We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a …
Join Dr. Rob Knight for a Reddit AMA tomorrow, September 17, 10-11:30am MT. This will be a great opportunity to ask one of the foremost microbiome researchers in the world about anything and everything related to the human microbiome, the American Gut Project, the Earth Microbiome Project, and, well, anything you can think of related …
We recently submitted a paper to biorxiv on the estimation of average genome size from shotgun metagenomics data and it’s application to the human microbiome (http://biorxiv.org/content/biorxiv/early/2014/09/11/009001.full.pdf). It is currently undergoing peer review. This study was motivated by the troubling observation that many universal single-copy genes appear to vary significantly across metagenomes. How can this be? …
Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 Progress on the microbiology of the built environment, especially through amplicon studies, has been extremely rapid. However, analyzing and combining datasets has been increasingly challenging, especially as investigators use different strategies and techniques to collect their individual …
Announcement: Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 Application Deadline — October 30, 2014 Progress on the microbiology of the built environment, especially through amplicon studies, has been extremely rapid. However, analyzing and combining datasets has been increasingly challenging, especially as investigators use …
Back in May, I had the pleasure of attending a talk at ASM 2014 by Didier Raoult on the the importance of culturomics. At one point in the talk he mentioned that they just came out with a paper that showed that they could get anaerobes to grow in the presence of oxygen if you …
While not exactly the microbiology of the built environment, studies of the human microbiome are the next closest thing and and understanding of both will be critical to creating healthier living environments. The American Gut project is the largest, crowdfunded/citizen science human microbiome effort, with over 3,000 participants so far (including myself). In addition to …
In response to Hal Levin’s comment on my previous post: Thank you ISIAQ for the “Vocabulary of the Indoor Air Sciences” I am starting to put together some definitions and background information on the terminology of microbial ecology studies. Please suggest any / all terms that you think would be useful to define and I will …
Just wrapped up the 3rd Annual Sloan Conference in the Microbiology of the Built Environment. We saw 20 presentations, a number of posters, and had some time to set up new collaborations, argue methods, and eat good food. I’m going to take a different approach to my conference report here, I’m only going to talk …
Microbiology is on a roll, it’s been an amazing couple decades of discoveries that have transformed our understanding of the roles that microbes play in human health. And this knowledge has pushed its way into popular culture. Every couple of days I see another popular media article about the influence of microbes on something else; …