Sequenced a marine actinobacterium for 16S, assembled and identified in Eztaxon. Obtained 98.58% similarity with Citricoccus yambaruensis. Can it be a new species? Can I go for whole genome sequencing to find out the novelty?
Seeking for valuable comments and directions...
Thanks in Advance.
Hello Sivasankar, if the 16S rRNA sequence similarity of your isolate with the referenced strain is 98.58% which is greater than 97%, then it means that your isolate is neither a new strain, which % similarity should be
Hi Siva. As per sequence details given in above image. You have 1338 bp 16S rRNA gene only. What I understand in taxonomy, one base can change identity of any bacterium. It may be correct or wrong amplification. You need at-least more than 1400 bp 16S rRNA gene sequence after trimming and removing chimeras if any. Then see at EzTaxon what it says. Later you may think on other experiments.
I hope this will be useful.
With that % identity, it's hard to tell if it's a new species, but it's likely Citricoccus or closely related. You'd need to sequence more genes or the whole genome or do the experiments suggested by Dilipan E and Maurice Ekpenyong to be sure. Perhaps sequencing is easier...
Anyway, I would rely on any interesting phenotypic characteristics to consider if it's worth to sequence. Why are you isolating marine actinobacteria in the first place? If you are just looking for something "new", it should have less than 97% 16S gene identity.
Sivasankar Palaniappan hey mate.
Do you have the whole genome?
If you do then compare it to it's closest 16S match that has a whole genome using ANI/AAI analysis - http://enve-omics.ce.gatech.edu/aai/
http://enve-omics.ce.gatech.edu/ani/
Then if it's close to a known species then you can try DDH to see if it's a new subspecies.
You can message me anytime if you have questions?
I do this all the time and I am always in search of species.
I am "Microbe Hunter"! - haha.
Good luck
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