Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process?

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 …

How Cosmetic Use Changes the Microbiome

Almost everyone in developed countries uses cosmetics, from body washes to make-up. In the US, the cosmetics industry makes over $56 billion dollars in revenue. As a society, we use a lot of personal care products. And in order for those products to have a useful shelf-life, they contain antimicrobials – no one wants to open their …

The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)

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 …

Genomic data sharing via BitTorrent, part 2 – BioTorrents to BitTorious

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 …

Healthcare Design discusses design issues relating to hospital acquired infections

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 …

Open Source Building Science Sensors

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 …

Comparing the new 16S rRNA V4 and ITS primers to the old primers-RESULTS!

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 …

“Strategy for American Innovation” – feedback being requested – drown them in microbe-themed emails

Well, it looks like the White House is requesting feedback on funding priorities relating to Science and Technology topics.  See  Federal Register | Strategy for American Innovation.  In the summary they write: The Office of Science and Technology Policy and the National Economic Council request public comments to provide input into an upcoming update of …