ArticleInternational journal of systematic and evolutionary microbiology2024
EzBioCloud: a genome-driven database and platform for microbiome identification and discovery.
Article in International journal of systematic and evolutionary microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 231 papers.
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231 citing papers in PubMed.
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- Production and Structural/Physicochemical Characteristics of Exopolysaccharides from the Halotolerant Strain Oceanobacillus sp. DT-Z6.Applied biochemistry and biotechnology · 2026Article
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- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- Taxonomic characterization of Kribbella broussonetiae sp. nov., a novel rare actinomycete isolated from the rhizosphere soil of Broussonetia papyrifera.The Journal of antibiotics · 2026Article
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- Draft genome sequence ofMicrobiology resource announcements · 2026Article
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- Bioprospecting of cultivable actinobacteria from tropical peat swamp forest soil reveals Streptomyces with potent antimicrobial activity.Antonie van Leeuwenhoek · 2026Article
- High-quality draft genome sequence data ofData in brief · 2026Article
- Occurrence of healthcare-associated infections caused by the zoonotic bacterium Pasteurella multocida subsp. gallicida in patients with severe motor and intellectual disabilities in Japan.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Distinct Host and Bacterial Profiles in Murine Single Versus Co-Infection with Foal-IsolatedMicroorganisms · 2026Article
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171 more citing papers are in PubMed but not listed here.
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15 authors.
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Abstract
With the continued evolution of DNA sequencing technologies, the role of genome sequence data has become more integral in the classification and identification of Bacteria and Archaea. Six years after introducing EzBioCloud, an integrated platform representing the taxonomic hierarchy of Bacteria and Archaea through quality-controlled 16S rRNA gene and genome sequences, we present an updated version, that further refines and expands its capabilities. The current update recognizes the growing need for accurate taxonomic information as defining a species increasingly relies on genome sequence comparisons. We also incorporated an advanced strategy for addressing underrepresented or less studied lineages, bolstering the comprehensiveness and accuracy of our database. Our rigorous quality control protocols remain, where whole-genome assemblies from the NCBI Assembly Database undergo stringent screening to remove low-quality sequence data. These are then passed through our enhanced identification bioinformatics pipeline which initiates a 16S rRNA gene similarity search and then calculates the average nucleotide identity (ANI). For genome sequences lacking a 16S rRNA sequence and without a closely related genomic representative for ANI calculation, we apply a different ANI approach using bacterial core genes for improved taxonomic placement (core gene ANI, cgANI). Because of the increase in genome sequences available in NCBI and our newly introduced cgANI method, EzBioCloud now encompasses a total of 109 835 species, of which 21 964 have validly published names. 47 896 are candidate species identified either through 16S rRNA sequence similarity (phylotypes) or through whole genome ANI (genomospecies), and the remaining 39 975 were positioned in the taxonomic tree by cgANI (species clusters). Our EzBioCloud database is accessible at www.ezbiocloud.net/db.
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