I was at a meeting a few weeks ago where the topic of fungal diversity surveys was discussed and many people there commented on how ITS based surveys (one of the main approaches for culture independent studies of fungi) had some limitations. ITS stands for the “internal transcribed sequence” and it is a region in …
Microbes in subways Bioaerosols in the Barcelona subway system – X. Triadó-Margarit – Indoor Air ($6 to rent, $38 to own) (…) We examined the microbiological composition and abundance in space and time of bioaerosols collected in the Barcelona subway system during a cold period. (…) Multitag 454 pyrosequencing of the 16S rRNA gene was used to …
So having gained a reputation as the toilet guy (e.g. Slate, RedOrbit, microBEnet) I felt like I just had to write about this article. Plus it sounds really cool. This article is by Jennifer Fouquier (also cool) who is in Scott Kelly’s lab at UC San Diego San Diego State. The title “Rapid assemblage of …
A recent post highlighted issues with analyzing fungal ITS data, and that inspired my labmate Sydney Glassman and me to want to share our experiences with using amplicons to characterize fungal communities. We are very excited that people are interested in delving into the wonderful world of fungi, and we wish to share our love …
I wrote a post on the Seagrass Microbiome website yesterday about my struggles with fungal ITS sequencing data which I thought I’d share here as well in case anyone is looking to jump into the fungal fray. To summarize: changing the default method of the QIIME assign_taxonomy.py script from “UCLUST” to “blast” dramatically increased the …
Another SIGS meeting report of interest: Meeting Report: Fungal ITS Workshop (October 2012) | Bates | Standards in Genomic Sciences. This one discusses issues in sampling and characterizing fungi using ITS sequencing.