{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T16:08:21Z","timestamp":1745856501018},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-242","type":"journal-article","created":{"date-parts":[[2014,7,16]],"date-time":"2014-07-16T03:01:43Z","timestamp":1405479703000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Accurate genome relative abundance estimation for closely related species in a metagenomic sample"],"prefix":"10.1186","volume":"15","author":[{"given":"Michael B","family":"Sohn","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingling","family":"An","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naruekamol","family":"Pookhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qike","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,7,16]]},"reference":[{"issue":"6","key":"6526_CR1","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1093\/bib\/bbs039","volume":"13","author":"H Teeling","year":"2012","unstructured":"Teeling H, Gl\u00f6ckner FO: Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. Brief Bioinform. 2012, 13 (6): 728-742.","journal-title":"Brief Bioinform"},{"key":"6526_CR2","volume-title":"Metagenomics - a guide from sampling to data analysis","author":"T Thomas","year":"2012","unstructured":"Thomas T, Gilbert J, Meyer F: Metagenomics - a guide from sampling to data analysis. Microb Inform Exp. 2012, 2 (3): [http:\/\/www.microbialinformaticsj.com\/content\/2\/1\/3],"},{"issue":"6","key":"6526_CR3","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1093\/bib\/bbs031","volume":"13","author":"J Dr\u00f6ge","year":"2012","unstructured":"Dr\u00f6ge J, McHardy AC: Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinform. 2012, 13 (6): 645-655.","journal-title":"Brief Bioinform"},{"issue":"6","key":"6526_CR4","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1093\/bib\/bbs054","volume":"13","author":"SS Mande","year":"2012","unstructured":"Mande SS, Mohammed MH, Ghosh TS: Classification of metagenomic sequences: methods and challenges. Brief Bioinform. 2012, 13 (6): 669-681.","journal-title":"Brief Bioinform"},{"key":"6526_CR5","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1101\/gr.5969107","volume":"17","author":"DH Huson","year":"2007","unstructured":"Huson DH, Auch AF, Qi J, Schuster SC: Megan analysis of metagenomic data. Genome Res. 2007, 17: 377-386.","journal-title":"Genome Res"},{"key":"6526_CR6","doi-asserted-by":"publisher","first-page":"1722","DOI":"10.1093\/bioinformatics\/btp317","volume":"25","author":"MM Haque","year":"2009","unstructured":"Haque MM, Ghosh TS, Komanduri D, Mande SS: Sort-items: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics. 2009, 25: 1722-1730.","journal-title":"Bioinformatics"},{"issue":"14","key":"6526_CR7","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1093\/nar\/gkr225","volume":"39","author":"W Gerlach","year":"2011","unstructured":"Gerlach W, Stoye J: Taxonomic classification of metagenomic shotgun sequences with carma3. Nucleic Acids Res. 2011, 39 (14): 91-","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"6526_CR8","doi-asserted-by":"publisher","first-page":"1000593","DOI":"10.1371\/journal.pcbi.1000593","volume":"5","author":"FE Angly","year":"2009","unstructured":"Angly FE, Willner D, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barrott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F, Prieto-Dav\u00f3 A: The gaas metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009, 5 (12): 1000593-","journal-title":"PLoS Comput Biol"},{"issue":"12","key":"6526_CR9","first-page":"27992","volume":"6","author":"LC Xia","year":"2011","unstructured":"Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F: Accurate genome relative abundance estimation based on shotgun metagenomic reads. Brief Bioinform. 2011, 6 (12): 27992-","journal-title":"Brief Bioinform"},{"issue":"1","key":"6526_CR10","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1093\/nar\/gks803","volume":"41","author":"MS Lindner","year":"2013","unstructured":"Lindner MS, Renard BY: Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res. 2013, 41 (1): 10-","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"6526_CR11","doi-asserted-by":"publisher","first-page":"46450","DOI":"10.1371\/journal.pone.0046450","volume":"7","author":"H Jiang","year":"2012","unstructured":"Jiang H, An L, Lin SM, Feng G, Qiu Y: A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads. PLoS ONE. 2012, 7 (10): 46450-","journal-title":"PLoS ONE"},{"key":"6526_CR12","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL: Fast gapped-read alignment with bowtie 2. Nat Methods. 2012, 9: 357-359.","journal-title":"Nat Methods"},{"key":"6526_CR13","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1214\/009053604000000067","volume":"32","author":"B Efron","year":"2004","unstructured":"Efron B, Hastie T, Johnstone I, Tibshirani R: Least angle regression. Ann Stat. 2004, 32: 407-499.","journal-title":"Ann Stat"},{"issue":"1","key":"6526_CR14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","volume":"39","author":"AP Dempster","year":"1977","unstructured":"Dempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via the em algorithm. J R Stat Soc. 1977, 39 (1): 1-38.","journal-title":"J R Stat Soc"},{"key":"6526_CR15","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/ismej.2011.85","volume":"6","author":"P Belda-Ferre","year":"2012","unstructured":"Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Sim\u00f3n-Soro A, Pignatelli M, Mira A: The oral metagenome in health and disease. ISME. 2012, 6: 45-56.","journal-title":"ISME"},{"key":"6526_CR16","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/gb-2012-13-9-r79","volume":"13","author":"XC Morgan","year":"2012","unstructured":"Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C: Dysfunction of the intestinal micro biome in inflammatory bowel disease and treatment. Genome Biol. 2012, 13: 79-","journal-title":"Genome Biol"},{"key":"6526_CR17","unstructured":"The ncbi ftp site. 2012, [ftp:\/\/ftp.ncbi.nih.gov\/genomes\/bacteria\/],"},{"issue":"3","key":"6526_CR18","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/biomet\/68.3.589","volume":"68","author":"B Efron","year":"1981","unstructured":"Efron B: Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods. Biometrika. 1981, 68 (3): 589-599.","journal-title":"Biometrika"},{"key":"6526_CR19","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nmeth1043","volume":"4","author":"K Mavromatis","year":"2007","unstructured":"Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007, 4: 495-500.","journal-title":"Nat Methods"},{"issue":"10","key":"6526_CR20","doi-asserted-by":"publisher","first-page":"3373","DOI":"10.1371\/journal.pone.0003373","volume":"3","author":"DC Richter","year":"2008","unstructured":"Richter DC, Ott F, Auch AF, Schmid R, Huson DH: Metasima sequencing simulator for genomics and metagenomics. PLoS ONE. 2008, 3 (10): 3373-","journal-title":"PLoS ONE"},{"issue":"6","key":"6526_CR21","doi-asserted-by":"publisher","first-page":"37919","DOI":"10.1371\/journal.pone.0037919","volume":"7","author":"B Liu","year":"2012","unstructured":"Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Pop M, Amar S, Segr\u00e8 D: Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS ONE. 2012, 7 (6): 37919-","journal-title":"PLoS ONE"},{"issue":"19","key":"6526_CR22","doi-asserted-by":"publisher","first-page":"5002","DOI":"10.1128\/JB.00542-10","volume":"192","author":"FE Dewhirst","year":"2010","unstructured":"Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG: The human oral microbiome. J Bacteriol. 2010, 192 (19): 5002-5017.","journal-title":"J Bacteriol"},{"issue":"4","key":"6526_CR23","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1097\/00007611-200194040-00018","volume":"94","author":"J Ricaurte","year":"2001","unstructured":"Ricaurte J, Klein O, Labombardi V, Martinez V, Serpe A, Joy M: Rothia dentocariosa endocarditis complicated by multiple intracranial hemorrhages. Southern Med J. 2001, 94 (4): 438-440.","journal-title":"Southern Med J"},{"issue":"3","key":"6526_CR24","doi-asserted-by":"publisher","first-page":"195","DOI":"10.17796\/jcpd.32.3.vp657177815618l1","volume":"32","author":"S Tanaka","year":"2008","unstructured":"Tanaka S, Yoshida M, Murakami Y, Ogiwara T, Shoji M, Kobayashi S, Watanabe S, Machino M, Fujisawa S: The relationship of prevotella intermedia, prevotella nigrescens and prevotella melaninogenica in the supragingival plaque of children, caries and oral malodor. J Clin Pediatr Dent. 2008, 32 (3): 195-200.","journal-title":"J Clin Pediatr Dent"},{"issue":"2-3","key":"6526_CR25","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/0928-8244(93)90093-J","volume":"6","author":"E Kononen","year":"1993","unstructured":"Kononen E: Pigmented prevotella species in the periodontally healthy oral cavity. FEMS Immunol Med Microbiol. 1993, 6 (2-3): 201-205.","journal-title":"FEMS Immunol Med Microbiol"},{"key":"6526_CR26","unstructured":"Medical dictionary. 2013, [http:\/\/medical-dictionary.thefreedictionary.com\/prevotella+denticola],"},{"issue":"3","key":"6526_CR27","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.anaerobe.2008.04.004","volume":"14","author":"E Eribe","year":"2008","unstructured":"Eribe E, Olsen I: Leptotrichia species in human infections. Anaerobe. 2008, 14 (3): 131-137.","journal-title":"Anaerobe"},{"issue":"12","key":"6526_CR28","doi-asserted-by":"publisher","first-page":"1804","DOI":"10.1128\/CVI.00310-09","volume":"16","author":"G Matera","year":"2009","unstructured":"Matera G, Muto V, Vinci M, Zicca E, Abdollahi-Roodsaz S, van de Veerdonk, Kullberg BJ, Liberto MC, van der Meer, Netea MG, Joosten LA, Foc\u00e8\u0103 A: Receptor recognition of and immune intracellular pathways for veillonella parvula lipopolysaccharide. Clin Vaccine Immunol. 2009, 16 (12): 1804-1809.","journal-title":"Clin Vaccine Immunol"},{"issue":"6","key":"6526_CR29","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1111\/j.1600-0765.2012.01485.x","volume":"47","author":"L Gonalves","year":"2012","unstructured":"Gonalves L, Fermiano D, Feres M, Figueiredo L, Teles F, Mayer M, Faveri M: Levels of selenomonas species in generalized aggressive periodontitis. J Periodontal Res. 2012, 47 (6): 711-718.","journal-title":"J Periodontal Res"},{"key":"6526_CR30","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1111\/j.1600-0757.2009.00345.x","volume":"54","author":"K Ishihara","year":"2010","unstructured":"Ishihara K: Virulence factors of treponema denticola. Periodontology 2000. 2010, 54: 117-135.","journal-title":"Periodontology 2000"},{"issue":"1","key":"6526_CR31","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1111\/j.1399-302X.2007.00388.x","volume":"23","author":"C Van Hoogmoed","year":"2008","unstructured":"Van Hoogmoed C, Geertsema-Doornbusch G, Teughels W, Quirynen M, Busscher H, der Mei HC V: Reduction of periodontal pathogens adhesion by antagonistic strains. Oral Microbiol Immunol. 2008, 23 (1): 43-48.","journal-title":"Oral Microbiol Immunol"},{"key":"6526_CR32","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1201\/b10848-57","volume-title":"Molecular Detection of Human Bacterial Pathogens","author":"M Avita-Campos","year":"2011","unstructured":"Avita-Campos M, Simionato M, Gaetti-Jardim E: Prevotella. Molecular Detection of Human Bacterial Pathogens. Edited by: Liu D. 2011, CRC Press, Taylor & Francis Group, 585-600."},{"issue":"6","key":"6526_CR33","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1093\/bib\/bbs019","volume":"13","author":"C Ngom-Bru","year":"2012","unstructured":"Ngom-Bru C, Barretto C: Gut microbiota: methodological aspects to describe taxonomy and functionality. Brief Bioinform. 2012, 13 (6): 747-750.","journal-title":"Brief Bioinform"},{"issue":"6","key":"6526_CR34","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1093\/bib\/bbs002","volume":"13","author":"M Collison","year":"2011","unstructured":"Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR: Data mining the human gut microbiota for therapeutic targets. Brief Bioinform. 2011, 13 (6): 751-768.","journal-title":"Brief Bioinform"},{"key":"6526_CR35","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1126\/science.1110591","volume":"308","author":"PB Eckburg","year":"2005","unstructured":"Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA: Diversity of the human intestinal microbial flora. Science. 2005, 308: 1635-1638.","journal-title":"Science"},{"key":"6526_CR36","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1097\/MOG.0b013e328339536b","volume":"26","author":"H Sokol","year":"2010","unstructured":"Sokol H, Seksik P: The intestinal microbiota in inflammatory bowel diseases: time to connect with the host. Curr Opin Gastroenterol. 2010, 26: 327-331.","journal-title":"Curr Opin Gastroenterol"},{"key":"6526_CR37","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.ijantimicag.2012.10.012","volume":"41","author":"G Dubourg","year":"2013","unstructured":"Dubourg G, Lagier J, Armougom F, Robert C, Audoly G, Papazian L, Raoult D: High-level colonisation of the human gut by verrucomicrobia following broad-spectrum antibiotic treatment. Int J Antimicrob Agents. 2013, 41: 149-155.","journal-title":"Int J Antimicrob Agents"},{"key":"6526_CR38","doi-asserted-by":"publisher","first-page":"595","DOI":"10.2217\/fmb.11.31","volume":"6","author":"V Thota","year":"2011","unstructured":"Thota V, Dacha S, Natarajan A, Nerad J: Eggerthella lenta bacteremia in a crohn\u2019s disease patient after ileocecal resection. Future Microbiol. 2011, 6: 595-597.","journal-title":"Future Microbiol"},{"key":"6526_CR39","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1053\/j.gastro.2007.11.059","volume":"134","author":"R Sartor","year":"2008","unstructured":"Sartor R: Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008, 134: 577-594.","journal-title":"Gastroenterology"},{"key":"6526_CR40","doi-asserted-by":"publisher","first-page":"595","DOI":"10.2217\/fmb.11.108","volume":"6","author":"Y Liu","year":"2011","unstructured":"Liu Y, van Kruiningen H, West A, Cartun R, Cortot A, Colombel J: Immunocytochemical evidence of listeria, escherichia coli, and streptococcus antigens in crohn\u2019s disease. Future Microbiol. 2011, 6: 595-597.","journal-title":"Future Microbiol"},{"key":"6526_CR41","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/ctg.2013.9","volume":"4","author":"V P\u00e9rez-Brocal","year":"2013","unstructured":"P\u00e9rez-Brocal V, Garc\u00eda-L\u00f3pez R, V\u00e1zquez-Castellanos J, Nos P, Beltr\u00e1n B, Latorre A, Moya A: Study of the viral and microbial communities associated with crohn\u2019s disease: a metagenomic approach. Clin Transl Gastroenterol. 2013, 4: 36-","journal-title":"Clin Transl Gastroenterol"},{"key":"6526_CR42","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/nrgastro.2011.3","volume":"8","author":"S Man","year":"2011","unstructured":"Man S, Kaakoush N, Mitchell H: The role of bacteria and pattern-recognition receptors in crohn\u2019s disease. Nat Rev Gastroenterol Hepatol. 2011, 8: 152-168.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"6526_CR43","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1099\/jmm.0.021170-0","volume":"59","author":"A Rehman","year":"2010","unstructured":"Rehman A, Lepage P, Nolte A, Hellmig S, Schreiber S, Ott S: Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol. 2010, 59: 1114-1122.","journal-title":"J Med Microbiol"},{"key":"6526_CR44","doi-asserted-by":"publisher","first-page":"13780","DOI":"10.1073\/pnas.0706625104","volume":"104","author":"D Frank","year":"2007","unstructured":"Frank D, Amand A, Feldman R, Boedeker E, Harpaz N, Pace N: Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA. 2007, 104: 13780-13785.","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-242.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T08:24:10Z","timestamp":1717057450000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-242"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,7,16]]},"references-count":44,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6526"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-242","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,7,16]]},"assertion":[{"value":"17 January 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 July 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"242"}}