TY - JOUR
T1 - STROBE-metagenomics
T2 - a STROBE extension statement to guide the reporting of metagenomics studies
AU - Bharucha, Tehmina
AU - Oeser, Clarissa
AU - Balloux, Francois
AU - Brown, Julianne R.
AU - Carbo, Ellen C.
AU - Charlett, Andre
AU - Chiu, Charles Y.
AU - Claas, Eric C.J.
AU - de Goffau, Marcus C.
AU - de Vries, Jutte J.C.
AU - Eloit, Marc
AU - Hopkins, Susan
AU - Huggett, Jim F.
AU - MacCannell, Duncan
AU - Morfopoulou, Sofia
AU - Nath, Avindra
AU - O'Sullivan, Denise M.
AU - Reoma, Lauren B.
AU - Shaw, Liam P.
AU - Sidorov, Igor
AU - Simner, Patricia J.
AU - Van Tan, Le
AU - Thomson, Emma C.
AU - van Dorp, Lucy
AU - Wilson, Michael R.
AU - Breuer, Judith
AU - Field, Nigel
N1 - 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
PY - 2020/10
Y1 - 2020/10
N2 - 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.
AB - 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.
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U2 - 10.1016/S1473-3099(20)30199-7
DO - 10.1016/S1473-3099(20)30199-7
M3 - Review article
C2 - 32768390
AN - SCOPUS:85089959054
VL - 20
SP - e251-e260
JO - The Lancet Infectious Diseases
JF - The Lancet Infectious Diseases
SN - 1473-3099
IS - 10
ER -