After taxonomy assignment, I received some unassigned taxa. I balsted the sequences an I understood they are uncultured bacterium clone.
Now, I have three questions:
1. why they have nor got the special name (genus and spaces)
2. why it is written (clone) after the bacterium word
3. is it a typical result after taxonomy assignment (for soil sample)
-Some names are shared in a photo here.
Hi Mehrdad,
An uncultured bacterium, as the name suggests, is a bacterium you can't get a culture from. A lot of described species of unculturable bacteria carry the "Candidatus" name in front of the genus. For example, the primary symbiont of psyllids, Carsonella rudii, is unculturable and can be found as Candidatus Carsonella rudii. Due to the fact they are not culturable, it is easy to find undescribed "Uncultured bacteria" in many database. It is due to the fact that whoever uploaded the sequence didn't/couldn't described it.
Based on the blast, I assume you are working with bacterial 16S. This might be another issue. Often, the 16S gene is not specific enough to give you a Genus- or Species-level identification.
The word clone was probably added by whoever uploaded the sequence. They had multiple clones and they uploaded all of them.
Finally, yes, for the reasons just listed above, it is common to have unassigned reads from your soil samples.
However, from your picture are cropped the value of similarity of the blast. Is your sequence 100% identical to the list you uploaded? Or are these simply the most similar results? If the % is lower than ~97% your samples are almost certainly something different. BLAST provides you with the most similar results, but if the similarity is not high, it does not mean your sequence is exactly that organism.
Hope this helps
Francesco Martoni
Thanks for reply!
All the assigned and unassigned taxa show 100% coverage.
Finally we reach the conclusion that the unknown microorganisms are unassigned taxa?
Hi mehrdad,
The value that reports 100% for your results is the query% which indicates how much of your sequence is covered by the sequence on genbank (i.e. If they are long the same). The value that tells you how similar they are is the 97.85%
This is usually suggesting they are very closely related, surely from the same genus. But borderline on the species 'general threshold'. Clearly different haplotypes.. Since you haven't received any hit for a similar genus, however, I would say it is something undescribed..
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