Hello Qiime team,
My lab is interested in the fungal gut microbiome and recently I started exploring fungal amplicon sequencing, either with ITS or 18S. Many papers mentioned targeting ITS1 (ITS1f-ITS2) but that doesn't reach up to species (as per my current search). Since we are expecting a change in some fungal species like C. albicans & Aspergillus fumigatus in our treatment group but now we can do only amplicon sequencing. Please can someone suggest to me a target region and database or a reference paper that can reach up to species level?
Depending of the specific fungal group you're targeting might want to sequence Calmodulin (this is specifically good with Aspergillus, Talaromyces, Penicillium and Fusarium as a barcode), Transcription Elongation Factor 1 (TEF) and Beta-tubulin (I think these two are good ones for filamentous fungi in a general picture), RPB1 and RPB2 are also widely used.
Hypothetically you could use RESCRIPt to generate a NCBI database as long as it has a bioproject code, but I don't see one for those specific genes. Maybe from OrthoMCL database you can mine it. But as standalone databases... I haven't seen one yet, that'd be a nice endeavour for a fungi gang.
Thanks for your suggestion. Of course, we are expecting changes in specific fungal sps. but we cant ignore other unexpected ones. One of the objectives is to report the fungal gut microbiome. I was thinking if I could use ITS or 18S region and probably try with UNITE or RDP database.
If it's either one of those two, I'd recommend you this article Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation - ScienceDirect.
I mentioned the previous barcodes as they're the ones that are coloquially used in fungal species delimitation and have enough resolution power to reach species level most of the times (TEF and CMD together are truly informative), as long for ITS and LSU, the article mentions (see below a portion of the abstract) that ITS has more power to identify species but a moderate portion of your species will be not resolved by neither, together or individually, that's one of the reasons of needing other barcodes.
Thanks, Luis, this is helpful,
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