engleski

Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes

Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long- read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5× ; Canu), higher contiguity than short-read (~10× NGA50 ; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2× ; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near- complete genomes with higher coverage. We used OPERA- MS to assemble 28 gut metagenomes of antibiotic- treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High- quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.

metagenome ; assembler ; microbiome

nije evidentirano