DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses

Hou，Shengwei1,2; Tang，Tianqi3; Cheng，Siliangyu3; Liu，Yuanhao1; Xia，Tian1; Chen，Ting4; Fuhrman，Jed A.2; Sun，Fengzhu3

2024-06-01

10.1093/nargab/lqae044

NAR Genomics and Bioinformatics   影响因子和分区

2631-9268

Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.

ESCI

英语

第一 ; 通讯

2-s2.0-85192960850

Scopus

1.Department of Ocean Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China
2.Marine and Environmental Biology,Department of Biological Sciences,University of Southern California,Los Angeles,90089,United States
3.Department of Quantitative and Computational Biology,University of Southern California,Los Angeles,90089,United States
4.Department of Computer Science and Technology,Institute of Artificial Intelligence and BNRist,Tsinghua University,Beijing,100084,China

Hou，Shengwei,Tang，Tianqi,Cheng，Siliangyu,et al. DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses[J]. NAR Genomics and Bioinformatics,2024,6(2).

Hou，Shengwei.,Tang，Tianqi.,Cheng，Siliangyu.,Liu，Yuanhao.,Xia，Tian.,...&Sun，Fengzhu.(2024).DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.NAR Genomics and Bioinformatics,6(2).

Hou，Shengwei,et al."DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses".NAR Genomics and Bioinformatics 6.2(2024).