Hi Caroline, 

In case of bacterial 16S rRNA gene, using the primers is one of the prerequisite criteria to get sequences related to bacteria. For example using primers such as V3-V4 gives you higher percentage of not sequencing other organisms such as eukaryotic cells.  For fungal ITS, I don't know if this the same but anyway if it trues you need to know such scenario for your case.

Hope answered your question

Best

Hi,

try this link and let us know.

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes

Thanks, that appears to be for prokaryotes. But I've identified them through UNITE database

did you tryed also to use blastn using the option Organism: fungi (taxid:4751)

It gives you back the results only in such kingdom, and may be more accurate because its frequent update!! Actually is the best way to identify using alignment against a database. then, if you get ambiguous results, you can use alternative taxonomically relevant marker that allow you to disambigue your data. in he link you can find an impressive job done, during which the authors designed universal primers for fungal identification.

Hope it will be usefull,

Regards

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713107/

H165

Hi Caroline

See this paper 1

https://www.ncbi.nlm.nih.gov/pubmed/17228792

2

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC88253/

3

https://mmy.oxfordjournals.org/content/41/5/369.abstract

4

https://jcm.asm.org/content/48/3/741.full

5

https://jhs.pharm.or.jp/data/49(6)/49_531.pdf