{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,11]],"date-time":"2026-11-11T03:59:06Z","timestamp":1794369546009,"version":"4.9.0"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T00:00:00Z","timestamp":1732665600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T00:00:00Z","timestamp":1732665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/s41467-024-54797-8","type":"journal-article","created":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T13:50:31Z","timestamp":1732715431000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":76,"title":["Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn\u2019s disease"],"prefix":"10.1038","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0727-7638","authenticated-orcid":false,"given":"Shintaro","family":"Akiyama","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8444-9272","authenticated-orcid":false,"given":"Suguru","family":"Nishijima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasushi","family":"Kojima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2202-5527","authenticated-orcid":false,"given":"Moto","family":"Kimura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitsuru","family":"Ohsugi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohjiro","family":"Ueki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5269-4006","authenticated-orcid":false,"given":"Masashi","family":"Mizokami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahira","family":"Hattori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1977-8707","authenticated-orcid":false,"given":"Kiichiro","family":"Tsuchiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi","family":"Uemura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Kawai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2627-833X","authenticated-orcid":false,"given":"Peer","family":"Bork","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7255-4024","authenticated-orcid":false,"given":"Naoyoshi","family":"Nagata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,11,27]]},"reference":[{"key":"54797_CR1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-9-r79","volume":"13","author":"XC Morgan","year":"2012","unstructured":"Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).","journal-title":"Genome Biol."},{"key":"54797_CR2","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","volume":"4","author":"EA Franzosa","year":"2019","unstructured":"Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293\u2013305 (2019).","journal-title":"Nat. Microbiol."},{"key":"54797_CR3","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/j.chom.2015.09.008","volume":"18","author":"JD Lewis","year":"2015","unstructured":"Lewis, J. D. et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric crohn\u2019s disease. Cell Host Microbe 18, 489\u2013500 (2015).","journal-title":"Cell Host Microbe"},{"key":"54797_CR4","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","volume":"15","author":"D Gevers","year":"2014","unstructured":"Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn\u2019s disease. Cell Host Microbe 15, 382\u2013392 (2014).","journal-title":"Cell Host Microbe"},{"key":"54797_CR5","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655\u2013662 (2019).","journal-title":"Nature"},{"key":"54797_CR6","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1038\/nbt.2939","volume":"32","author":"HB Nielsen","year":"2014","unstructured":"Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822\u2013828 (2014).","journal-title":"Nat. Biotechnol."},{"key":"54797_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix050","volume":"6","author":"Q He","year":"2017","unstructured":"He, Q. et al. Two distinct metacommunities characterize the gut microbiota in Crohn\u2019s disease patients. Gigascience 6, 1\u201311 (2017).","journal-title":"Gigascience"},{"key":"54797_CR8","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1136\/gutjnl-2017-314903","volume":"67","author":"C Palmela","year":"2018","unstructured":"Palmela, C. et al. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 67, 574\u2013587 (2018).","journal-title":"Gut"},{"key":"54797_CR9","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1879-9","volume":"20","author":"J Seishima","year":"2019","unstructured":"Seishima, J. et al. Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host. Genome Biol. 20, 252 (2019).","journal-title":"Genome Biol."},{"key":"54797_CR10","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1002\/ibd.22971","volume":"19","author":"B Dogan","year":"2013","unstructured":"Dogan, B. et al. Multidrug resistance is common in Escherichia coli associated with ileal Crohn\u2019s disease. Inflamm. Bowel Dis. 19, 141\u2013150 (2013).","journal-title":"Inflamm. Bowel Dis."},{"key":"54797_CR11","doi-asserted-by":"publisher","first-page":"3018","DOI":"10.1111\/jam.15154","volume":"131","author":"Y Xia","year":"2021","unstructured":"Xia, Y. et al. Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease. J. Appl. Microbiol. 131, 3018\u20133031 (2021).","journal-title":"J. Appl. Microbiol."},{"key":"54797_CR12","doi-asserted-by":"publisher","first-page":"2879","DOI":"10.1016\/j.cell.2022.07.003","volume":"185","author":"S Federici","year":"2022","unstructured":"Federici, S. et al. Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation. Cell 185, 2879\u20132898 e2824 (2022).","journal-title":"Cell"},{"key":"54797_CR13","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1007\/s10123-020-00121-5","volume":"23","author":"JL Balcazar","year":"2020","unstructured":"Balcazar, J. L. Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment. Int. Microbiol. 23, 475\u2013479 (2020).","journal-title":"Int. Microbiol."},{"key":"54797_CR14","doi-asserted-by":"publisher","first-page":"10400","DOI":"10.1073\/pnas.1601060113","volume":"113","author":"P Manrique","year":"2016","unstructured":"Manrique, P. et al. Healthy human gut phageome. Proc. Natl. Acad. Sci. USA 113, 10400\u201310405 (2016).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"54797_CR15","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1016\/j.chom.2019.10.009","volume":"26","author":"AG Clooney","year":"2019","unstructured":"Clooney, A. G. et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe 26, 764\u2013778.e765 (2019).","journal-title":"Cell Host Microbe"},{"key":"54797_CR16","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.cell.2015.01.002","volume":"160","author":"JM Norman","year":"2015","unstructured":"Norman, J. M. et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160, 447\u2013460 (2015).","journal-title":"Cell"},{"key":"54797_CR17","doi-asserted-by":"publisher","first-page":"e969","DOI":"10.1016\/S2666-5247(22)00203-8","volume":"3","author":"F Zhang","year":"2022","unstructured":"Zhang, F., Aschenbrenner, D., Yoo, J. Y. & Zuo, T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. Lancet Microbe 3, e969\u2013e983 (2022).","journal-title":"Lancet Microbe"},{"key":"54797_CR18","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","volume":"66","author":"H Sokol","year":"2017","unstructured":"Sokol, H. et al. Fungal microbiota dysbiosis in IBD. Gut 66, 1039\u20131048 (2017).","journal-title":"Gut"},{"key":"54797_CR19","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1136\/gut.42.6.788","volume":"42","author":"JF Quinton","year":"1998","unstructured":"Quinton, J. F. et al. Anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease: prevalence and diagnostic role. Gut 42, 788\u2013791 (1998).","journal-title":"Gut"},{"key":"54797_CR20","doi-asserted-by":"publisher","first-page":"e66019","DOI":"10.1371\/journal.pone.0066019","volume":"8","author":"C Hoffmann","year":"2013","unstructured":"Hoffmann, C. et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE 8, e66019 (2013).","journal-title":"PLoS ONE"},{"key":"54797_CR21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34535-8","volume":"13","author":"Q Liu","year":"2022","unstructured":"Liu, Q. et al. Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome. Nat. Commun. 13, 6806 (2022).","journal-title":"Nat. Commun."},{"key":"54797_CR22","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1038\/s41591-021-01289-7","volume":"27","author":"M Mac Aogain","year":"2021","unstructured":"Mac Aogain, M. et al. Integrative microbiomics in bronchiectasis exacerbations. Nat. Med. 27, 688\u2013699 (2021).","journal-title":"Nat. Med."},{"key":"54797_CR23","doi-asserted-by":"crossref","unstructured":"Mearin, F. et al. Bowel Disorders. Gastroenterology 150, 1393\u20131407 (2016).","DOI":"10.1053\/j.gastro.2016.02.031"},{"key":"54797_CR24","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1053\/j.gastro.2020.09.056","volume":"160","author":"M Lee","year":"2021","unstructured":"Lee, M. & Chang, E. B. Inflammatory bowel diseases (IBD) and the microbiome-searching the crime scene for clues. Gastroenterology 160, 524\u2013537 (2021).","journal-title":"Gastroenterology"},{"key":"54797_CR25","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1053\/j.gastro.2019.11.294","volume":"158","author":"R Pittayanon","year":"2020","unstructured":"Pittayanon, R. et al. Differences in gut microbiota in patients with vs without inflammatory bowel diseases: a systematic review. Gastroenterology 158, 930\u2013946.e931 (2020).","journal-title":"Gastroenterology"},{"key":"54797_CR26","doi-asserted-by":"publisher","first-page":"e00181","DOI":"10.1128\/CMR.00181-19","volume":"33","author":"DMP De Oliveira","year":"2020","unstructured":"De Oliveira, D. M. P. et al. Antimicrobial resistance in ESKAPE pathogens. Clin. Microbiol. Rev. 33, e00181\u201319 (2020).","journal-title":"Clin. Microbiol. Rev."},{"key":"54797_CR27","doi-asserted-by":"publisher","first-page":"100839","DOI":"10.1016\/j.genrep.2020.100839","volume":"21","author":"M Puzari","year":"2020","unstructured":"Puzari, M., Baishya, S., Choudhury, M. D. & Chetia, P. Gene network analysis of efflux pump proteins in Shigella spp. Gene Reports 21, 100839 (2020).","journal-title":"Gene Reports"},{"key":"54797_CR28","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1111\/j.1600-065X.2012.01146.x","volume":"249","author":"D Tang","year":"2012","unstructured":"Tang, D., Kang, R., Coyne, C. B., Zeh, H. J. & Lotze, M. T. PAMPs and DAMPs: signal 0s that spur autophagy and immunity. Immunol. Rev. 249, 158\u2013175 (2012).","journal-title":"Immunol. Rev."},{"key":"54797_CR29","first-page":"78","volume":"5","author":"TC Yang","year":"2012","unstructured":"Yang, T. C. et al. Screening of the Salmonella paratyphi A CMCC 50973 strain outer membrane proteins for the identification of potential vaccine targets. Mol. Med. Rep. 5, 78\u201383 (2012).","journal-title":"Mol. Med. Rep."},{"key":"54797_CR30","doi-asserted-by":"publisher","first-page":"6099","DOI":"10.1128\/AEM.69.10.6099-6105.2003","volume":"69","author":"C Fitzgerald","year":"2003","unstructured":"Fitzgerald, C., Sherwood, R., Gheesling, L. L., Brenner, F. W. & Fields, P. I. Molecular analysis of the rfb O antigen gene cluster of Salmonella enterica serogroup O:6,14 and development of a serogroup-specific PCR assay. Appl. Environ. Microbiol. 69, 6099\u20136105 (2003).","journal-title":"Appl. Environ. Microbiol."},{"key":"54797_CR31","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1099\/mic.0.051599-0","volume":"158","author":"S Heuston","year":"2012","unstructured":"Heuston, S., Begley, M., Gahan, C. G. M. & Hill, C. Isoprenoid biosynthesis in bacterial pathogens. Microbiology 158, 1389\u20131401 (2012).","journal-title":"Microbiology"},{"key":"54797_CR32","doi-asserted-by":"publisher","first-page":"173750","DOI":"10.1016\/j.ejphar.2020.173750","volume":"891","author":"AS Bhagavathula","year":"2021","unstructured":"Bhagavathula, A. S., Clark, C. & Rahmani, J. Statin use and new-onset of inflammatory bowel disease: a systematic review and meta-analysis of over ten million participants. Eur. J. Pharmacol. 891, 173750 (2021).","journal-title":"Eur. J. Pharmacol."},{"key":"54797_CR33","doi-asserted-by":"publisher","first-page":"1955","DOI":"10.1126\/science.1109051","volume":"307","author":"JL Sonnenburg","year":"2005","unstructured":"Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955\u20131959 (2005).","journal-title":"Science"},{"key":"54797_CR34","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/nrgastro.2013.35","volume":"10","author":"ME Johansson","year":"2013","unstructured":"Johansson, M. E., Sjovall, H. & Hansson, G. C. The gastrointestinal mucus system in health and disease. Nat. Rev. Gastroenterol. Hepatol. 10, 352\u2013361 (2013).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"54797_CR35","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1093\/ecco-jcc\/jjv223","volume":"10","author":"M Alipour","year":"2016","unstructured":"Alipour, M. et al. Mucosal barrier depletion and loss of bacterial diversity are primary abnormalities in paediatric ulcerative colitis. J. Crohns Colitis 10, 462\u2013471 (2016).","journal-title":"J. Crohns Colitis"},{"key":"54797_CR36","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","volume":"399","author":"Antimicrobial Resistance Collaborators","year":"2022","unstructured":"Antimicrobial Resistance Collaborators Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629\u2013655 (2022).","journal-title":"Lancet"},{"key":"54797_CR37","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1128\/AAC.45.1.263-266.2001","volume":"45","author":"KV Singh","year":"2001","unstructured":"Singh, K. V., Malathum, K. & Murray, B. E. Disruption of an Enterococcus faecium species-specific gene, a homologue of acquired macrolide resistance genes of staphylococci, is associated with an increase in macrolide susceptibility. Antimicrob. Agents Chemother. 45, 263\u2013266 (2001).","journal-title":"Antimicrob. Agents Chemother."},{"key":"54797_CR38","doi-asserted-by":"publisher","first-page":"251","DOI":"10.3390\/antibiotics9050251","volume":"9","author":"M Martinez-Medina","year":"2020","unstructured":"Martinez-Medina, M. et al. Antimicrobial resistance profiles of adherent invasive Escherichia coli show increased resistance to beta-lactams. Antibiotics 9, 251 (2020).","journal-title":"Antibiotics"},{"key":"54797_CR39","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1093\/ecco-jcc\/jjac064","volume":"16","author":"M Titecat","year":"2022","unstructured":"Titecat, M. et al. Safety and efficacy of an AIEC-targeted bacteriophage cocktail in a mice colitis model. J Crohns Colitis 16, 1617\u20131627 (2022).","journal-title":"J Crohns Colitis"},{"key":"54797_CR40","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.1172\/JCI30504","volume":"117","author":"N Barnich","year":"2007","unstructured":"Barnich, N. et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease. J. Clin. Invest. 117, 1566\u20131574 (2007).","journal-title":"J. Clin. Invest."},{"key":"54797_CR41","doi-asserted-by":"publisher","first-page":"462","DOI":"10.3390\/antibiotics9080462","volume":"9","author":"S Zhang","year":"2020","unstructured":"Zhang, S. et al. Short chain fatty acids modulate the growth and virulence of pathosymbiont escherichia coli and host response. Antibiotics 9, 462 (2020).","journal-title":"Antibiotics"},{"key":"54797_CR42","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1053\/j.gastro.2022.03.054","volume":"163","author":"N Nagata","year":"2022","unstructured":"Nagata, N. et al. Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study. Gastroenterology 163, 222\u2013238 (2022).","journal-title":"Gastroenterology"},{"key":"54797_CR43","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1053\/j.gastro.2022.06.070","volume":"163","author":"N Nagata","year":"2022","unstructured":"Nagata, N. et al. Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome. Gastroenterology 163, 1038\u20131052 (2022).","journal-title":"Gastroenterology"},{"key":"54797_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32832-w","volume":"13","author":"S Nishijima","year":"2022","unstructured":"Nishijima, S. et al. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat. Commun. 13, 5252 (2022).","journal-title":"Nat. Commun."},{"key":"54797_CR45","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/j.cgh.2012.12.034","volume":"11","author":"N Nagata","year":"2013","unstructured":"Nagata, N. et al. Combined endoscopy, aspiration, and biopsy analysis for identifying infectious colitis in patients with ileocecal ulcers. Clin. Gastroenterol. Hepatol. 11, 673\u2013680.e672 (2013).","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"54797_CR46","doi-asserted-by":"publisher","first-page":"256","DOI":"10.5582\/ddt.2019.01071","volume":"13","author":"N Nagata","year":"2019","unstructured":"Nagata, N. et al. Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota. Drug Discov. Ther. 13, 256\u2013260 (2019).","journal-title":"Drug Discov. Ther."},{"key":"54797_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-40182-9","volume":"9","author":"N Nagata","year":"2019","unstructured":"Nagata, N. et al. Effects of bowel preparation on the human gut microbiome and metabolome. Sci. Rep. 9, 4042 (2019).","journal-title":"Sci. Rep."},{"key":"54797_CR48","doi-asserted-by":"publisher","first-page":"2265","DOI":"10.1002\/(SICI)1097-0258(19981015)17:19<2265::AID-SIM918>3.0.CO;2-B","volume":"17","author":"RB D\u2019Agostino Jr.","year":"1998","unstructured":"D\u2019Agostino, R. B. Jr. Propensity score methods for bias reduction in the comparison of a treatment to a non-randomized control group. Stat. Med. 17, 2265\u20132281 (1998).","journal-title":"Stat. Med."},{"key":"54797_CR49","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1093\/dnares\/dsw002","volume":"23","author":"S Nishijima","year":"2016","unstructured":"Nishijima, S. et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res. 23, 125\u2013133 (2016).","journal-title":"DNA Res."},{"key":"54797_CR50","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","volume":"27","author":"R Schmieder","year":"2011","unstructured":"Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863\u2013864 (2011).","journal-title":"Bioinformatics"},{"key":"54797_CR51","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1089\/cmb.2017.0096","volume":"24","author":"A Kechin","year":"2017","unstructured":"Kechin, A., Boyarskikh, U., Kel, A. & Filipenko, M. cutPrimers: a new tool for accurate cutting of primers from reads of targeted next generation sequencing. J Comput. Biol. 24, 1138\u20131143 (2017).","journal-title":"J Comput. Biol."},{"key":"54797_CR52","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"54797_CR53","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01410-z","volume":"10","author":"HJ Ruscheweyh","year":"2022","unstructured":"Ruscheweyh, H. J. et al. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome 10, 212 (2022).","journal-title":"Microbiome"},{"key":"54797_CR54","doi-asserted-by":"publisher","first-page":"D587","DOI":"10.1093\/nar\/gkac963","volume":"51","author":"M Kanehisa","year":"2023","unstructured":"Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587\u2013D592 (2023).","journal-title":"Nucleic Acids Res."},{"key":"54797_CR55","doi-asserted-by":"crossref","first-page":"D517","DOI":"10.1093\/nar\/gkz1136","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517\u2013D525 (2020).","journal-title":"Nucleic Acids Res."},{"key":"54797_CR56","doi-asserted-by":"publisher","first-page":"2848","DOI":"10.1038\/ismej.2017.139","volume":"11","author":"F Beghini","year":"2017","unstructured":"Beghini, F. et al. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME J. 11, 2848\u20132863 (2017).","journal-title":"ISME J."},{"key":"54797_CR57","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"54797_CR58","doi-asserted-by":"publisher","first-page":"bbaa290","DOI":"10.1093\/bib\/bbaa290","volume":"22","author":"S Peschel","year":"2021","unstructured":"Peschel, S., Muller, C. L., von Mutius, E., Boulesteix, A. L. & Depner, M. NetCoMi: network construction and comparison for microbiome data in R. Brief. Bioinform. 22, bbaa290 (2021).","journal-title":"Brief. Bioinform."},{"key":"54797_CR59","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14021369","author":"S Akiyama","year":"2024","unstructured":"Akiyama, S. ShintaroAkiyama\/IBD-multi-biome: IBD multi-biome analysis (v1.0.0). Zenodo. https:\/\/doi.org\/10.5281\/zenodo.14021369 (2024).","journal-title":"Zenodo."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-54797-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-54797-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-54797-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T15:07:35Z","timestamp":1732720055000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-54797-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,27]]},"references-count":59,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["54797"],"URL":"https:\/\/doi.org\/10.1038\/s41467-024-54797-8","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,27]]},"assertion":[{"value":"27 January 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 November 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"10291"}}