Spike-in genomic DNA for validating performance of metagenomics workflows. (27th November 2018)

• Record Type: Journal Article
• Authors: Venkataraman, Arvind; Parlov, Mirjana; Hu, Ping; Schnell, Dan; Wei, Xingtao; Tiesman, Jay P
• Is Part Of: Biotechniques. Volume 65:Number 6(2018)
• Page Start: 315
• Page End: 321
• Publication Date: 2018-11-27
• Subjects: Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/btn-2018-0089
• Languages: English
• ISSNs: 0736-6205

Abstract

Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool – spike-in DNA – to assess performance of metagenomics workflows. The spike-in is DNA from two organisms – Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.