High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

By Chirag Jain, L. Rodriguez-R., Adam M. Phillippy, Konstantinos T. Konstantinidis, Srinivas Aluru. Nature Communications, 2017

4,858 citations recorded by the source corpus.

A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases. Average Nucleotide Identity (ANI) is a robust and useful measure to gauge genetic relatedness between two genomes. Here, the authors develop FastANI, a method to compute ANI using alignment-free approximate sequence mapping, and show 95% ANI is an accurate threshold for demarcating prokaryotic species by analyzing about 90,000 prokaryotic genomes.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c0f91b5779a67e29f26da96ce2aa474354cf5c5

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Citations in the corpus

CoverM: read alignment statistics for metagenomics (2025, positive): “Since aligning against multiple near-identical reference genomes can distort read alignments, CoverM uses Galah (Aroney et al. 2024) to dereplicate input genomes, interpreting ANI calculated by skani (Shaw and Yu 2023), FastANI (Jain et al. 2018), or Dashing (Baker and Langmead 2019).”
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. (2020, background): “Although proposals have been made to apply a methodfree species concept that is based on cohesive evolutionary forces [6], an ANI value of 95 % (94–96 %) has been almost consistently used in recent years to describe new bacterial species [7, 8] and was suggested to reflect the biological significanc”
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (2023, background): “Briefly, an SGB 42 delineates a microbial species purely based on the clustering of whole-genome genetic distances at 5% genomic identity 47 and a taxonomic label can then be assigned to the SGB based on the presence (or not) of characterized genomes from isolate sequencing.”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, positive): “2 Cell 176, 1–14, January 24, 2019 tent with the definition of known species (see STAR Methods) and with other reports (Jain et al., 2018).”
Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth (2019, positive): “To illustrate the population structure of the closely related Enterobacter and Klebsiella strain isolates, FastANI(Jain et al. 2017) was used to estimate the pairwise average nucleotide identity distance between all public and BBS genome assemblies, which was then used as an input to generate a…”