ArticleNature communications2024
Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Biochar and Quicklime Co-Application Enhances Soil Fertility and Nut Yield in Acidic Pecan Orchards.Plants (Basel, Switzerland) · 2026Article
- Bioprospecting of the Phylum Bacteroidota for Sustainable Agriculture.Plants (Basel, Switzerland) · 2026Review
- Article
- The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.Nature communications · 2026Article
- Bacterial Siderophore Production in Metal-Rich Environments: Underexplored Sources of Siderophores and Insights into Bioremediation.Journal of natural products · 2026Review
- Sulfur Oxidation by New and Non-Canonical Bacteria in a Subsurface Flow Constructed Wetland Treating Domestic Wastewater.Microorganisms · 2026Article
- Modeling neutrophilic iron-oxidizing bacteria: a KBase narrative resource describing newly integrated metabolic reactions.Microbiology resource announcements · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.Frontiers in microbiology · 2026Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.Entropy (Basel, Switzerland) · 2025Article
- Multi-omics elucidation ofFrontiers in nutrition · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
The low cultivability of environmental bacteria has been widely acknowledged, but most previous estimates focused on the proportion of cultivable cells rather than cultivable taxa. Here, we estimate the proportions of cultivable cells and cultivable taxa for two sample types (soil and activated sludge) using cell counting, 16S rRNA gene amplicon sequencing, metagenomics, and cultivation on agar plates under various conditions. We find that the proportion of cultivable taxa exceeds that of cultivable cells at the sample level. A large proportion of cultivable taxa are taxonomically novel but tend to be present at very low abundance on agar plates, forming microcolonies, and some of them cease to grow during subculture. Compared with uncultivable taxa (under the conditions used in our study), cultivatable taxa tend to display higher metabolic activity as inferred by measuring rRNA copies per cell. Finally, we use the generated taxonomic and genomic information as a guide to isolate a strain representing a yet-uncultured class within the Bacteroidota and to enhance the cultivable diversity of Burkholderiales from activated sludge.
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