{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:48:04Z","timestamp":1765234084396,"version":"3.46.0"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,8]]},"DOI":"10.7759\/cureus.98748","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:38:26Z","timestamp":1765233506000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-Cell Sequencing of a Bile Sample From an Acute Cholecystitis Patient"],"prefix":"10.7759","author":[{"given":"Mari","family":"Tohya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazunori","family":"Murase","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masaaki","family":"Minagawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akio","family":"Saiura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ichiro","family":"Nakagawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teruo","family":"Kirikae","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shin","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4469","article-title":"The trajectory of microbial single-cell sequencing","volume":"14","author":"Woyke T","year":"2017","unstructured":"Woyke T, Doud DF, Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods. 2017, 14:1045-54. 10.1038\/nmeth.4469","journal-title":"Nat Methods"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-020-10844-0","article-title":"Microbial single-cell omics: the crux of the matter","volume":"104","author":"Kaster AK","year":"2020","unstructured":"Kaster AK, Sobol MS. Microbial single-cell omics: the crux of the matter. Appl Microbiol Biotechnol. 2020, 104:8209-20. 10.1007\/s00253-020-10844-0","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01152-4","article-title":"Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics","volume":"9","author":"Arikawa K","year":"2021","unstructured":"Arikawa K, Ide K, Kogawa M, et al.. Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics. Microbiome. 2021, 9:202. 10.1186\/s40168-021-01152-4","journal-title":"Microbiome"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.06.040","article-title":"Single-cell approaches in human microbiome research","volume":"185","author":"Llor\u00e9ns-Rico V","year":"2022","unstructured":"Llor\u00e9ns-Rico V, Simcock JA, Huys GR, Raes J. Single-cell approaches in human microbiome research. Cell. 2022, 185:2725-38. 10.1016\/j.cell.2022.06.040","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.955404","article-title":"Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing","volume":"13","author":"Ide K","year":"2022","unstructured":"Ide K, Saeki T, Arikawa K, et al.. Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing. Front Microbiol. 2022, 13:955404. 10.3389\/fmicb.2022.955404","journal-title":"Front Microbiol"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick RR","year":"2017","unstructured":"Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017, 13:e1005595. 10.1371\/journal.pcbi.1005595","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann T","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014, 30:2068-9. 10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis KT","year":"2005","unstructured":"Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A. 2005, 102:2567-72. 10.1073\/pnas.0409727102","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1007\/s10482-017-0844-4","article-title":"A large-scale evaluation of algorithms to calculate average nucleotide identity","volume":"110","author":"Yoon SH","year":"2017","unstructured":"Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek. 2017, 110:1281-6. 10.1007\/s10482-017-0844-4","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref10","unstructured":"Genome-to-genome distance calculator 3.0. (2023). Accessed. June 23, 2023: https:\/\/ggdc.dsmz.de\/ggdc.php."},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon SH","year":"2017","unstructured":"Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017, 67:1613-7. 10.1099\/ijsem.0.001755","journal-title":"Int J Syst Evol Microbiol"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-019-0779-2","article-title":"Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota","volume":"8","author":"Chijiiwa R","year":"2020","unstructured":"Chijiiwa R, Hosokawa M, Kogawa M, et al.. Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota. Microbiome. 2020, 8:5. 10.1186\/s40168-019-0779-2","journal-title":"Microbiome"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen S","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018, 34:i884-90. 10.1093\/bioinformatics\/bty560","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li H","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25:1754-60. 10.1093\/bioinformatics\/btp324","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li H","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010, 26:589-95. 10.1093\/bioinformatics\/btp698","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-376","article-title":"GenomeMatcher: a graphical user interface for DNA sequence comparison","volume":"9","author":"Ohtsubo Y","year":"2008","unstructured":"Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics. 2008, 9:376. 10.1186\/1471-2105-9-376","journal-title":"BMC Bioinformatics"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1126\/science.1167140","article-title":"The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria","volume":"323","author":"Moran NA","year":"2009","unstructured":"Moran NA, McLaughlin HJ, Sorek R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science. 2009, 323:379-82. 10.1126\/science.1167140","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia V","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E, et al.. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020, 75:3491-500. 10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho C","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009, 10:421. 10.1186\/1471-2105-10-421","journal-title":"BMC Bioinformatics"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen KG","year":"2014","unstructured":"Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014, 52:1501-10. 10.1128\/JCM.03617-13","journal-title":"J Clin Microbiol"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01269-20","article-title":"In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data","volume":"58","author":"Malberg Tetzschner AM","year":"2020","unstructured":"Malberg Tetzschner AM, Johnson JR, Johnston BD, Lund O, Scheutz F. In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data. J Clin Microbiol. 2020, 58:10.1128\/JCM.01269-20","journal-title":"J Clin Microbiol"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2011.455","article-title":"Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research","volume":"7","author":"Zhang M","year":"2012","unstructured":"Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, Zhang HB. Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nat Protoc. 2012, 7:467-78. 10.1038\/nprot.2011.455","journal-title":"Nat Protoc"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02598","article-title":"Corrigendum: phylogenetic analyses of Shigella and enteroinvasive Escherichia coli for the identification of molecular epidemiological markers: Whole-genome comparative analysis does not support distinct genera designation","volume":"8","author":"Pettengill EA","year":"2017","unstructured":"Pettengill EA, Pettengill JB, Binet R. Corrigendum: phylogenetic analyses of Shigella and enteroinvasive Escherichia coli for the identification of molecular epidemiological markers: Whole-genome comparative analysis does not support distinct genera designation. Front Microbiol. 2017, 8:2598. 10.3389\/fmicb.2017.02598","journal-title":"Front Microbiol"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01790-16","article-title":"Identification of Escherichia coli and Shigella Species from whole-genome sequences","volume":"55","author":"Chattaway MA","year":"2017","unstructured":"Chattaway MA, Schaefer U, Tewolde R, Dallman TJ, Jenkins C. Identification of Escherichia coli and Shigella Species from whole-genome sequences. J Clin Microbiol. 2017, 55:616-23. 10.1128\/JCM.01790-16","journal-title":"J Clin Microbiol"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00021-17","article-title":"Non-toxin-producing Bacillus cereus Strains belonging to the B. anthracis clade isolated from the international space station","volume":"2","author":"Venkateswaran K","year":"2017","unstructured":"Venkateswaran K, Singh NK, Checinska Sielaff A, et al.. Non-toxin-producing Bacillus cereus Strains belonging to the B. anthracis clade isolated from the international space station. mSystems. 2017, 2:10.1128\/mSystems.00021-17","journal-title":"mSystems"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0020122","article-title":"Anthrax, but not Bacillus anthracis?","volume":"2","author":"Okinaka R","year":"2006","unstructured":"Okinaka R, Pearson T, Keim P. Anthrax, but not Bacillus anthracis?. PLoS Pathog. 2006, 2:e122. 10.1371\/journal.ppat.0020122","journal-title":"PLoS Pathog"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1126\/science.abm1483","article-title":"High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome","volume":"376","author":"Zheng W","year":"2022","unstructured":"Zheng W, Zhao S, Yin Y, et al.. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science. 2022, 376:eabm1483. 10.1126\/science.abm1483","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1080\/01635589109514161","article-title":"Bile salt\/acid induction of DNA damage in bacterial and mammalian cells: implications for colon cancer","volume":"16","author":"Kandell RL","year":"1991","unstructured":"Kandell RL, Bernstein C. Bile salt\/acid induction of DNA damage in bacterial and mammalian cells: implications for colon cancer. Nutr Cancer. 1991, 16:227-38. 10.1080\/01635589109514161","journal-title":"Nutr Cancer"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.26769-0","article-title":"Bile-salt-mediated induction of antimicrobial and bile resistance in Salmonella typhimurium","volume":"150","author":"Prouty AM","year":"2004","unstructured":"Prouty AM, Brodsky IE, Falkow S, Gunn JS. Bile-salt-mediated induction of antimicrobial and bile resistance in Salmonella typhimurium. Microbiology (Reading). 2004, 150:775-83. 10.1099\/mic.0.26769-0","journal-title":"Microbiology (Reading)"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0074647","article-title":"Bile salts affect expression of Escherichia coli O157:H7 genes for virulence and iron acquisition, and promote growth under iron limiting conditions","volume":"8","author":"Hamner S","year":"2013","unstructured":"Hamner S, McInnerney K, Williamson K, Franklin MJ, Ford TE. Bile salts affect expression of Escherichia coli O157:H7 genes for virulence and iron acquisition, and promote growth under iron limiting conditions. PLoS One. 2013, 8:e74647. 10.1371\/journal.pone.0074647","journal-title":"PLoS One"}],"container-title":["Cureus"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cureus.com\/articles\/380837-single-cell-sequencing-of-a-bile-sample-from-an-acute-cholecystitis-patient","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:38:27Z","timestamp":1765233507000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cureus.com\/articles\/380837-single-cell-sequencing-of-a-bile-sample-from-an-acute-cholecystitis-patient"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,8]]},"references-count":30,"URL":"https:\/\/doi.org\/10.7759\/cureus.98748","relation":{},"ISSN":["2168-8184"],"issn-type":[{"value":"2168-8184","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12,8]]}}}