Hi,
I have an isolated species from environmental samples, what is the best way to identify it? I think using Sanger sequencing with total 16S will be enough, but I heard that NGS (shotgun method or 16S too) can give better results.
Our study target is just identification without any further biological studies on the isolated species.
If you are sure that you have a single colony pure culture, then you can use Sanger and 16S for the easiest analysis. If you have more than 100 samples, NGS is the same cost or cheaper than Sanger.
However, if you have a mixed culture with more than one type of bacteria, then you should use NGS. Sanger can't distinguish between multiple templates and you'll get "messy" results showing the most common template with a strong background of the rest. I hope that helps!
NGS is relevant in case of environmental samples and is quite expensive. Go for Sanger sequencing if you have a single isolate.
16S Sangers' is still the gold standard for pure isolates. if you think that your isolate is novel or otherwise important, you may rather consider performing an NGS based whole genome sequencing of the isolate.
16S hardly brings you to identify the species rather genera; if this is enough for you, considering you have a pure isolate, I agree with previous comments. If you need to identify the species more precisely, then you could go for a NGS (MiSeq maybe) run for whole-genome sequencing
If it's pure and culturable, I would also advise doing some phenotyping of your bacterium after you sequence the 16S rDNA; in my experience, you usually get an unambiguous assignment of the genus that way, but you will need additional information if you wish to determine if it is a novel species.
A polyphasic approach is still superior to relying solely on sequence-based methods.
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