ArticleNucleic acids research2025
FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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40 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
- A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential.Nature communications · 2026Article
- Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation.Nature communications · 2026Article
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- Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.Nature communications · 2026Article
- Phylogenomic reclassification of Cellulophaga species to Paracellulophaga gen. nov. and description of Allocellulophaga tsushimaensis gen. nov., sp. nov., a novel bacterium from coastal seawater of Tsushima Island, Japan.Antonie van Leeuwenhoek · 2026Article
- Single-cell sequencing reveals unexpected genetic diversity amongMicrobial genomics · 2026Article
- A novel polyhydroxyalkanoate-storing bacterium Thauera carbonocopians sp. nov. isolated from a sequencing batch reactor fed with volatile fatty acids.Scientific reports · 2026Article
- Genomic and phenotypic characterization of a human gutFuture microbiology · 2026Article
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7 authors.
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Abstract
Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.
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