[1]

Okeke IN, de Kraker MEA, Van Boeckel TP, Kumar CK, Schmitt H, et al. 2024. The scope of the antimicrobial resistance challenge. The Lancet 403:2426−2438

doi: 10.1016/S0140-6736(24)00876-6
[2]

Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Aguilar GR, et al. 2022. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet 399:629−655

doi: 10.1016/S0140-6736(21)02724-0
[3]

Kavanagh K. 2025. The rise of 'nightmare bacteria': antimicrobial resistance in five charts. Nature 646:526−527

doi: 10.1038/d41586-025-03218-x
[4]

Arnold BJ, Huang IT, Hanage WP. 2022. Horizontal gene transfer and adaptive evolution in bacteria. Nature Reviews Microbiology 20:206−218

doi: 10.1038/s41579-021-00650-4
[5]

Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth's biogeochemical cycles. Science 320:1034−1039

doi: 10.1126/science.1153213
[6]

Mueller UG, Sachs JL. 2015. Engineering microbiomes to improve plant and animal health. Trends in Microbiology 23:606−617

doi: 10.1016/j.tim.2015.07.009
[7]

Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, et al. 2024. Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Nature Microbiology 9:2262−2277

doi: 10.1038/s41564-024-01735-5
[8]

Yan J, Bassler BL. 2019. Surviving as a community: antibiotic tolerance and persistence in bacterial biofilms. Cell Host & Microbe 26:15−21

doi: 10.1016/j.chom.2019.06.002
[9]

Wang Q, Wei S, Silva AF, Madsen JS. 2023. Cooperative antibiotic resistance facilitates horizontal gene transfer. The ISME Journal 17:846−854

doi: 10.1038/s41396-023-01393-1
[10]

Bottery MJ, Matthews JL, Wood AJ, Johansen HK, Pitchford JW, et al. 2022. Inter-species interactions alter antibiotic efficacy in bacterial communities. The ISME Journal 16:812−821

doi: 10.1038/s41396-021-01130-6
[11]

Kelsic ED, Zhao J, Vetsigian K, Kishony R. 2015. Counteraction of antibiotic production and degradation stabilizes microbial communities. Nature 521:516−519

doi: 10.1038/nature14485
[12]

Newton DP, Ho PY, Huang KC. 2023. Modulation of antibiotic effects on microbial communities by resource competition. Nature Communications 14:2398

doi: 10.1038/s41467-023-37895-x
[13]

Gullberg E, Cao S, Berg OG, Ilbäck C, Sandegren L, et al. 2011. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathogens 7:e1002158

doi: 10.1371/journal.ppat.1002158
[14]

Andersson DI, Hughes D. 2010. Antibiotic resistance and its cost: is it possible to reverse resistance? Nature Reviews Microbiology 8:260−271

doi: 10.1038/nrmicro2319
[15]

Banerjee S, Schlaeppi K, van der Heijden MG. 2018. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology 16:567−576

doi: 10.1038/s41579-018-0024-1
[16]

Yu Z, Henderson IR, Guo J. 2023. Non-caloric artificial sweeteners modulate conjugative transfer of multi-drug resistance plasmid in the gut microbiota. Gut Microbes 15:2157698

doi: 10.1080/19490976.2022.2157698
[17]

Lu J, Yu Z, Ding P, Guo J. 2022. Triclosan promotes conjugative transfer of antibiotic resistance genes to opportunistic pathogens in environmental microbiome. Environmental Science & Technology 56:15108−15119

doi: 10.1021/acs.est.2c05537
[18]

Cantón R, Morosini MI. 2011. Emergence and spread of antibiotic resistance following exposure to antibiotics. FEMS Microbiology Reviews 35:977−991

doi: 10.1111/j.1574-6976.2011.00295.x
[19]

Pérez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, et al. 2013. Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62:1591−1601

doi: 10.1136/gutjnl-2012-303184
[20]

Willing BP, Russell SL, Finlay BB. 2011. Shifting the balance: antibiotic effects on host–microbiota mutualism. Nature Reviews Microbiology 9:233−243

doi: 10.1038/nrmicro2536
[21]

De La Cochetière MF, Durand T, Lepage P, Bourreille A, Galmiche JP, et al. 2005. Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. Journal of Clinical Microbiology 43:5588−5592

doi: 10.1128/JCM.43.11.5588-5592.2005
[22]

Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, et al. 2010. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 5:e9836

doi: 10.1371/journal.pone.0009836
[23]

Gomaa EZ. 2020. Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek 113:2019−2040

doi: 10.1007/s10482-020-01474-7
[24]

Stewart PS. 2015. Antimicrobial tolerance in biofilms. Microbiology Spectrum 3:MB-0010-2014

doi: 10.1128/microbiolspec.MB-0010-2014
[25]

Bottery MJ, Pitchford JW, Friman VP. 2021. Ecology and evolution of antimicrobial resistance in bacterial communities. The ISME Journal 15:939−948

doi: 10.1038/s41396-020-00832-7
[26]

Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, et al. 2013. The long-term stability of the human gut microbiota. Science 341:1237439

doi: 10.1126/science.1237439
[27]

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, et al. 2016. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Science Translational Medicine 8:343ra81

doi: 10.1126/scitranslmed.aad0917
[28]

Li X, Brejnrod A, Thorsen J, Zachariasen T, Trivedi U, et al. 2023. Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults. Nature Communications 14:8526

doi: 10.1038/s41467-023-44289-6
[29]

Dhariwal A, Haugli Bråten LC, Sturød K, Salvadori G, Bargheet A, et al. 2023. Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut Microbes 15:2157200

doi: 10.1080/19490976.2022.2157200
[30]

Reyman M, Van Houten MA, Watson RL, Chu MLJN, Arp K, et al. 2022. Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial. Nature Communications 13:893

doi: 10.1038/s41467-022-28525-z
[31]

de Nies L, Busi SB, Tsenkova M, Halder R, Letellier E, et al. 2022. Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nature Communications 13:2296

doi: 10.1038/s41467-022-29919-9
[32]

Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, et al. 2016. The initial state of the human gut microbiome determines its reshaping by antibiotics. The ISME Journal 10:707−720

doi: 10.1038/ismej.2015.148
[33]

Baldi A, Braat S, Imrul Hasan M, Bennett C, Barrios M, et al. 2024. Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children. Nature Communications 15:6980

doi: 10.1038/s41467-024-51326-5
[34]

Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, et al. 2018. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology 3:1255−1265

doi: 10.1038/s41564-018-0257-9
[35]

Grießhammer A, de la Cuesta-Zuluaga J, Müller P, Gekeler C, Homolak J, et al. 2025. Non-antibiotics disrupt colonization resistance against enteropathogens. Nature 644:641−649

doi: 10.1038/s41586-025-09217-2
[36]

de la Cuesta-Zuluaga J, Boldt L, Maier L. 2024. Response, resistance, and recovery of gut bacteria to human-targeted drug exposure. Cell Host & Microbe 32:786−793

doi: 10.1016/j.chom.2024.05.009
[37]

Lynch M, Ackerman MS, Gout JF, Long H, Sung W, et al. 2016. Genetic drift, selection and the evolution of the mutation rate. Nature Reviews Genetics 17:704−714

doi: 10.1038/nrg.2016.104
[38]

Brauner A, Fridman O, Gefen O, Balaban NQ. 2016. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nature Reviews Microbiology 14:320−330

doi: 10.1038/nrmicro.2016.34
[39]

Pu Y, Zhao Z, Li Y, Zou J, Ma Q, et al. 2016. Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Molecular Cell 62:284−294

doi: 10.1016/j.molcel.2016.03.035
[40]

Schenk MF, Zwart MP, Hwang S, Ruelens P, Severing E, et al. 2022. Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution. Nature Ecology & Evolution 6:439−447

doi: 10.1038/s41559-022-01669-3
[41]

Fogle CA, Nagle JL, Desai MM. 2008. Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics 180:2163−2173

doi: 10.1534/genetics.108.090019
[42]

Mahrt N, Tietze A, Künzel S, Franzenburg S, Barbosa C, et al. 2021. Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. Nature Ecology & Evolution 5:1233−1242

doi: 10.1038/s41559-021-01511-2
[43]

Nordholt N, Kanaris O, Schmidt SBI, Schreiber F. 2021. Persistence against benzalkonium chloride promotes rapid evolution of tolerance during periodic disinfection. Nature Communications 12:6792

doi: 10.1038/s41467-021-27019-8
[44]

Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, et al. 2012. The molecular diversity of adaptive convergence. Science 335:457−461

doi: 10.1126/science.1212986
[45]

Card KJ, Thomas MD, Graves JL Jr, Barrick JE, Lenski RE. 2021. Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 118:e2016886118

doi: 10.1073/pnas.2016886118
[46]

Lee H, Popodi E, Tang H, Foster PL. 2012. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proceedings of the National Academy of Sciences of the United States of America 109:E2774−E2783

doi: 10.1073/pnas.1210309109
[47]

Cabot G, Zamorano L, Moyà B, Juan C, Navas A, et al. 2016. Evolution of Pseudomonas aeruginosa antimicrobial resistance and fitness under low and high mutation rates. Antimicrobial Agents and Chemotherapy 60:1767−1778

doi: 10.1128/AAC.02676-15
[48]

Szendro IG, Franke J, de Visser JAG, Krug J. 2013. Predictability of evolution depends nonmonotonically on population size. Proceedings of the National Academy of Sciences of the United States of America 110:571−576

doi: 10.1073/pnas.1213613110
[49]

Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, et al. 2021. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 371:eaba0862

doi: 10.1126/science.aba0862
[50]

Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, et al. 2023. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nature Communications 14:7366

doi: 10.1038/s41467-023-42998-6
[51]

Knöppel A, Näsvall J, Andersson DI. 2016. Compensating the fitness costs of synonymous mutations. Molecular Biology and Evolution 33:1461−1477

doi: 10.1093/molbev/msw028
[52]

Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, et al. 2016. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Molecular Biology and Evolution 33:885−897

doi: 10.1093/molbev/msv339
[53]

Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, et al. 2017. Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecology & Evolution 1:1354−1363

doi: 10.1038/s41559-017-0243-2
[54]

Bakkeren E, Diard M, Hardt WD. 2020. Evolutionary causes and consequences of bacterial antibiotic persistence. Nature Reviews Microbiology 18:479−490

doi: 10.1038/s41579-020-0378-z
[55]

Li J, Rettedal EA, van der Helm E, Ellabaan M, Panagiotou G, et al. 2019. Antibiotic treatment drives the diversification of the human gut resistome. Genomics, Proteomics & Bioinformatics 17:39−51

doi: 10.1016/j.gpb.2018.12.003
[56]

Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genetics 36:760−766

doi: 10.1038/ng1381
[57]

Gillings MR. 2017. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Annals of the New York Academy of Sciences 1389:20−36

doi: 10.1111/nyas.13213
[58]

Ramsay JP, Kwong SM, Murphy RJT, Yui Eto K, Price KJ, et al. 2016. An updated view of plasmid conjugation and mobilization in Staphylococcus. Mobile Genetic Elements 6:e1208317

doi: 10.1080/2159256X.2016.1208317
[59]

Yu Z, Wang Y, Lu J, Bond PL, Guo J. 2021. Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer. The ISME Journal 15:2117−2130

doi: 10.1038/s41396-021-00909-x
[60]

Wang Y, Lu J, Mao L, Li J, Yuan Z, et al. 2019. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera. The ISME Journal 13:509−522

doi: 10.1038/s41396-018-0275-x
[61]

Wang Q, Mao D, Luo Y. 2015. Ionic liquid facilitates the conjugative transfer of antibiotic resistance genes mediated by plasmid RP4. Environmental Science & Technology 49:8731−8740

doi: 10.1021/acs.est.5b01129
[62]

Klümper U, Dechesne A, Riber L, Brandt KK, Gülay A, et al. 2017. Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner. The ISME Journal 11:152−165

doi: 10.1038/ismej.2016.98
[63]

Wang Q, Liu L, Hou Z, Wang L, Ma D, et al. 2020. Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms. Science of The Total Environment 717:137055

doi: 10.1016/j.scitotenv.2020.137055
[64]

Pu Q, Fan XT, Li H, An XL, Lassen SB, et al. 2021. Cadmium enhances conjugative plasmid transfer to a fresh water microbial community. Environmental Pollution 268:115903

doi: 10.1016/j.envpol.2020.115903
[65]

Li L, Dechesne A, He Z, Madsen JS, Nesme J, et al. 2018. Estimating the transfer range of plasmids encoding antimicrobial resistance in a wastewater treatment plant microbial community. Environmental Science & Technology Letters 5:260−265

doi: 10.1021/acs.estlett.8b00105
[66]

Wang Y, Yu Z, Ding P, Lu J, Klümper U, et al. 2022. Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level. Microbiome 10:124

doi: 10.1186/s40168-022-01314-y
[67]

Li B, Qiu Y, Zhang J, Huang X, Shi H, et al. 2018. Real-time study of rapid spread of antibiotic resistance plasmid in biofilm using microfluidics. Environmental Science & Technology 52:11132−11141

doi: 10.1021/acs.est.8b03281
[68]

Godeux AS, Svedholm E, Barreto S, Potron A, Venner S, et al. 2022. Interbacterial transfer of carbapenem resistance and large antibiotic resistance islands by natural transformation in pathogenic Acinetobacter. mBio 13:e0263121

doi: 10.1128/mbio.02631-21
[69]

Yu Z, Wang Y, Henderson IR, Guo J. 2022. Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation. The ISME Journal 16:543−554

doi: 10.1038/s41396-021-01066-9
[70]

Hu X, Kang F, Yang B, Zhang W, Qin C, et al. 2019. Extracellular polymeric substances acting as a permeable barrier hinder the lateral transfer of antibiotic resistance genes. Frontiers in Microbiology 10:736

doi: 10.3389/fmicb.2019.00736
[71]

Mazaheri Nezhad Fard R, Barton MD, Heuzenroeder MW. 2011. Bacteriophage-mediated transduction of antibiotic resistance in enterococci. Letters in Applied Microbiology 52:559−564

doi: 10.1111/j.1472-765X.2011.03043.x
[72]

Haaber J, Penadés JR, Ingmer H. 2017. Transfer of antibiotic resistance in Staphylococcus aureus. Trends in Microbiology 25:893−905

doi: 10.1016/j.tim.2017.05.011
[73]

Winans JB, Wucher BR, Nadell CD. 2022. Multispecies biofilm architecture determines bacterial exposure to phages. PLoS Biology 20:e3001913

doi: 10.1371/journal.pbio.3001913
[74]

Ruan C, Ramoneda J, Kan A, Rudge TJ, Wang G, et al. 2024. Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nature Communications 15:5397

doi: 10.1038/s41467-024-49840-7
[75]

Palencia-Gándara C, Getino M, Moyano G, Redondo S, Fernández-López R, et al. 2021. Conjugation inhibitors effectively prevent plasmid transmission in natural environments. mBio 12:e01277-21

doi: 10.1128/mBio.01277-21
[76]

Jiang X, Hall AB, Xavier RJ, Alm EJ. 2019. Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PLoS One 14:e0223680

doi: 10.1371/journal.pone.0223680
[77]

Guo J, Li J, Chen H, Bond PL, Yuan Z. 2017. Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. Water Research 123:468−478

doi: 10.1016/j.watres.2017.07.002
[78]

Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, et al. 2022. Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nature Communications 13:1445

doi: 10.1038/s41467-022-29096-9
[79]

Fang Y, Wang Z, Liu X, Tyler BM. 2022. Biogenesis and biological functions of extracellular vesicles in cellular and organismal communication with microbes. Frontiers in Microbiology 13:817844

doi: 10.3389/fmicb.2022.817844
[80]

van Niel G, Carter DR, Clayton A, Lambert DW, Raposo G, et al. 2022. Challenges and directions in studying cell–cell communication by extracellular vesicles. Nature Reviews Molecular Cell Biology 23:369−382

doi: 10.1038/s41580-022-00460-3
[81]

Grande R, Di Marcantonio MC, Robuffo I, Pompilio A, Celia C, et al. 2015. Helicobacter pylori ATCC 43629/NCTC 11639 outer membrane vesicles (OMVs) from biofilm and planktonic phase associated with extracellular DNA (eDNA). Frontiers in Microbiology 6:1369

doi: 10.3389/fmicb.2015.01369
[82]

Michaelis C, Grohmann E. 2023. Horizontal gene transfer of antibiotic resistance genes in biofilms. Antibiotics 12:328

doi: 10.3390/antibiotics12020328
[83]

Zhou M, Ma L, Wang Z, Li S, Cai Y, et al. 2024. Nano-and microplastics drive the dynamic equilibrium of amoeba-associated bacteria and antibiotic resistance genes. Journal of Hazardous Materials 476:134958

doi: 10.1016/j.jhazmat.2024.134958
[84]

Nguyen TB, Bonkowski M, Dumack K, Chen QL, He JZ, et al. 2023. Protistan predation selects for antibiotic resistance in soil bacterial communities. The ISME Journal 17:2182−2189

doi: 10.1038/s41396-023-01524-8
[85]

Liu C, Wang Y, Zhou Z, Wang S, Wei Z, et al. 2024. Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions. The ISME Journal 18:wrae169

doi: 10.1093/ismejo/wrae169
[86]

Matsushita M, Okubo T, Hasegawa T, Matsuo J, Watanabe T, et al. 2018. Tetrahymena promotes interactive transfer of carbapenemase gene encoded in plasmid between fecal Escherichia coli and environmental Aeromonas caviae. Microbiology and Immunology 62:720−728

doi: 10.1111/1348-0421.12656
[87]

Bornier F, Zas E, Potheret D, Laaberki MH, Coupat-Goutaland B, et al. 2021. Environmental free-living amoebae can predate on diverse antibiotic-resistant human pathogens. Applied and Environmental Microbiology 87:e00747721

doi: 10.1128/AEM.00747-21
[88]

Lin C, Li LJ, Yang K, Xu JY, Fan XT, et al. 2025. Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance. The ISME Journal 19:wraf009

doi: 10.1093/ismej/wraf009
[89]

Ling X, Gu X, Shen Y, Fu C, Zhou Y, et al. 2024. Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes. mSphere 9:e00548-24

doi: 10.1128/msphere.00548-24
[90]

Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, et al. 2024. Amoebae as training grounds for microbial pathogens. mBio 15:e00827-24

doi: 10.1128/mbio.00827-24
[91]

Shi Y, Liang M, Zeng J, Wang Z, Zhang L, et al. 2024. Soil amoebae are unexpected hotspots of environmental antibiotics and antibiotic resistance genes. Environmental Science & Technology 58:21385−21904

doi: 10.1021/acs.est.4c10455
[92]

Sarink MJ, Grassi L, Tielens AGM, Verbon A, Vos MC, et al. 2025. Acanthamoeba castellanii can facilitate plasmid transfer between environmental Pseudomonas spp. Journal of Basic Microbiology 65:e70051

doi: 10.1002/jobm.2024070051
[93]

Nisbet B. 2012. Nutrition and feeding strategies in protozoa. Dordrecht: Springer. vii, 280 pp doi: 10.1007/978-94-011-6555-6

[94]

Denoncourt AM, Paquet VE, Charette SJ. 2017. Packaging of Mycobacterium smegmatis bacteria into fecal pellets by the ciliate Tetrahymena pyriformis. FEMS Microbiology Letters 364:fnx237

doi: 10.1093/femsle/fnx237
[95]

Hojo F, Sato D, Matsuo J, Miyake M, Nakamura S, et al. 2012. Ciliates expel environmental Legionella-laden pellets to stockpile food. Applied and Environmental Microbiology 78:5247−5257

doi: 10.1128/AEM.00421-12
[96]

Morón Á, Tarhouchi AE, Belinchón I, Valenzuela JM, de Francisco P, et al. 2024. Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response. The ISME Journal 18:wrae014

doi: 10.1093/ismejo/wrae014
[97]

Olanrewaju TO, Dooley JSG, Coleman HM, McGonigle C, Arnscheidt J. 2025. Bacterivorous ciliate Tetrahymena pyriformis facilitates vanA antibiotic resistance gene transfer in Enterococcus faecalis. Antibiotics 14:448

doi: 10.3390/antibiotics14040448
[98]

Rønn R, McCaig AE, Griffiths BS, Prosser JI. 2002. Impact of protozoan grazing on bacterial community structure in soil microcosms. Applied and Environmental Microbiology 68:6094−6105

doi: 10.1128/AEM.68.12.6094-6105.2002
[99]

Hahn MW, Höfle MG. 1999. Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition. Applied and Environmental Microbiology 65:4863−4872

doi: 10.1128/AEM.65.11.4863-4872.1999
[100]

Ratzke C, Barrere J, Gore J. 2020. Strength of species interactions determines biodiversity and stability in microbial communities. Nature Ecology & Evolution 4:376−383

doi: 10.1038/s41559-020-1099-4
[101]

Liu W, Jacquiod S, Brejnrod A, Russel J, Burmølle M, et al. 2019. Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. The ISME Journal 13:3054−3066

doi: 10.1038/s41396-019-0494-9
[102]

Rodríguez-Verdugo A, Ackermann M. 2021. Rapid evolution destabilizes species interactions in a fluctuating environment. The ISME Journal 15:450−460

doi: 10.1038/s41396-020-00787-9
[103]

Hansen SK, Rainey PB, Haagensen JAJ, Molin S. 2007. Evolution of species interactions in a biofilm community. Nature 445:533−536

doi: 10.1038/nature05514
[104]

Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, et al. 2011. Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications 2:589

doi: 10.1038/ncomms1597
[105]

Dieltjens L, Appermans K, Lissens M, Lories B, Kim W, et al. 2020. Inhibiting bacterial cooperation is an evolutionarily robust anti-biofilm strategy. Nature Communications 11:107

doi: 10.1038/s41467-019-13660-x
[106]

Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, et al. 2016. Biofilms: an emergent form of bacterial life. Nature Reviews Microbiology 14:563−575

doi: 10.1038/nrmicro.2016.94
[107]

Secor PR, Michaels LA, Ratjen A, Jennings LK, Singh PK. 2018. Entropically driven aggregation of bacteria by host polymers promotes antibiotic tolerance in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America 115:10780−10785

doi: 10.1073/pnas.1806005115
[108]

Clardy J, Fischbach MA, Walsh CT. 2006. New antibiotics from bacterial natural products. Nature Biotechnology 24:1541−1550

doi: 10.1038/nbt1266
[109]

Brook I. 2009. The role of beta-lactamase-producing-bacteria in mixed infections. BMC Infectious Diseases 9:202

doi: 10.1186/1471-2334-9-202
[110]

Pearl Mizrahi S, Goyal A, Gore J. 2023. Community interactions drive the evolution of antibiotic tolerance in bacteria. Proceedings of the National Academy of Sciences of the United States of America 120:e2209043119

doi: 10.1073/pnas.2209043119
[111]

Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. 2023. Metabolic exchanges are ubiquitous in natural microbial communities. Nature Microbiology 8:2244−2252

doi: 10.1038/s41564-023-01511-x
[112]

Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, et al. 2021. Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology & Evolution 5:195−203

doi: 10.1038/s41559-020-01353-4
[113]

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, et al. 2015. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America 112:6449−6454

doi: 10.1073/pnas.1421834112
[114]

Wu Y, Fu C, Peacock CL, Sørensen SJ, Redmile-Gordon MA, et al. 2023. Cooperative microbial interactions drive spatial segregation in porous environments. Nature Communications 14:4226

doi: 10.1038/s41467-023-39991-4
[115]

Nadell CD, Ricaurte D, Yan J, Drescher K, Bassler BL. 2017. Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms. eLife 6:e21855

doi: 10.7554/eLife.21855
[116]

Li L, Wu T, Wang Y, Ran M, Kang Y, et al. 2019. Spatial coordination in a mutually beneficial bacterial community enhances its antibiotic resistance. Communications Biology 2:301

doi: 10.1038/s42003-019-0533-0
[117]

Palmer JD, Foster KR. 2022. Bacterial species rarely work together. Science 376:581−582

doi: 10.1126/science.abn5093
[118]

García-Bayona L, Comstock LE. 2018. Bacterial antagonism in host-associated microbial communities. Science 361:eaat2456

doi: 10.1126/science.aat2456
[119]

Suckow G, Seitz P, Blokesch M. 2011. Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner. Journal of Bacteriology 193:4914−4924

doi: 10.1128/JB.05396-11
[120]

Borgeaud S, Metzger LC, Scrignari T, Blokesch M. 2015. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science 347:63−67

doi: 10.1126/science.1260064
[121]

Stefanic P, Belcijan K, Kraigher B, Kostanjšek R, Nesme J, et al. 2021. Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis. Nature Communications 12:3457

doi: 10.1038/s41467-021-23685-w
[122]

Ringel PD, Hu D, Basler M. 2017. The role of type VI secretion system effectors in target cell lysis and subsequent horizontal gene transfer. Cell Reports 21:3927−3940

doi: 10.1016/j.celrep.2017.12.020
[123]

Morgado S, Vicente AC. 2022. Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids. Scientific Reports 12:8249

doi: 10.1038/s41598-022-12382-3
[124]

Thomas J, Watve SS, Ratcliff WC, Hammer BK. 2017. Horizontal gene transfer of functional type VI killing genes by natural transformation. mBio 8:e00654-17

doi: 10.1128/mbio.00654-00617
[125]

Schwechheimer C, Kuehn MJ. 2015. Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. Nature Reviews Microbiology 13:605−619

doi: 10.1038/nrmicro3525
[126]

Li C, Zhu L, Wang D, Wei Z, Hao X, et al. 2022. T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer. The ISME Journal 16:500−510

doi: 10.1038/s41396-021-01093-8
[127]

Ciofu O, Beveridge TJ, Kadurugamuwa J, Walther-Rasmussen J, Høiby N. 2000. Chromosomal β-lactamase is packaged into membrane vesicles and secreted from Pseudomonas aeruginosa. Journal of Antimicrobial Chemotherapy 45:9−13

doi: 10.1093/jac/45.1.9
[128]

Shi Y, Ma L, Zhou M, He Z, Zhao Y, et al. 2024. Copper stress shapes the dynamic behavior of amoebae and their associated bacteria. The ISME Journal 18:wrae100

doi: 10.1093/ismej/wrae100
[129]

Zielenkiewicz U, Cegłowski P. 2001. Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochimica Polonica 48:1003−1023

doi: 10.18388/abp.12001_13863
[130]

Li L, Dechesne A, Madsen JS, Nesme J, Sørensen SJ, et al. 2020. Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes. The ISME Journal 14:1170−1181

doi: 10.1038/s41396-020-0596-4
[131]

Aviv G, Rahav G, Gal-Mor O. 2016. Horizontal transfer of the Salmonella enterica serovar infantis resistance and virulence plasmid pESI to the gut microbiota of warm-blooded hosts. mBio 7:e01395-16

doi: 10.1128/mBio.01395-16
[132]

De Gelder L, Ponciano JM, Joyce P, Top EM. 2007. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology 153:452−463

doi: 10.1099/mic.0.2006/001784-0
[133]

Yang QE, Ma X, Zeng L, Wang Q, Li M, et al. 2024. Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study. The Lancet Microbe 5:e13−e23

doi: 10.1016/S2666-5247(23)00227-6
[134]

MacPherson DW, Gushulak BD, Baine WB, Bala S, Gubbins PO, et al. 2009. Population mobility, globalization, and antimicrobial drug resistance. Emerging Infectious Diseases 15:1727−1732

doi: 10.3201/eid1511.090419
[135]

Miller WR, Arias CA. 2024. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nature Reviews Microbiology 22:598−616

doi: 10.1038/s41579-024-01054-w
[136]

Economist Intelligence Unit. 2019. It's time to end drug-resistant tuberculosis. The Economist. www.eiu.com/graphics/marketing/pdf/its-time-to-end-drug-resistant-tuberculosis-full-report.pdf

[137]

Unemo M, Seifert HS, Hook EW III, Hawkes S, Ndowa F, et al. 2019. Gonorrhoea. Nature Reviews Disease Primers 5:79

doi: 10.1038/s41572-019-0128-6
[138]

Debroas D, Siguret C. 2019. Viruses as key reservoirs of antibiotic resistance genes in the environment. The ISME Journal 13:2856−2867

doi: 10.1038/s41396-019-0478-9
[139]

Polz MF, Alm EJ, Hanage WP. 2013. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends in Genetics 29:170−175

doi: 10.1016/j.tig.2012.12.006
[140]

Amaro F, Martín-González A. 2021. Microbial warfare in the wild—the impact of protists on the evolution and virulence of bacterial pathogens. International Microbiology 24:559−571

doi: 10.1007/s10123-021-00192-y
[141]

Król-Turmińska K, Olender A. 2017. Human infections caused by free-living amoebae. Annals of Agricultural and Environmental Medicine 24:254−260

doi: 10.5604/12321966.1233568
[142]

Debroas D. 2025. Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems. Microbiome 13:77

doi: 10.1186/s40168-025-02062-5
[143]

Brockhurst MA, Harrison E. 2022. Ecological and evolutionary solutions to the plasmid paradox. Trends in Microbiology 30:534−543

doi: 10.1016/j.tim.2021.11.001
[144]

Wein T, Hülter NF, Mizrahi I, Dagan T. 2019. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nature Communications 10:2595

doi: 10.1038/s41467-019-10600-7
[145]

Frazão N, Sousa A, Lässig M, Gordo I. 2019. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proceedings of the National Academy of Sciences of the United States of America 116:17906−17915

doi: 10.1073/pnas.1906958116
[146]

Wu L, Wang XW, Tao Z, Wang T, Zuo W, et al. 2024. Data-driven prediction of colonization outcomes for complex microbial communities. Nature Communications 15:2406

doi: 10.1038/s41467-024-46766-y
[147]

Zhang P, Mao D, Gao H, Zheng L, Chen Z, et al. 2022. Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment. The ISME Journal 16:1284−1293

doi: 10.1038/s41396-021-01171-x
[148]

Alonso-del Valle A, León-Sampedro R, Rodríguez-Beltrán J, DelaFuente J, Hernández-García M, et al. 2021. Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nature Communications 12:2653

doi: 10.1038/s41467-021-22849-y
[149]

Colom J, Batista D, Baig A, Tang Y, Liu S, et al. 2019. Sex pilus specific bacteriophage to drive bacterial population towards antibiotic sensitivity. Scientific Reports 9:12616

doi: 10.1038/s41598-019-48483-9