I am using average nucleotide identity (ANI) to characterize newly sequenced bacteria genomes of the same species. Can ANI be used to determine whether or not two genomes represent difference isolation instances of the same strain? If so, what is the % shared ANI of two genomes of the same strain?
Yes logically average nucleotide identity can be used to characterize bacterial species. Since bacterial strains of variants of same bacterial species. The identity of nucleotide among different strains of bacteria will be very high. You can test your hypothesis by taking example of any one gene from different know strains of same bacterial species. But I feel rather than just looking for average identity in nucleotides you can check for relative divergence or conservation of nucleotides and compare among bacterial strain population. Thus least relative distance or max relative conservation will give you idea about different strains of same bacterial species. I hope, I have correctly understood your question.
The same strain is tricky, as there is to my best knowledge no clear definition of what constitutes a strain.
Based on experience (we sequenced quite a number of Corynebacterium glutamicum strains), the difference between strains was in the order of >10k SNPs and a couple of dozen singletons. So ANIs would most likely be >99%. But that is just an observation without statistical backing.
Christian, out of curiosity, is the observation that Corynebacterium glutamicum strains differ at around >10k SNPs/genomes published?
Unfortunately not (yet). We decided to do all type strains of the genus first and that is still some way to go.
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