ArticleNature communications2024
Towards estimating the number of strains that make up a natural bacterial population.
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 50 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
50 citing papers in PubMed.
- Trial
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- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
- Unmasking pathogen traits for chronic colonization in neurogenic bladder.Cell reports · 2026Article
- Genomic and Phenotypic Evaluation of the Gliadin-Degrading Probiotic Bacillus amyloliquefaciens EG025 from Cheonggukjang for Celiac Disease Treatment.Probiotics and antimicrobial proteins · 2026Article
- Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agentMicrobiology spectrum · 2026Article
- Assessment of genome evolution inmSystems · 2026Article
- Community conservatism is widespread across microbial phyla and environments.Nature ecology & evolution · 2026Article
- Identification and characterization of RacX, a new broad-specificity amino acid racemase from a novel taxon within the orderApplied and environmental microbiology · 2026Article
- Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.The ISME journal · 2026Article
- Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.The ISME journal · 2026Article
- Transfer potential of F-like plasmids inISME communications · 2026Article
- Accessible, robust ultrahigh-throughput microbiome analysis via integration of uniform droplet-templated emulsification and FACS.PloS one · 2026Article
- An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.ISME communications · 2026Article
- Metagenomics reveal unrestricted dispersal of extreme halophiles and higher connectivity among coastal vs. inland solar salterns and hypersaline lakes.ISME communications · 2026Article
- Leveraging strain competition to address antimicrobial resistance with microbiota therapies.Gut microbes · 2025Review
- Article
- Developing genome typing strategies for the emerging zoonotic pathogenJournal of clinical microbiology · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
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