ArticleEnvironmental microbiology2020
Sequencing effort dictates gene discovery in marine microbial metagenomes.
Article in Environmental microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- Microbial functional diversity and redundancy: moving forward.FEMS microbiology reviews · 2025Review
- Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.GigaScience · 2025Article
- Article
- Comparative biodegradation analysis of three compostable polyesters by a marine microbial community.Applied and environmental microbiology · 2023Article
- Abiotic selection of microbial genome size in the global ocean.Nature communications · 2023Article
- Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.Science advances · 2023Article
- The Simrad EK60 echosounder dataset from the Malaspina circumnavigation.Scientific data · 2021Article
- Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume.Frontiers in microbiology · 2021Article
- Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics.Frontiers in microbiology · 2021Article
- Distances Between Extension Spaces of Phylogenetic Trees.IEEE transactions on computational biology and bioinformaticsArticle
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Authors and funding
11 authors.
Funding
Abstract
Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red Sea plankton community to uncover that the rate of gene discovery increases continuously with sequencing effort, with no indication that the retrieved 2.83 million non-redundant (complete) genes predicted from the experiment represented a nearly complete inventory of the genes present in the sampled community (i.e., no evidence of saturation). The underlying reason is the Pareto-like distribution of the abundance of genes in the plankton community, resulting in a very long tail of millions of genes present at remarkably low abundances, which can only be retrieved through massive sequencing. Microbial metagenomic projects retrieve a variable number of unique genes per Tera base-pair (Tbp), with a median value of 14.7 million unique genes per Tbp sequenced across projects. The increase in the rate of gene discovery in microbial metagenomes with sequencing effort implies that there is ample room for new gene discovery in further ocean and holobiont sequencing studies.
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