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

Tehmina Bharucha*, Clarissa Oeser, Francois Balloux, Julianne R. Brown, Ellen C. Carbo, Andre Charlett, Charles Y. Chiu, Eric C.J. Claas, Marcus C. de Goffau, Jutte J.C. de Vries, Marc Eloit, Susan Hopkins, Jim F. Huggett, Duncan MacCannell, Sofia Morfopoulou, Avindra Nath, Denise M. O'Sullivan, Lauren B. Reoma, Liam P. Shaw, Igor SidorovPatricia J. Simner, Le Van Tan, Emma C. Thomson, Lucy van Dorp, Michael R. Wilson, Judith Breuer, Nigel Field

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

24 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)e251-e260
JournalThe Lancet Infectious Diseases
Volume20
Issue number10
DOIs
Publication statusPublished - Oct 2020

Bibliographical note

Funding Information:
AN and LBR are National Institute of Health (NIH) employees and are in receipt on an NIH grant (NS003130). TB is supported by the University of Oxford and the Medical Research Council (grant number MR/N013468/1). MW is funded by a National Institute of Neurological Disorders and Stroke (grant number K08NS096117). LVT is a Wellcome Research Fellow (grant number 204904/Z/16/Z).

Funding Information:
AN and LBR are National Institute of Health (NIH) employees and are in receipt on an NIH grant (NS003130). TB is supported by the University of Oxford and the Medical Research Council (grant number MR/N013468/1). MW is funded by a National Institute of Neurological Disorders and Stroke (grant number K08NS096117). LVT is a Wellcome Research Fellow (grant number 204904/Z/16/Z).

Publisher Copyright:
© 2020 Elsevier Ltd

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