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Nat Biotechnol. 2017 Nov;35(11):1077-1086. doi: 10.1038/nbt.3981. Epub 2017 Oct 2.

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium.

Author information

1
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.
2
Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
3
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
4
Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, North Carolina, USA.
5
Pediatrics, University of California, San Diego, La Jolla, California, USA.
6
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.
7
Computer Science and Engineering and Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA.

Abstract

In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

PMID:
28967885
PMCID:
PMC5839636
DOI:
10.1038/nbt.3981
[Indexed for MEDLINE]
Free PMC Article

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