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 …
This week in eLife, our lab published a study entitled Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis (NEC) development. Spearheaded by a talented Banfield Lab post-doc, Tali Raveh-Sadka, in collaboration with Michael Morowitz’s Lab, the study aimed to find the causative agent in an outbreak of NEC cases that …
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 …
I’ve gone public with my default QIIME workflow. I hope this will be helpful to some, and I encourage anyone with QIIME skills to read through it to see if I’m missing anything. Brief blog post about it is here: http://jennomics.com/2015/02/20/ipython-notebook-for-basic-microbial-ecology-analysis-using-qiime/ and the notebook is hosted here: jennomics.github.io/QIIMEbyJennomics/
IBM and Mars put out a joint press release today announcing a new effort to use metagenomics to study microorganisms in the food supply chain. The new initiative, called the Sequencing the Food Supply Chain Consortium (SFSC), will use metagenomics and metatranscriptomics to establish what they call a “microbial baseline” that can later be used …
I was recently contacted by a SRA curator to submit the raw pacbio datasets that go with genomes that were deposited to NCBI. I did go through with the submission and will share what I did and my experience doing so. Be prepared to answer a lot of questions regarding your project as well as …
In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to …
As someone who uses sequence data for most of my research, I am continually happy with the fact that sequencing continues to get cheaper and easier and faster and bigger and better and more and more and more. Along with such continued advances, sharing the data produced by such sequencing has become somewhat challenging at …
The Knight lab has been working hard testing new primers for 16S rRNA amplicon production and its time to share our progress. So far, the 16S rRNA V4 region forward primer (designated 515f) has been paired with five different reverse primers (806r, 926r, 967r, 1048r, and 1391r) to amplify ribosomal RNA from bacteria, Archaea, and …
The idea for GenomePeek began two years ago when I was working with Karl Klose, Liz Dinsdale, and Rob Edwards to assemble a P. salmonis genome that was being particularly difficult, even though we had 9 gigabases of sequencing. To check whether it was a single isolated genome I pulled out all the 16S reads …