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/
So – we have been having a running discussion with people in my lab about one key issue in microbiome studies – how does one store samples prior to doing DNA extractions and does it matter? As background for those who do not do this kind of work – the general principle behind DNA based …
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 …
Just a quick post here pointing people to an article of possible interest: Healthcare-associated Infections Keep Industry On High Alert. In the article Sara Marberry discusses some issues relating to microbes and the built environment in hospital design. Among the topics covered are hydrogen peroxide vapor systems, UV irradiation devices, and copper as possible antimicrobials. Also …
This is just a quick post to introduce some early work products resulting from a really exciting project my team has been working on: the Open Source Building Science Sensors (OSBSS) Project (funded by the Sloan Foundation). The goal of OSBSS is to to design and develop a network of inexpensive, open source devices based on …