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

• Published in: Nature biotechnology Vol. 37; no. 8; pp. 937 - 944
• Main Authors: Bertrand, Denis, Shaw, Jim, Kalathiyappan, Manesh, Ng, Amanda Hui Qi, Kumar, M. Senthil, Li, Chenhao, Dvornicic, Mirta, Soldo, Janja Paliska, Koh, Jia Yu, Tong, Chengxuan, Ng, Oon Tek, Barkham, Timothy, Young, Barnaby, Marimuthu, Kalisvar, Chng, Kern Rei, Sikic, Mile, Nagarajan, Niranjan
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.08.2019; Nature Publishing Group
• Subjects: 631/114/2785/2302; 631/326/107; 631/326/2565/2142; Agriculture; Antibiotics; Assemblies; Assembly; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Clustering; DNA sequencing; Genetic aspects; Genomes; Genomics; Intestinal microflora; Life Sciences; Methods; Microbiomes; Microbiota (Symbiotic organisms); Nucleotide sequencing; Phages; Physiological aspects; Porosity; Rare species; Scaffolding; Singapore
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/s41587-019-0191-2

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. A more accurate metagenomics approach uses a hybrid assembler to incorporate short- and long-read sequences.