{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T09:57:48Z","timestamp":1773827868221,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,9,2]],"date-time":"2024-09-02T00:00:00Z","timestamp":1725235200000},"content-version":"vor","delay-in-days":39,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["P20GM125503"],"award-info":[{"award-number":["P20GM125503"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA143130"],"award-info":[{"award-number":["R01CA143130"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count\u2013based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.<\/jats:p>","DOI":"10.1093\/bib\/bbae424","type":"journal-article","created":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T18:07:56Z","timestamp":1723572476000},"source":"Crossref","is-referenced-by-count":7,"title":["CAIM: coverage-based analysis for identification of microbiome"],"prefix":"10.1093","volume":"25","author":[{"given":"Daniel A","family":"Acheampong","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States"},{"name":"Stowers Institute for Medical Research , 1000 E 50 St, Kansas City, MO 64110, United 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Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand"},{"name":"Mahidol University , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alongkorn","family":"Kurilung","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1070-3047","authenticated-orcid":false,"given":"Yotsawat","family":"Pomyen","sequence":"additional","affiliation":[{"name":"Translational Research Unit, Chulabhorn Research Institute , 54 Kamphaeng Phet Rd., Laksi, Bangkok 10210, 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Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natthaya","family":"Chuaypen","sequence":"additional","affiliation":[{"name":"Center of Excellence in Hepatitis and Liver Cancer , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand"},{"name":"Chulalongkorn University , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kanthida","family":"Kusonmano","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Program , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand"},{"name":"King Mongkut\u2019s University of Technology Thonburi , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand"},{"name":"Systems Biology and Bioinformatics Research Laboratory , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand"},{"name":"King Mongkut\u2019s University of Technology Thonburi , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8901-1088","authenticated-orcid":false,"given":"Intawat","family":"Nookaew","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States"},{"name":"Division of Endocrinology , Department of Medicine, , 4301 W Markham St, Little Rock, AR 72205, United States"},{"name":"University 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