Strainberry: Automated strain separation in low-complexity metagenomes using long reads

Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E. and Chikhi, Rayan (2021) Strainberry: Automated strain separation in low-complexity metagenomes using long reads. Nature Communications, 12. ISSN 2041-1723

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Abstract

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.

Item Type:	Article
Additional Information:	Acknowledgements: R.V. and R.C. are funded by ANR INCEPTION (PIA/ANR-16-CONV-0005) and R.C. by ANR PRAIRIE (ANR-19-P3IA-0001) and ANR SeqDigger (ANR-19-CE45-0008). C.Q. is funded through "Strain resolved metagenomics for medical microbiology" MRC MR/S037195/1 and the "CLIMB-BIG-DATA" consortium MR/T030062/1. A.E.D.’s contributions to this research were supported in part by the Australian Government through the Australian Research Council Discovery Projects funding scheme (project DP180101506). The authors thank Eduardo Rocha for his advice on the manuscript.
Uncontrolled Keywords:	chemistry(all),biochemistry, genetics and molecular biology(all),physics and astronomy(all) ,/dk/atira/pure/subjectarea/asjc/1600
Faculty \ School:	Faculty of Science > School of Biological Sciences
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	12 Sep 2022 11:30
Last Modified:	21 Oct 2022 01:39
URI:	https://ueaeprints.uea.ac.uk/id/eprint/88125
DOI:	10.1038/s41467-021-24515-9

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