Publications

Publications Search

Search for publications by author
Search for publications by abstract keyword(s)

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

Abstract

The complexity of microbial communities, combined with technical biases in next-generation sequencing, pose a challenge to metagenomic analysis. Here, we develop a set of internal DNA standards, termed "sequins" (sequencing spike-ins), that together constitute a synthetic community of artificial microbial genomes. Sequins are added to environmental DNA samples prior to library preparation, and undergo concurrent sequencing with the accompanying sample. We validate the performance of sequins by comparison to mock microbial communities, and demonstrate their use in the analysis of real metagenome samples. We show how sequins can be used to measure fold change differences in the size and structure of accompanying microbial communities, and perform quantitative normalization between samples. We further illustrate how sequins can be used to benchmark and optimize new methods, including nanopore long-read sequencing technology. We provide metagenome sequins, along with associated data sets, protocols, and an accompanying software toolkit, as reference standards to aid in metagenomic studies.

Type Journal
ISBN 2041-1723
Authors Hardwick, S. A.; Chen, W. Y.; Wong, T.; Kanakamedala, B. S.; Deveson, I. W.; Ongley, S. E.; Santini, N. S.; Marcellin, E.; Smith, M. A.; Nielsen, L. K.; Lovelock, C. E.; Neilan, B. A.; Mercer, T. R.
Responsible Garvan Author Dr Timothy Mercer
Publisher Name Nature Communications
Published Date 2018-08-06
Published Volume 9
Published Issue 1
Published Pages 3096
Status Published in-print
DOI 10.1038/s41467-018-05555-0