{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T16:03:41Z","timestamp":1765382621019,"version":"3.44.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T00:00:00Z","timestamp":1754438400000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R00 AI147165"],"award-info":[{"award-number":["R00 AI147165"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM151045"],"award-info":[{"award-number":["R35 GM151045"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2\u2019s accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084\/m9.figshare.29420780.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf440","type":"journal-article","created":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T18:01:55Z","timestamp":1755021715000},"source":"Crossref","is-referenced-by-count":2,"title":["StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities"],"prefix":"10.1093","volume":"41","author":[{"given":"Kerim","family":"Heber","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, PA 16802,","place":["United States"]}]},{"given":"Shuchang","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, PA 16802,","place":["United States"]}]},{"given":"Daniela","family":"Betancurt-Anzola","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, PA 16802,","place":["United States"]}]},{"given":"Heejung","family":"Koo","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, PA 16802,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8649-1706","authenticated-orcid":false,"given":"Jordan E","family":"Bisanz","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, PA 16802,","place":["United States"]},{"name":"One Health Microbiome Center, Huck Life Sciences Institute , University Park, PA 16802,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,6]]},"reference":[{"key":"2025082519465408900_btaf440-B1","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1038\/s41564-021-00966-0","article-title":"Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes","volume":"6","author":"Aggarwala","year":"2021","journal-title":"Nat Microbiol"},{"key":"2025082519465408900_btaf440-B2","doi-asserted-by":"crossref","first-page":"1057883","DOI":"10.3389\/fmicb.2023.1057883","article-title":"A three-species synthetic community model whose rapid response to antagonism allows the study of higher-order dynamics and emergent properties in minutes","volume":"14","author":"Aguilar-Salinas","year":"2023","journal-title":"Front Microbiol"},{"key":"2025082519465408900_btaf440-B3","doi-asserted-by":"crossref","first-page":"1117122","DOI":"10.3389\/fmicb.2023.1117122","article-title":"Challenges and opportunities of strain diversity in gut microbiome research","volume":"14","author":"Anderson","year":"2023","journal-title":"Front Microbiol"},{"key":"2025082519465408900_btaf440-B4","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"2025082519465408900_btaf440-B5","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"2025082519465408900_btaf440-B7","doi-asserted-by":"crossref","first-page":"25","DOI":"10.4161\/gmic.2.1.14651","article-title":"Human intestinal microbiota: characterization of a simplified and stable gnotobiotic rat model","volume":"2","author":"Becker","year":"2011","journal-title":"Gut Microbes"},{"key":"2025082519465408900_btaf440-B8","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1016\/j.chom.2020.04.006","article-title":"A genomic toolkit for the mechanistic dissection of intractable human gut bacteria","volume":"27","author":"Bisanz","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2025082519465408900_btaf440-B9","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4","volume":"41","author":"Blanco-M\u00edguez","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025082519465408900_btaf440-B10","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1126\/science.aaw9285","article-title":"Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome","volume":"366","author":"Carri\u00f3n","year":"2019","journal-title":"Science"},{"key":"2025082519465408900_btaf440-B11","doi-asserted-by":"crossref","first-page":"e1009056","DOI":"10.1371\/journal.ppat.1009056","article-title":"Strain diversity in the microbiome: lessons from Bacteroides fragilis","volume":"16","author":"Carrow","year":"2020","journal-title":"PLoS Pathog"},{"key":"2025082519465408900_btaf440-B12","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1038\/s41467-020-15508-1","article-title":"Developing a new class of engineered live bacterial therapeutics to treat human diseases","volume":"11","author":"Charbonneau","year":"2020","journal-title":"Nat Commun"},{"key":"2025082519465408900_btaf440-B13","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2025082519465408900_btaf440-B14","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1016\/j.cell.2022.08.003","article-title":"Design, construction, and in vivo augmentation of a complex gut microbiome","volume":"185","author":"Cheng","year":"2022","journal-title":"Cell"},{"key":"2025082519465408900_btaf440-B15","doi-asserted-by":"crossref","first-page":"e0095122","DOI":"10.1128\/msystems.00951-22","article-title":"A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology","volume":"7","author":"Coker","year":"2022","journal-title":"mSystems"},{"key":"2025082519465408900_btaf440-B16","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1186\/s12864-018-4703-0","article-title":"Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms","volume":"19","author":"Costello","year":"2018","journal-title":"BMC Genomics"},{"key":"2025082519465408900_btaf440-B17","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1016\/j.cell.2018.10.020","article-title":"Microbial interkingdom interactions in roots promote Arabidopsis survival","volume":"175","author":"Dur\u00e1n","year":"2018","journal-title":"Cell"},{"key":"2025082519465408900_btaf440-B18","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.chom.2024.12.002","article-title":"Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization","volume":"33","author":"Fishbein","year":"2025","journal-title":"Cell Host Microbe"},{"key":"2025082519465408900_btaf440-B19","doi-asserted-by":"crossref","first-page":"3656","DOI":"10.1073\/pnas.1917265117","article-title":"Ecological drivers of bacterial community assembly in synthetic phycospheres","volume":"117","author":"Fu","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082519465408900_btaf440-B20","doi-asserted-by":"crossref","first-page":"6346","DOI":"10.1016\/j.cell.2024.08.037","article-title":"Emergence of community behaviors in the gut microbiota upon drug treatment","volume":"187","author":"Garcia-Santamarina","year":"2024","journal-title":"Cell"},{"key":"2025082519465408900_btaf440-B21","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s40793-023-00536-3","article-title":"Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction","volume":"18","author":"Gon\u00e7alves","year":"2023","journal-title":"Environ Microbiome"},{"key":"2025082519465408900_btaf440-B22","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/bty630","article-title":"Simulating Illumina metagenomic data with InSilicoSeq","volume":"35","author":"Gourl\u00e9","year":"2019","journal-title":"Bioinformatics"},{"key":"2025082519465408900_btaf440-B23","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.mib.2014.02.002","article-title":"Synthetic microbial communities","volume":"18","author":"Grosskopf","year":"2014","journal-title":"Curr Opin Microbiol"},{"key":"2025082519465408900_btaf440-B24","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1038\/s41467-019-13036-1","article-title":"Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis","volume":"10","author":"Johnson","year":"2019","journal-title":"Nat Commun"},{"key":"2025082519465408900_btaf440-B25","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1111\/nph.12536","article-title":"Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia","volume":"201","author":"Knoth","year":"2014","journal-title":"New Phytol"},{"key":"2025082519465408900_btaf440-B26","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae047","article-title":"YACHT: an ANI-based statistical test to detect microbial presence\/absence in a metagenomic sample","volume":"40","author":"Koslicki","year":"2024","journal-title":"Bioinformatics"},{"key":"2025082519465408900_btaf440-B27","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1080\/19490976.2019.1702431","article-title":"Following the community development of SIHUMIx\u2014a new intestinal in vitro model for bioreactor use","volume":"11","author":"Krause","year":"2020","journal-title":"Gut Microbes"},{"key":"2025082519465408900_btaf440-B28","first-page":"3","article-title":"E. coli as an all-rounder: the thin line between commensalism and pathogenicity","volume":"358","author":"Leimbach","year":"2013","journal-title":"Curr Top Microbiol Immunol"},{"key":"2025082519465408900_btaf440-B29","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.3389\/fimmu.2019.01420","article-title":"Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis","volume":"10","author":"Lengfelder","year":"2019","journal-title":"Front Immunol"},{"key":"2025082519465408900_btaf440-B30","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1186\/s40168-023-01615-w","article-title":"High-resolution strain-level microbiome composition analysis from short reads","volume":"11","author":"Liao","year":"2023","journal-title":"Microbiome"},{"key":"2025082519465408900_btaf440-B31","doi-asserted-by":"crossref","first-page":"12819","DOI":"10.3390\/ijms252312819","article-title":"Synthetic microbial community isolated from intercropping system enhances P uptake in rice","volume":"25","author":"Ma","year":"2024","journal-title":"Int J Mol Sci"},{"key":"2025082519465408900_btaf440-B32","doi-asserted-by":"crossref","first-page":"106ra106","DOI":"10.1126\/scitranslmed.3002701","article-title":"The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins","volume":"3","author":"McNulty","year":"2011","journal-title":"Sci Transl Med"},{"key":"2025082519465408900_btaf440-B33","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.gde.2005.09.006","article-title":"The microbial pan-genome","volume":"15","author":"Medini","year":"2005","journal-title":"Curr Opin Genet Dev"},{"key":"2025082519465408900_btaf440-B34","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41586-023-06431-8","article-title":"Mapping the T cell repertoire to a complex gut bacterial community","volume":"621","author":"Nagashima","year":"2023","journal-title":"Nature"},{"key":"2025082519465408900_btaf440-B35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19490976.2021.1919464","article-title":"A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects","volume":"13","author":"Perez","year":"2021","journal-title":"Gut Microbes"},{"key":"2025082519465408900_btaf440-B36","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/2049-2618-1-3","article-title":"Stool substitute transplant therapy for the eradication of Clostridium difficile infection: \u201cRePOOPulating\u201d the gut","volume":"1","author":"Petrof","year":"2013","journal-title":"Microbiome"},{"key":"2025082519465408900_btaf440-B37","doi-asserted-by":"crossref","first-page":"btac845","DOI":"10.1093\/bioinformatics\/btac845","article-title":"KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping","volume":"39","author":"Shen","year":"2023","journal-title":"Bioinformatics"},{"key":"2025082519465408900_btaf440-B38","doi-asserted-by":"crossref","first-page":"176","DOI":"10.4161\/gmic.28203","article-title":"Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine","volume":"5","author":"Slezak","year":"2014","journal-title":"Gut Microbes"},{"key":"2025082519465408900_btaf440-B39","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41586-019-0878-z","article-title":"A defined commensal consortium elicits CD8 T cells and anti-cancer immunity","volume":"565","author":"Tanoue","year":"2019","journal-title":"Nature"},{"key":"2025082519465408900_btaf440-B40","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.chom.2025.02.007","article-title":"A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance","volume":"33","author":"Tian","year":"2025","journal-title":"Cell Host Microbe"},{"key":"2025082519465408900_btaf440-B41","doi-asserted-by":"crossref","first-page":"3105","DOI":"10.1038\/s41467-021-23460-x","article-title":"Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis","volume":"12","author":"van der Lelie","year":"2021","journal-title":"Nat Commun"},{"key":"2025082519465408900_btaf440-B42","doi-asserted-by":"crossref","first-page":"fuad012","DOI":"10.1093\/femsre\/fuad012","article-title":"Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications","volume":"47","author":"van Leeuwen","year":"2023","journal-title":"FEMS Microbiol Rev"},{"key":"2025082519465408900_btaf440-B43","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/s41579-020-0368-1","article-title":"Diversity within species: interpreting strains in microbiomes","volume":"18","author":"Van Rossum","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"2025082519465408900_btaf440-B44","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.coph.2019.07.005","article-title":"Design of synthetic microbial consortia for gut microbiota modulation","volume":"49","author":"V\u00e1zquez-Castellanos","year":"2019","journal-title":"Curr Opin Pharmacol"},{"key":"2025082519465408900_btaf440-B45","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1016\/j.cell.2023.05.037","article-title":"Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome","volume":"186","author":"Wang","year":"2023","journal-title":"Cell"},{"key":"2025082519465408900_btaf440-B46","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.chom.2019.09.001","article-title":"Bioremediation of a common product of food processing by a human gut bacterium","volume":"26","author":"Wolf","year":"2019","journal-title":"Cell Host Microbe"},{"key":"2025082519465408900_btaf440-B47","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol"},{"key":"2025082519465408900_btaf440-B48","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1002\/mnfr.201500249","article-title":"Alleviation of high fat diet-induced obesity by oligofructose in gnotobiotic mice is independent of presence of Bifidobacterium longum","volume":"59","author":"Woting","year":"2015","journal-title":"Mol Nutr Food Res"},{"key":"2025082519465408900_btaf440-B49","doi-asserted-by":"crossref","first-page":"e01530","DOI":"10.1128\/mBio.01530-14","article-title":"Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models","volume":"5","author":"Woting","year":"2014","journal-title":"mBio"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf440\/63967712\/btaf440.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/8\/btaf440\/63967712\/btaf440.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/8\/btaf440\/63967712\/btaf440.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T23:47:06Z","timestamp":1756165626000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf440\/8223223"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":48,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2025,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf440","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,8]]},"published":{"date-parts":[[2025,8]]},"article-number":"btaf440"}}