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STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

ABSTRACT: The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.

SUBMITTER: Bharucha T

PROVIDER: S-EPMC7406238 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

Bharucha Tehmina T Oeser Clarissa C Balloux Francois F Brown Julianne R JR Carbo Ellen C EC Charlett Andre A Chiu Charles Y CY Claas Eric C J ECJ de Goffau Marcus C MC de Vries Jutte J C JJC Eloit Marc M Hopkins Susan S Huggett Jim F JF MacCannell Duncan D Morfopoulou Sofia S Nath Avindra A O'Sullivan Denise M DM Reoma Lauren B LB Shaw Liam P LP Sidorov Igor I Simner Patricia J PJ Van Tan Le L Thomson Emma C EC van Dorp Lucy L Wilson Michael R MR Breuer Judith J Field Nigel N

The Lancet. Infectious diseases 20200805 10

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep process ...[more]

PMID: 32768390

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Project description:BackgroundObservational studies are the most frequently published studies in literature. When randomized controlled trials cannot be conducted because of ethical or practical considerations, an observational study design is the first choice. The STROBE Statement (STrengthening the Reporting of OBservational studies in Epidemiology) was developed to provide guidance on how to adequately report observational studies.ObjectivesThe objectives were 1) to evaluate the quality of reporting of observational studies of otorhinolaryngologic literature using the STROBE Statement checklist, 2) to compare the quality of reporting of observational studies in the top 5 Ear, Nose, Throat (ENT) journals versus the top 5 general medical journals and 3) to formulate recommendations to improve adequate reporting of observational research in otorhinolaryngologic literature.MethodsThe top 5 general medical journals and top 5 otorhinolaryngologic journals were selected based on their ISI Web of Knowledge impact factors. On August 3rd, 2015, we performed a PubMed search using different filters to retrieve observational articles from these journals. Studies were selected from 2010 to 2014 for the general medical journals and from 2015 for the ENT journals. We assessed all STROBE items to examine how many items were reported adequately for each journal type.ResultsThe articles in the top 5 general medical journals (n = 11) reported a mean of 69.2% (95% confidence interval (CI): 65.8%-72.7%; median 70.6%), whereas the top 5 ENT journals (n = 29) reported a mean of 51.4% (95% CI: 47.7%-55.0%; median 50.0%). The two journal types reported STROBE items significantly different (p < .001).ConclusionQuality of reporting of observational studies in otorhinolaryngologic articles can considerably enhance. The quality of reporting was better in general medical journals compared to ENT journals. To improve the quality of reporting of observational studies, we recommend authors and editors to endorse and actively implement the STROBE Statement.

Dataset Information

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

Publications

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

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