ArticleCommunications biology2020
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.Environmental microbiology · 2026Article
- Microbial model communities exhibit widespread metabolic interdependencies.Communications biology · 2025Article
- Article
- GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.Bioinformatics (Oxford, England) · 2025Article
- Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.Scientific data · 2025Article
- Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.Microbiome · 2025Article
- A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.Computational and structural biotechnology journal · 2025Article
- New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.ISME communications · 2025Article
- Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?bioRxiv : the preprint server for biology · 2024Article
- Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches.Environmental microbiome · 2024Article
- Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.FEMS microbiology reviews · 2024Review
- Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.Nature communications · 2024Article
- Article
- Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth.PNAS nexus · 2024Article
- A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems · 2024Article
- The road forward to incorporate seawater microbes in predictive reef monitoring.Environmental microbiome · 2024Review
- A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.Scientific data · 2024Article
- Quantifying microbial guilds.ISME communications · 2024Article
- Deterministic and stochastic processes generating alternative states of microbiomes.ISME communications · 2024Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
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