A survey on computational strategies for genome-resolved gut metagenomics

Abstract Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe–phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation....

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Bibliographic Details
Published in:Briefings in bioinformatics 2023-05, Vol.24 (3)
Main Authors: Jia, Longhao, Wu, Yingjian, Dong, Yanqi, Chen, Jingchao, Chen, Wei-Hua, Zhao, Xing-Ming
Format: Article
Language:English
Subjects:
Antibiotic resistance
Assemblies
Bacteria - genetics
Computer applications
Digestive system
Gastrointestinal Tract
Genomes
Humans
Metagenome
Metagenomics
Microorganisms
Phenotypes
Platforms
Sequence Analysis, DNA
Software
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Summary:Abstract Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe–phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbad162