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微生物组质量控制项目:基线研究设计与未来方向。

The microbiome quality control project: baseline study design and future directions.

作者信息

Sinha Rashmi, Abnet Christian C, White Owen, Knight Rob, Huttenhower Curtis

机构信息

Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland, 20892, USA.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

出版信息

Genome Biol. 2015 Dec 9;16:276. doi: 10.1186/s13059-015-0841-8.

Abstract

Microbiome research has grown exponentially over the past several years, but studies have been difficult to reproduce across investigations. Relevant variation in measurements between laboratories, from a variety of sources, has not been systematically assessed. This is coupled with a growing concern in the scientific community about the lack of reproducibility in biomedical research. The Microbiome Quality Control project (MBQC) was initiated to identify sources of variation in microbiome studies, to quantify their magnitudes, and to assess the design and utility of different positive and negative control strategies. Here we report on the first MBQC baseline study project and workshop.

摘要

在过去几年中,微生物组研究呈指数级增长,但各项研究之间很难重复。实验室之间因各种来源导致的测量相关差异尚未得到系统评估。这与科学界对生物医学研究缺乏可重复性的日益担忧相呼应。微生物组质量控制项目(MBQC)旨在识别微生物组研究中的变异来源,量化其大小,并评估不同阳性和阴性对照策略的设计和效用。在此,我们报告首个MBQC基线研究项目及研讨会的情况。

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本文引用的文献

1
Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model.
J Microbiol Methods. 2015 Jan;108:36-44. doi: 10.1016/j.mimet.2014.11.007. Epub 2014 Nov 20.
2
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1.
4
UPARSE: highly accurate OTU sequences from microbial amplicon reads.
Nat Methods. 2013 Oct;10(10):996-8. doi: 10.1038/nmeth.2604. Epub 2013 Aug 18.
6
Structure, function and diversity of the healthy human microbiome.
Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234.
7
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
ISME J. 2012 Aug;6(8):1621-4. doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.
8
PANDAseq: paired-end assembler for illumina sequences.
BMC Bioinformatics. 2012 Feb 14;13:31. doi: 10.1186/1471-2105-13-31.
9
QIIME allows analysis of high-throughput community sequencing data.
Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11.
10
A human gut microbial gene catalogue established by metagenomic sequencing.
Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.

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