Towards minimizing second-generation mis-identification of Blastocystis - continued

Hi all,

I hope you're well!

A great of deal of Blastocystis research involves surveys and increasing our insight into Blastocystis epidemiology. We do this in order to understand what role this organism plays in health and disease, how we get it, where we get it from, etc. 

Central to such research is our ability to 'speak together' - to have a standardised languge - standardised systems. When we analyse Blastocystis DNA sequences obtained from the stool of human individuals or from the environment (including water and faeces from animals), we need to be able to compare them with other sequences to find out whether they are different or not. That's why we developed the subtype system back in 2007, a terminology that is still in use. However, it is becoming increasingly difficult to 'rely' on Blastocystis reference data because of an increasing amount of misinformation in the NCBI Database, a resource that holds genetic information on the many forms that life has taken, and which is probably used by tens of thousands of people across the globe for reference.  

Last year, we published "Towards minimizing second-generation mis-identification of Blastocystis" in Trends in Parasitology, with a view to make our colleagues aware of DNA sequences in the NCBI Database wrongly annotated as 'Blastocystis'. You will there find a collection of sequences that are not Blastocystis even though it says that they are. I hope you think it's informative and helpful. 

Since then, however, more sequences have come to my attention that are named 'Blastocystis' but that are not (they are sequences of yeast):

There are 16 sequences from Yunnan, China: PQ817670-PQ817679 and PV363977-PV363982. 

Moreover, I believe that these four sequences from Korea are also yeast: OR447548-OR447551. 

There may be other recent ones in GenBank that I haven't noticed yet, so watch out.

Therefore: For sequence comparisons, including sequence alignment and phylogentic analyses, I highly recommend using the collection of reference strains collated by Prof Graham Clark available here. I consider these my 'go-to collection', and they can be considered curated. It's the best database we have at the moment for identifying Blastocystis at subtype level.

If you're in doubt, you're always welcome to take contact to me.