ArticleISME communications2022
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes.
Article in ISME communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass,Microbial genomics · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.Environmental microbiome · 2025Article
- Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.Communications biology · 2025Article
- Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.Frontiers in microbiology · 2025Article
- Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.ISME communications · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.Microbiome · 2024Article
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.Genome biology · 2024Article
- Microbiota succession influences nematode physiology in a beetle microcosm ecosystem.Nature communications · 2024Article
- Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.Biophysical reviews · 2024Review
- scMicrobe PTA: Near Complete Genomes from Single Bacterial Cells.bioRxiv : the preprint server for biology · 2024Article
- Article
- Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants.The ISME journal · 2023Article
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2 authors.
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Abstract
Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from metagenomes remains a computationally difficult task. Repetitive or exogenous sequences, such as ribosomal RNA and horizontally transferred genes, are frequently absent from MAGs because of misassembly and binning errors. Here, we report that ribosomal protein genes are also often absent from MAGs, although they are neither repetitive nor exogenous. Comprehensive analyses of more than 190,000 MAGs revealed that these genes could be missing in more than 20-40% of near-complete (i.e., with completeness of 90% or higher) MAGs. While some uncultivated environmental microbes intrinsically lack some ribosomal protein genes, we found that this unexpected absence is largely due to special evolutionary patterns of codon usage bias in ribosomal protein genes and algorithmic characteristics of metagenomic binning, which is dependent on tetranucleotide frequencies of contigs. This problem reflects the microbial life-history strategy. Fast-growing microbes tend to have this difficulty, likely because of strong evolutionary pressures on ribosomal protein genes toward the efficient assembly of ribosomes. Our observations caution those who study genomics and phylogeny of uncultivated microbes, the diversity and evolution of microbial genes in the central dogma, and bioinformatics in metagenomics.
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