Taxonomy assignment_query

Hello Sir/Ma’am,

After the taxonomy assignment, Basidiobolus species otu was high in all twelve ITS sequencing samples (which was taken from twelve different patient’s eye) . I did open reference clustering (99% identity), I got this same problem.

How come Basidiobolus; haptosporus var. minor organism was abundant in all twelve different sample when compared to other organism?

I didnt get this kind of problem in my 16SrRNA sequencing sample data taxonomic assignment. The only difference between two taxonomic assignment analysis was I didn’t do training the Naive Bayes classifier analysis with our ITS primer sequence before performing the taxonomy analysis with unite database. will it affect the taxonomic assignment analysis?

I have attached my otu file here for your reference. Kindly have a look and let me know your suggestions.

Thanking you in advance. Looking forward to your reply.
[taxonomy.csv|attachment]
(upload://pKBYtWuPZSPsHkW3AxQ351V9exB.csv) (105.3 KB)

Hi @Asha1,
Are you saying that one taxon is prominent across all of your ITS samples, but this is unexpected?
If so, why is it unexpected? If not, please clarify your situation. Any chance you sequenced mock communities alongside your samples? If an unexpected taxon showed up in your mocks, that would be a good sign there is indeed a problem.

A number of things could be happening here. It could be the case that the taxon is abundant, that there was an error or contamination event in storage, lab, or sequencing, or that there are issues with the bioinformatics methods used. Any further information you can share about your process and reasoning will make it easier to help.

Best,
Chris :wolf:

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Thank you so much for your reply sir

I still cant troubleshoot where the problem occurred. Our objective is to find the ocular microbiome of fungal keratitis (corneal infection). So, we got corneal swab sample from 12 different fungal keratitis patients and did ITS sequencing (outsourcing: Genotypic technology, Bangalore).The taxonomy result was Basidiobolous species was abundant in all 12 samples.

I followed qiime protocol only for ITS sequencing data analysis. I have attached commandline for your perusal. Kindly let me know If there is any mistake.

Itsdata_qiimecommandline.tsv (2.5 KB)

Thanks for the background info, @Asha1.

I’m happy to help you troubleshoot, but I do not know anything about your study domain. Please address the questions from my reply:

Thanks,
CK

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