{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T09:35:46Z","timestamp":1790501746570,"version":"4.1.0"},"reference-count":40,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2022,9,30]],"date-time":"2022-09-30T00:00:00Z","timestamp":1664496000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/R022526\/1"],"award-info":[{"award-number":["BB\/R022526\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/R012504\/1"],"award-info":[{"award-number":["BB\/R012504\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/CCG1720\/1"],"award-info":[{"award-number":["BB\/CCG1720\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/P022073\/1"],"award-info":[{"award-number":["BB\/P022073\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:p>Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for <jats:italic>in vitro<\/jats:italic> evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of <jats:italic>\n                     <jats:named-content content-type=\"genus\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3291\" xlink:type=\"simple\">Salmonella<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.<\/jats:p>","DOI":"10.1099\/mgen.0.000871","type":"journal-article","created":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T17:16:56Z","timestamp":1663694216000},"source":"Crossref","is-referenced-by-count":8,"title":["Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella"],"prefix":"10.1099","volume":"8","author":[{"given":"Matt","family":"Bawn","sequence":"first","affiliation":[{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johana","family":"Hernandez","sequence":"additional","affiliation":[{"name":"Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleftheria","family":"Trampari","sequence":"additional","affiliation":[{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaetan","family":"Thilliez","sequence":"additional","affiliation":[{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Quince","sequence":"additional","affiliation":[{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark A.","family":"Webber","sequence":"additional","affiliation":[{"name":"Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UA, UK"},{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert A.","family":"Kingsley","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK"},{"name":"Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil","family":"Hall","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK"},{"name":"Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iain C.","family":"Macaulay","sequence":"additional","affiliation":[{"name":"Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK"},{"name":"School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1038\/nature18959"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2019.02.003"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.48"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-017-0012-7"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188470"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1126\/science.aav6390"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6976.12015"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4469"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-019-0779-2"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1126\/science.1248575"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-021-01178-4"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.082089499"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.6.3342-3347.2005"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0704662104"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0006864"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0010314"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2720"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201700312"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-019-0557-y"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.46"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2015.23"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1126\/science.1099390"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1126\/science.277.5331.1453"},{"key":"R24","article-title":"BBMap: A Fast, Accurate, Splice-Aware Aligner. United States","author":"Bushnell","year":"2014"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0554-6_12"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl446"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14694.1"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2014.04.007"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1126\/science.aak9787"},{"key":"R32","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/S0021-9258(18)48474-8","article-title":"8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G----T and A----C substitutions","volume":"267","author":"Cheng","year":"1992","journal-title":"J Biol Chem"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00121-18"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01415-16"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M405048200"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1038\/s43705-021-00041-z"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.05903.x"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14685-3"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1016\/j.resmic.2018.01.003"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3370"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000871?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T18:26:46Z","timestamp":1702578406000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000871"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,30]]},"references-count":40,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2022,9,30]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000871","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,30]]}}}