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.
Highlights
High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities
It requires two inputs: a strain-oblivious metagenome assembly, and a set of long reads aligned to the assembly
We use those single-nucleotide variants (SNVs) to perform haplotype phasing and separate reads originating from different haplotypes
Summary
High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. 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. 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. Current techniques for de novo metagenome assembly are able to reconstruct the chromosomal sequences of sufficiently abundant species within a microbial sample, but ideally should aim at reconstructing each strain present. SAVAGE13 is a method that performs the assembly of viral quasispecies from deepcoverage short-read sequencing data and is able to reconstruct individual haplotypes of intra-host virus strains. StrainEst[16] is a referencebased method exploiting the single-nucleotide variant profiles of available genomes of selected species to determine the number and identity of coexisting strains and their relative abundances in mixed metagenomic samples
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