ArticleMicrobiology spectrum2024
Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes.
Article in Microbiology spectrum, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Different grazing intensities affect soil nitrogen cycling by altering microbial nitrogen metabolism in alpine wetlands.iScience · 2026Article
- Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.Microbiology spectrum · 2026Article
- Multi-Omics Insights into Microbial Interactions and Fermented Food Quality.Microorganisms · 2025Review
- Spatio-Temporal Resolution of Microbial Functions and Taxa Associated With Cyanobacterial Harmful Algae Blooms Along a 500-Km Aquatic Continuum in the Lake Erie Watershed.Environmental microbiology · 2025Article
- Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.Microbiology spectrum · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes. IMPORTANCE: Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.
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Registered trials
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