I don't think there is such threshold. You will get different identities based on which regions of genome you are looking at. Why not identify both bacterias and take a look on how close they are in evolutionary tree?
I'm using whole genome sequence (chromosomal + plasmids) as comparisons. So it should give an idea if my samples are of the same species or not. These species have not yet been documented previously . By the way, I have found an article saying that ANI values between genomes of the same species are above 95% .
The species boundary is 94-95% depending on the reference you choose. Other boundaries such as genus and family have also been done using AAI (average amino acid identity).
Check out the following references:
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. PNAS106: 19126-19131
Konstantinidis, K.T. and Tiedje, J.M. (2005) Towards a Genome-Based Taxonomy for Prokaryotes. Journal of Bacteriology187: 6258-6264.
Konstantinidis, K.T. and Tiedje, J.M. (2005) Genomic insights that advance the species definition for prokaryotes. PNAS102: 2567-2572.
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I don't think there is such threshold. You will get different identities based on which regions of genome you are looking at. Why not identify both bacterias and take a look on how close they are in evolutionary tree?
I'm using whole genome sequence (chromosomal + plasmids) as comparisons. So it should give an idea if my samples are of the same species or not. These species have not yet been documented previously . By the way, I have found an article saying that ANI values between genomes of the same species are above 95% .