To give some background, I was instructed by my supervisor to analyse the relationship between the bacteria using the measurements listed in the title and to see whether they were in the same genus using 16S rRNA, ANI, AF and DDH value measurements. So I have had no problems finding the percentage genus cutoff for the 16S rRNA, but I can't find anything for the ANI, AF and DDH and this is particularly problematic because from my understanding, you can't just rely on 16S rRNA to determine whether they're in a different genus, because the 16S rRNA gene is only one gene and very short and so I would imagine you'd need other measurements to back up the idea that they're in different genera. What would be the best way to go about doing this?
"because the 16S rRNA gene is only one gene and very short and so I would imagine you'd need other measurements to back up the idea that they're in different genera. What would be the best way to go about doing this?"
>> This is a wrong assumption of yours if you talk about genus level. For genus level, 16S rRNA gene is a very good marker even for the very diverse (complicated) genera like Bacillus.
For your main question, check out the following:
Varghese et al; 2015, Microbial species delineation using whole genome sequences, Nucleic Acids Research, Volume 43, Issue 14, 18 August 2015, Pages 6761–6771, https://doi.org/10.1093/nar/gkv657
You could check out those literatures:
Barco RA, Garrity GM, Scott JJ, et al. A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index. Mbio. 2020 Jan;11(1):e02475-19. DOI: 10.1128/mbio.02475-19. PMID: 31937639; PMCID: PMC6960282.
Meehan CJ, Barco RA, Loh YE, Cogneau S, Rigouts L. Reconstituting the genus Mycobacterium. Int J Syst Evol Microbiol. 2021 Sep;71(9):004922. doi: 10.1099/ijsem.0.004922. PMID: 34554081; PMCID: PMC8549266.
However, I still could not find the recommended DDH threshold for genus delineanation. If you have any information, welcome to reply me.
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