- Title
- Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
- Creator
- Hardwick, Simon A.; Chen, Wendy Y.; Lovelock, Catherine E.; Neilan, Brett A.; Mercer, Tim R.; Wong, Ted; Kanakamedala, Bindu S.; Deveson, Ira W.; Ongley, Sarah E.; Santini, Nadia S.; Marcellin, Esteban; Smith, Martin A.; Nielsen, Lars K.
- Relation
- Funding BodyNHMRCGrant Number1062470 http://purl.org/au-research/grants/nhmrc/1062470
- Relation
- Nature Communication Vol. 9, no. 3096
- Publisher Link
- http://dx.doi.org/10.1038/s41467-018-05555-0
- Publisher
- Nature Publishing Group
- Resource Type
- journal article
- Date
- 2018
- Description
- 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.
- Subject
- microbial communities; synthetic microbe communities; metagenome sequencing; metagenomic analysis; sequins; metagenomic studies
- Identifier
- http://hdl.handle.net/1959.13/1390898
- Identifier
- uon:33145
- Identifier
- ISSN:2041-1723
- Rights
- This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Language
- eng
- Full Text
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