.1176950
[128]

Stanaway IB, Wallace JC, Shojaie A, Griffith WC, Hong S, et al. 2017. Human oral buccal microbiomes are associated with farmworker status and azinphos-methyl agricultural pesticide exposure. Applied and Environmental Microbiology 83(2):e02149-16

doi: 10.1128/AEM.02149-16
[129]

Pearson AL, Pechal J, Lin Z, Benbow ME, Schmidt C, et al. 2020. Associations detected between measures of neighborhood environmental conditions and human microbiome diversity. Science of The Total Environment 745:141029

doi: 10.1016/j.scitotenv.2020.141029
[130]

Letten AD, Hall AR, Levine JM. 2021. Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nature Ecology & Evolution 5(4):431−441

doi: 10.1038/s41559-020-01385-w
[131]

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431−437

doi: 10.1038/nature12352
[132]

Schulz F, Eloe-Fadrosh EA, Bowers RM, Jarett J, Nielsen T, et al. 2017. Towards a balanced view of the bacterial tree of life. Microbiome 5(1):140

doi: 10.1186/s40168-017-0360-9
[133]

Cui P, Bai Y, Li X, Peng Z, Chen D, et al. 2020. Enhanced removal of antibiotic resistance genes and mobile genetic elements during sewage sludge composting covered with a semi-permeable membrane. Journal of Hazardous Materials 396:122738

doi: 10.1016/j.jhazmat.2020.122738
[134]

Waglechner N, Wright GD. 2017. Antibiotic resistance: it's bad, but why isn't it worse? BMC Biology 15(1):84

doi: 10.1186/s12915-017-0423-1
[135]

Nijsingh N, Munthe C, Joakim Larsson DG. 2019. Managing pollution from antibiotics manufacturing: charting actors, incentives and disincentives. Environmental Health 18(1):95

doi: 10.1186/s12940-019-0531-1
[136]

Sundin GW, Wang N. 2018. Antibiotic resistance in plant-pathogenic bacteria. Annual Review of Phytopathology 56:161−180

doi: 10.1146/annurev-phyto-080417-045946
[137]

Zhu M, Dai X. 2024. Shaping of microbial phenotypes by trade-offs. Nature Communications 15(1):4238

doi: 10.1038/s41467-024-48591-9