RT Journal Article
SR Electronic
T1 Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 456905
DO 10.1101/456905
A1 Denis Bertrand
A1 Jim Shaw
A1 Manesh Kalathiappan
A1 Amanda Hui Qi Ng
A1 Senthil Muthiah
A1 Chenhao Li
A1 Mirta Dvornicic
A1 Janja Paliska Soldo
A1 Jia Yu Koh
A1 Ng Oon Tek
A1 Timothy Barkham
A1 Barnaby Young
A1 Kalisvar Marimuthu
A1 Chng Kern Rei
A1 Mile Sikic
A1 Niranjan Nagarajan
YR 2018
UL http://biorxiv.org/content/early/2018/10/30/456905.abstract
AB The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing. The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9× long read coverage, thus enabling high quality assembly of lowly abundant species (<1%). Furthermore, OPERA-MS’s fine-grained clustering is able to deconvolute and assemble multiple genomes of the same species in a single sample, allowing us to study the complex dynamics of the human microbiome at the sub-species level. Applying nanopore sequencing to gut metagenomes of patients undergoing antibiotic treatment, we show that long reads can be obtained from stool samples in clinical studies to produce more meaningful metagenomic assemblies (up to 200× improvement over short-read assemblies), including the closed assembly of >80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences.