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Pregled bibliografske jedinice broj: 1015416

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


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 et al.
Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes // Nature Biotechnology, 37 (2019), 8; 937-944 doi:10.1038/s41587-019-0191-2 (međunarodna recenzija, članak, znanstveni)


CROSBI ID: 1015416 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

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

Autori
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

Izvornik
Nature Biotechnology (1087-0156) 37 (2019), 8; 937-944

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
metagenome, assembler, microbiome

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo



POVEZANOST RADA


Projekti:
HRZZ-IP-2018-01-5886 - De novo sastavljanje genoma i metagenoma (SIGMA) (Šikić, Mile, HRZZ - 2018-01) ( POIROT)

Ustanove:
Fakultet elektrotehnike i računarstva, Zagreb

Profili:

Avatar Url Mile Šikić (autor)

doi

Citiraj ovu publikaciju

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 et al.
Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes // Nature Biotechnology, 37 (2019), 8; 937-944 doi:10.1038/s41587-019-0191-2 (međunarodna recenzija, članak, znanstveni)
Bertrand, D., Shaw, J., Kalathiyappan, M., Ng, A., Kumar, M., Li, C., Dvornicic, M., Soldo, J., Koh, J. & Tong, C. (2019) Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes. Nature Biotechnology, 37 (8), 937-944 doi:10.1038/s41587-019-0191-2.
@article{article, year = {2019}, pages = {937-944}, DOI = {10.1038/s41587-019-0191-2}, keywords = {metagenome, assembler, microbiome}, journal = {Nature Biotechnology}, doi = {10.1038/s41587-019-0191-2}, volume = {37}, number = {8}, issn = {1087-0156}, title = {Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes}, keyword = {metagenome, assembler, microbiome} }
@article{article, year = {2019}, pages = {937-944}, DOI = {10.1038/s41587-019-0191-2}, keywords = {metagenome, assembler, microbiome}, journal = {Nature Biotechnology}, doi = {10.1038/s41587-019-0191-2}, volume = {37}, number = {8}, issn = {1087-0156}, title = {Hybrid metagenomic assembly enables high- resolution analysis of resistance determinants and mobile elements in human microbiomes}, keyword = {metagenome, assembler, microbiome} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
  • Scopus
  • MEDLINE


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