{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T00:14:34Z","timestamp":1758759274684,"version":"3.44.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T00:00:00Z","timestamp":1757376000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T00:00:00Z","timestamp":1757376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Humanidades, Ciencias y Tecnolog\u00edas","doi-asserted-by":"publisher","award":["CF 2023-G-1274"],"award-info":[{"award-number":["CF 2023-G-1274"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Microbiol"],"published-print":{"date-parts":[[2025,10]]},"DOI":"10.1007\/s00203-025-04437-6","type":"journal-article","created":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T06:45:00Z","timestamp":1757400300000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Escherichia coli strain O55 contains two cryptic plasmids that depend on each other to replicate"],"prefix":"10.1007","volume":"207","author":[{"given":"Jos\u00e9 A.","family":"Mart\u00ednez-\u00c1lvarez","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra Ethelvina","family":"Coria-Alcaraz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F\u00e1tima Berenice","family":"Ram\u00edrez-Montiel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana Laura","family":"Medina-Nieto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sairy Yarely","family":"Andrade-Guillen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F\u00e1tima Tornero-","family":"Guti\u00e9rrez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c1ngeles","family":"Rangel-Serrano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naur\u00fa Idalia","family":"Vargas-Maya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodolfo","family":"Garc\u00eda-Contreras","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felipe","family":"Padilla-Vaca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernardo","family":"Franco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,9,9]]},"reference":[{"key":"4437_CR1","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","volume":"630","author":"J Abramson","year":"2024","unstructured":"Abramson J, Adler J, Dunger J et al (2024) Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630:493\u2013500. https:\/\/doi.org\/10.1038\/s41586-024-07487-w","journal-title":"Nature"},{"key":"4437_CR2","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20204114","author":"WA Al-Megrin","year":"2021","unstructured":"Al-Megrin WA, Mohamed SH, Saleh MM, Yehia HM (2021) Preventive role of probiotic bacteria against gastrointestinal diseases in mice caused by Giardia lamblia. Biosci Rep. https:\/\/doi.org\/10.1042\/BSR20204114"},{"issue":"3","key":"4437_CR3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403\u2013410. https:\/\/doi.org\/10.1016\/S0022-2836(05)80360-2","journal-title":"J Mol Biol"},{"issue":"2","key":"4437_CR4","first-page":"183","volume":"23","author":"F Anaya-Vel\u00e1zquez","year":"1992","unstructured":"Anaya-Vel\u00e1zquez F, Padilla-Vaca F (1992) Effect of intestinal bacteria on the virulence of Entamoeba histolytica. Arch Med Res 23(2):183\u2013185","journal-title":"Arch Med Res"},{"issue":"Spec No","key":"4437_CR5","first-page":"195","volume":"28","author":"F Anaya-Vel\u00e1zquez","year":"1997","unstructured":"Anaya-Vel\u00e1zquez F, Padilla-Vaca F, Barrios-Rodiles M, Vaca-Ch\u00e1vez A, Gonz\u00e1lez-Robles A (1997) Selective interaction of Entamoeba histolytica with lactobacilli and other intestinal bacteria. Arch Med Res 28(Spec No):195\u2013196","journal-title":"Arch Med Res"},{"issue":"6557","key":"4437_CR6","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1126\/science.abj8754","volume":"373","author":"M Baek","year":"2021","unstructured":"Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD et al (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science 373(6557):871\u2013876. https:\/\/doi.org\/10.1126\/science.abj8754","journal-title":"Science"},{"issue":"12","key":"4437_CR7","doi-asserted-by":"publisher","first-page":"e1035","DOI":"10.1016\/S2666-5247(23)00281-1","volume":"4","author":"KS Baker","year":"2023","unstructured":"Baker KS, Jauneikaite E, Nunn JG, Midega JT, Atun R, Holt KE, Walia K, Howden BP, Tate H, Okeke IN, Carattoli A, Hsu LY, Hopkins KL, Muloi DM, Wheeler NE, Aanensen DM, Mason LCE, Rodgus J, Hendriksen RS, Essack SY, Egyir B, Halpin AL, MacCannell DR, Campos J, Srikantiah P, Feasey NA, Peacock SJ, SEDRIC Genomics Surveillance Working Group (2023) Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group. Lancet Microbe 4(12):e1035\u2013e1039. https:\/\/doi.org\/10.1016\/S2666-5247(23)00281-1","journal-title":"Lancet Microbe"},{"issue":"1_supplement","key":"4437_CR8","doi-asserted-by":"publisher","first-page":"131.1","DOI":"10.1096\/fasebj.27.1_supplement.131.1","volume":"27","author":"J Beatty","year":"2013","unstructured":"Beatty J, Akierman S, Rioux K, Beck P, McKnight W, Feener T, Wallace J, Buret A (2013) Gut microbiota biofilm disruptions by Giardia: pathology in human enterocytes and germ-free mice. FASEB J 27(1_supplement):131.1-131.1. https:\/\/doi.org\/10.1096\/fasebj.27.1_supplement.131.1","journal-title":"FASEB J"},{"issue":"45","key":"4437_CR9","doi-asserted-by":"publisher","first-page":"34349","DOI":"10.1074\/jbc.M603365200","volume":"281","author":"JG Bird","year":"2006","unstructured":"Bird JG, Sharma S, Roshwalb SC, Hoskins JR, Wickner S (2006) Functional analysis of CbpA, a DnaJ homolog and nucleoid-associated DNA-binding protein. J Biol Chem 281(45):34349\u201334356. https:\/\/doi.org\/10.1074\/jbc.M603365200","journal-title":"J Biol Chem"},{"issue":"3","key":"4437_CR10","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1128\/iai.40.3.882-887.1983","volume":"40","author":"R Bracha","year":"1983","unstructured":"Bracha R, Mirelman D (1983) Adherence and ingestion of Escherichia coli serotype 055 by trophozoites of Entamoeba histolytica. Infect Immun 40(3):882\u2013887. https:\/\/doi.org\/10.1128\/iai.40.3.882-887.1983","journal-title":"Infect Immun"},{"issue":"6","key":"4437_CR11","doi-asserted-by":"publisher","first-page":"e65793","DOI":"10.1371\/journal.pone.0065793","volume":"8","author":"A Brolund","year":"2013","unstructured":"Brolund A, Franz\u00e9n O, Melefors O, Tegmark-Wisell K, Sandegren L (2013) Plasmidome-analysis of ESBL-producing Escherichia coli using conventional typing and high-throughput sequencing. PLoS ONE 8(6):e65793. https:\/\/doi.org\/10.1371\/journal.pone.0065793","journal-title":"PLoS ONE"},{"issue":"6\u20137","key":"4437_CR12","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.ijmm.2013.02.001","volume":"303","author":"A Carattoli","year":"2013","unstructured":"Carattoli A (2013) Plasmids and the spread of resistance. Int J Med Microbiol 303(6\u20137):298\u2013304. https:\/\/doi.org\/10.1016\/j.ijmm.2013.02.001","journal-title":"Int J Med Microbiol"},{"key":"4437_CR13","doi-asserted-by":"publisher","first-page":"6640","DOI":"10.1073\/pnas.120163297","volume":"97","author":"KA Datsenko","year":"2000","unstructured":"Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640\u20136645. https:\/\/doi.org\/10.1073\/pnas.120163297","journal-title":"Proc Natl Acad Sci U S A"},{"key":"4437_CR14","doi-asserted-by":"publisher","first-page":"783","DOI":"10.2307\/2408678","volume":"39","author":"J Felsenstein","year":"1985","unstructured":"Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783\u2013791","journal-title":"Evolution"},{"issue":"1","key":"4437_CR15","doi-asserted-by":"publisher","first-page":"9332","DOI":"10.1038\/s41598-020-66239-8","volume":"10","author":"JA Gama","year":"2020","unstructured":"Gama JA, Kloos J, Johnsen PJ, Samuelsen \u00d8 (2020) Host dependent maintenance of a blaNDM-1-encoding plasmid in clinical Escherichia coli isolates. Sci Rep 10(1):9332. https:\/\/doi.org\/10.1038\/s41598-020-66239-8","journal-title":"Sci Rep"},{"issue":"8","key":"4437_CR16","doi-asserted-by":"publisher","first-page":"608","DOI":"10.3390\/pathogens13080608","volume":"13","author":"JA Grondin","year":"2024","unstructured":"Grondin JA, Jamal A, Mowna S, Seto T, Khan WI (2024) Interaction between intestinal parasites and the gut microbiota: implications for the intestinal immune response and host defence. Pathogens 13(8):608. https:\/\/doi.org\/10.3390\/pathogens13080608","journal-title":"Pathogens"},{"issue":"14","key":"4437_CR17","doi-asserted-by":"publisher","first-page":"1169829","DOI":"10.3389\/fmicb.2023.1169829","volume":"5","author":"K Hoffmann","year":"2023","unstructured":"Hoffmann K, Riediger M, Tersteegen A, Marquardt P, Kahlfu\u00df S, Kaasch AJ, Hagen RM, Frickmann H, Zautner AE (2023) Molecular epidemiology of enterically colonizing Escherichia coli with resistance against third-generation cephalosporins isolated from stool samples of European soldiers with concomitant diarrhea on deployment in Western African mali. Front Microbiol 5(14):1169829. https:\/\/doi.org\/10.3389\/fmicb.2023.1169829","journal-title":"Front Microbiol"},{"key":"4437_CR18","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41587-023-01773-0","volume":"42","author":"M van Kempen","year":"2024","unstructured":"van Kempen M, Kim SS, Tumescheit C et al (2024) Fast and accurate protein structure search with Foldseek. Nat Biotechnol 42:243\u2013246. https:\/\/doi.org\/10.1038\/s41587-023-01773-0","journal-title":"Nat Biotechnol"},{"key":"4437_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/molbev\/msae263","volume":"41","author":"S Kumar","year":"2024","unstructured":"Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, Tamura K (2024) Molecular evolutionary genetics analysis version 12 for adaptive and green computing. Mol Biol Evol 41:1\u20139. https:\/\/doi.org\/10.1093\/molbev\/msae263","journal-title":"Mol Biol Evol"},{"key":"4437_CR20","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/B978-0-12-418687-3.00027-6","volume":"529","author":"JC Lessard","year":"2013","unstructured":"Lessard JC (2013) Transformation of E. coli via electroporation. Methods Enzym 529:321\u2013327. https:\/\/doi.org\/10.1016\/B978-0-12-418687-3.00027-6","journal-title":"Methods Enzym"},{"key":"4437_CR22","doi-asserted-by":"publisher","first-page":"1098386","DOI":"10.3389\/fmicb.2023.1098386","volume":"14","author":"MF Maciel-Fiuza","year":"2023","unstructured":"Maciel-Fiuza MF et al (2023) Role of gut microbiota in infectious and inflammatory diseases. Front Microbiol 14:1098386. https:\/\/doi.org\/10.3389\/fmicb.2023.1098386","journal-title":"Front Microbiol"},{"key":"4437_CR23","first-page":"3","volume-title":"Data sequence analysis and evolution bioinformatics","author":"NR Markham","year":"2008","unstructured":"Markham NR, Zuker MM (2008) UNAFold: software for nucleic acid folding and hybridization. In: Keith J (ed) Data sequence analysis and evolution bioinformatics. Humana Press Inc, Totowa, pp 3\u201331"},{"issue":"1","key":"4437_CR24","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/0092-8674(86)90491-5","volume":"44","author":"H Masukata","year":"1986","unstructured":"Masukata H, Tomizawa J (1986) Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript. Cell 44(1):125\u2013136. https:\/\/doi.org\/10.1016\/0092-8674(86)90491-5","journal-title":"Cell"},{"issue":"2","key":"4437_CR25","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.exppara.2008.10.0","volume":"121","author":"CL Mendoza-Mac\u00edas","year":"2009","unstructured":"Mendoza-Mac\u00edas CL, Barrios-Ceballos MP, de la Pe\u00f1a LP, Rangel-Serrano A, Anaya-Vel\u00e1zquez F, Mirelman D, Padilla-Vaca F (2009) Entamoeba histolytica: effect on virulence, growth and gene expression in response to monoxenic culture with Escherichia coli 055. Exp Parasitol 121(2):167\u2013174. https:\/\/doi.org\/10.1016\/j.exppara.2008.10.0","journal-title":"Exp Parasitol"},{"issue":"4","key":"4437_CR26","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1128\/jcm.11.4.328-331.1980","volume":"11","author":"D Mirelman","year":"1980","unstructured":"Mirelman D, Altmann G, Eshdat Y (1980) Screening of bacterial isolates for mannose-specific lectin activity by agglutination of yeasts. J Clin Microbiol 11(4):328\u2013331. https:\/\/doi.org\/10.1128\/jcm.11.4.328-331.1980","journal-title":"J Clin Microbiol"},{"issue":"5","key":"4437_CR27","doi-asserted-by":"publisher","first-page":"2096","DOI":"10.1128\/IAI.67.5.2096-2102.1999","volume":"67","author":"F Padilla-Vaca","year":"1999","unstructured":"Padilla-Vaca F, Ankri S, Bracha R, Koole LA, Mirelman D (1999) Down regulation of Entamoeba histolytica virulence by monoxenic cultivation with Escherichia coli O55 is related to a decrease in expression of the light (35-kilodalton) subunit of the Gal\/GalNAc lectin. Infect Immun 67(5):2096\u20132102. https:\/\/doi.org\/10.1128\/IAI.67.5.2096-2102.1999","journal-title":"Infect Immun"},{"issue":"3","key":"4437_CR28","doi-asserted-by":"publisher","first-page":"400","DOI":"10.2144\/00283bm02","volume":"28","author":"GJ Phillips","year":"2000","unstructured":"Phillips GJ, Park SK, Huber D (2000) High copy number plasmids compatible with commonly used cloning vectors. Biotechniques 28(3):400\u2013408. https:\/\/doi.org\/10.2144\/00283bm02","journal-title":"Biotechniques"},{"key":"4437_CR29","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406\u2013425","journal-title":"Mol Biol Evol"},{"issue":"11","key":"4437_CR30","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000685","volume":"7","author":"O Schwengers","year":"2021","unstructured":"Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom 7(11):000685. https:\/\/doi.org\/10.1099\/mgen.0.000685","journal-title":"Microb Genom"},{"key":"4437_CR31","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1038\/s41467-021-21734-y","volume":"12","author":"B Shao","year":"2021","unstructured":"Shao B, Rammohan J, Anderson DA, Alperovich N, Ross D (2021) Single-cell measurement of plasmid copy number and promoter activity. Nat Commun 12:1475. https:\/\/doi.org\/10.1038\/s41467-021-21734-y","journal-title":"Nat Commun"},{"issue":"7","key":"4437_CR32","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","volume":"11","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S\u00f6ding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol 11(7):539. https:\/\/doi.org\/10.1038\/msb.2011.75","journal-title":"Mol Syst Biol"},{"issue":"5803","key":"4437_CR33","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1038\/290264a0","volume":"290","author":"AR Stuitje","year":"1981","unstructured":"Stuitje AR, Spelt CE, Veltkamp E, Nijkamp HJ (1981) Identification of mutations affecting replication control of plasmid clo DF13. Nature 290(5803):264\u2013267. https:\/\/doi.org\/10.1038\/290264a0","journal-title":"Nature"},{"key":"4437_CR34","first-page":"512","volume":"10","author":"K Tamura","year":"1993","unstructured":"Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512\u2013526","journal-title":"Mol Biol Evol"},{"issue":"10","key":"4437_CR35","doi-asserted-by":"publisher","first-page":"4054","DOI":"10.1007\/s12325-020-01458-z","volume":"37","author":"GSE Tan","year":"2020","unstructured":"Tan GSE, Tay HL, Tan SH, Lee TH, Ng TM, Lye DC (2020) Gut microbiota modulation: implications for infection control and antimicrobial stewardship. Adv Ther 37(10):4054\u20134067. https:\/\/doi.org\/10.1007\/s12325-020-01458-z","journal-title":"Adv Ther"},{"issue":"D1","key":"4437_CR36","doi-asserted-by":"publisher","first-page":"D221","DOI":"10.1093\/nar\/gky1034","volume":"47","author":"The RNAcentral Consortium","year":"2019","unstructured":"The RNAcentral Consortium (2019) RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 47(D1):D221\u2013D229. https:\/\/doi.org\/10.1093\/nar\/gky1034","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"4437_CR37","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1099\/0022-1317-49-3-209","volume":"49","author":"MF Torres","year":"2000","unstructured":"Torres MF, Uetanabaro APT, Costa AF, Alves CA, Farias LM, Bambirra EA et al (2000) Influence of bacteria from the duodenal microbiota of patients with symptomatic giardiasis on the pathogenicity of Giardia duodenalis in gnotoxenic mice. J Med Microbiol 49(3):209\u2013215","journal-title":"J Med Microbiol"},{"issue":"3\u20134","key":"4437_CR38","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1111\/j.1574-6968.1986.tb01189.x","volume":"1","author":"JT Trevors","year":"1986","unstructured":"Trevors JT (1986) Plasmid curing in bacteria. FEMS Microbiol Rev 1(3\u20134):149\u2013157. https:\/\/doi.org\/10.1111\/j.1574-6968.1986.tb01189.x","journal-title":"FEMS Microbiol Rev"},{"issue":"1","key":"4437_CR39","doi-asserted-by":"publisher","first-page":"4031","DOI":"10.1038\/s41467-023-39778-7","volume":"14","author":"M Venkatesan","year":"2023","unstructured":"Venkatesan M, Fruci M, Verellen LA, Skarina T, Mesa N, Flick R, Pham C, Mahadevan R, Stogios PJ, Savchenko A (2023) Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat Commun 14(1):4031. https:\/\/doi.org\/10.1038\/s41467-023-39778-7","journal-title":"Nat Commun"},{"issue":"D1","key":"4437_CR40","doi-asserted-by":"publisher","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","volume":"51","author":"J Wang","year":"2023","unstructured":"Wang J, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A (2023) The conserved domain database in 2023. Nucleic Acids Res 51(D1):D384\u2013D388. https:\/\/doi.org\/10.1093\/nar\/gkac1096","journal-title":"Nucleic Acids Res"},{"key":"4437_CR41","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.831740","volume":"9","author":"J Wang","year":"2022","unstructured":"Wang J, Youkharibache P, Marchler-Bauer A, Lanczycki C, Zhang D, Lu S, Madej T, Marchler GH, Cheng T, Chong LC, Zhao S, Yang K, Lin J, Cheng Z, Dunn R, Malkaram SA, Tai C-H, Enoma D, Busby B, Johnson NL, Tabaro F, Song G, Ge Y (2022) Icn3d: from web-based 3d viewer to structural analysis tool in batch mode. Front Mol Biosci 9:831740. https:\/\/doi.org\/10.3389\/fmolb.2022.831740","journal-title":"Front Mol Biosci"},{"issue":"1","key":"4437_CR42","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bioinformatics\/btz502","volume":"36","author":"J Wang","year":"2020","unstructured":"Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A (2020a) iCn3D, a web-based 3D viewer for sharing 1D\/2D\/3D representations of biomolecular Structures. Bioinformatics 36(1):131\u2013135. https:\/\/doi.org\/10.1093\/bioinformatics\/btz502","journal-title":"Bioinformatics"},{"issue":"1","key":"4437_CR43","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bioinformatics\/btz502","volume":"36","author":"J Wang","year":"2020","unstructured":"Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A (2020b) Icn3D, a web-based 3D viewer for sharing 1D\/2D\/3D representations of biomolecular structures. Bioinformatics 36(1):131\u2013135. https:\/\/doi.org\/10.1093\/bioinformatics\/btz502","journal-title":"Bioinformatics"},{"issue":"6","key":"4437_CR44","doi-asserted-by":"publisher","DOI":"10.1111\/pim.12980","volume":"45","author":"N Winaris","year":"2023","unstructured":"Winaris N, Pawestri AR, Azizah S, Alifia LI, Asiyah R, Ayuningtyas TR, Fitri LE, Sardjono TW (2023) Plasmodium infection and dysbiosis: a new paradigm in the host-parasite interaction. Parasite Immunol 45(6):e12980. https:\/\/doi.org\/10.1111\/pim.12980","journal-title":"Parasite Immunol"},{"issue":"W1","key":"4437_CR45","doi-asserted-by":"publisher","first-page":"W459","DOI":"10.1093\/nar\/gkad276","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart DS, Ren L, Leong-Sit J, Saha S, Grant JR, Stothard P, Singh U, Kropielnicki A, Oler E, Peters H, Gautam V (2023) Plasmapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res 51(W1):W459\u2013W467. https:\/\/doi.org\/10.1093\/nar\/gkad276","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"4437_CR46","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.838698","volume":"24","author":"Y Yang","year":"2022","unstructured":"Yang Y, Yu Q, Wang M, Zhao R, Liu H, Xun L, Xia Y (2022) Escherichia coli BW25113 competent cells prepared using a simple chemical method have unmatched transformation and cloning efficiencies. Front Microbiol 24(13):838698. https:\/\/doi.org\/10.3389\/fmicb.2022.838698","journal-title":"Front Microbiol"},{"issue":"1","key":"4437_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1472-765X.2010.02958.x","volume":"52","author":"J Zhao","year":"2011","unstructured":"Zhao J, Dang H (2011) Identification of a globally distributed clinical streptomycin-resistance plasmid and other resistance determinants in a coastal bay of China. Lett Appl Microbiol 52(1):1\u20138. https:\/\/doi.org\/10.1111\/j.1472-765X.2010.02958.x","journal-title":"Lett Appl Microbiol"}],"container-title":["Archives of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-025-04437-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-025-04437-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-025-04437-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T13:24:52Z","timestamp":1758720292000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00203-025-04437-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,9]]},"references-count":46,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10]]}},"alternative-id":["4437"],"URL":"https:\/\/doi.org\/10.1007\/s00203-025-04437-6","relation":{"references":[{"id-type":"doi","id":"10.1042\/BSR20204114","asserted-by":"subject"}]},"ISSN":["0302-8933","1432-072X"],"issn-type":[{"type":"print","value":"0302-8933"},{"type":"electronic","value":"1432-072X"}],"subject":[],"published":{"date-parts":[[2025,9,9]]},"assertion":[{"value":"29 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2025","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 August 2025","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 September 2025","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"259"}}