ArticleFrontiers in microbiology2021
Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.The ISME journal · 2026Article
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.Environmental microbiome · 2025Article
- Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.Scientific data · 2025Article
- Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.mBio · 2025Article
- Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.Microbiome · 2025Article
- Microbial functional diversity and redundancy: moving forward.FEMS microbiology reviews · 2025Review
- HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes.BMC genomics · 2024Article
- Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59.mSystems · 2023Article
- Carotenoids in Health as Studied by Omics-Related Endpoints.Advances in nutrition (Bethesda, Md.) · 2023Review
- Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.Microbiology spectrum · 2023Article
- Flotillin-associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes.mSystems · 2023Article
- Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies.Microbiome · 2023Article
- An Environmental DNA Primer for Microbial and Restoration Ecology.Microbial ecology · 2023Review
- A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics.Environmental microbiome · 2023Article
- Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples.mSystems · 2022Article
- Improved Mobilome Delineation in Fragmented Genomes.Frontiers in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for
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