In scientific manuscripts, we tell stories of our research, generally in straight-line fashion with clear motivations and results. This type of research is rare (in my experience), with stories, motivations, and applications only realized post hoc. This is the nature of science, and our recent ISMEJ publication is no different. With “16Stimator: statistical estimation of …
Cheese has often been studied as a microbe-rich environment. The variety of interactions in one of the tastiest foods on earth (personal opinion) is still only just being discovered. A recent paper from Stellato et al attempts to study these interactions by swabbing and sequencing the food itself and the various surfaces it comes into contact with during the …
A new open access paper in Frontiers in Microbiology looked at the microbial communities found on buildings of the Auschwitz concentration camp in Poland. I’m currently travelling, so I only have time to post the abstract here. One Hundred Years by The Cure, a song about war and destruction, seemed a good choice for this post. …
This blog post by Jennifer Glass, assistant professor in the School of Earth and Atmospheric Sciences at Georgia Institute of Technology, chronicles her journey from first falling in love with marine science as a college freshman, to the first original research paper out of her own lab, now openly accessible: Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, …
A new PLoS One article from Dorado-GarcÃa et al. on the effectiveness of certain countermeasures to antimicrobial resistance shows some encouraging results. The study used MRSA levels as a positive indicator for antimicrobial resistance in Dutch veal farms. There were three methods of reducing MRSA levels in the farms that were studied: one program used protocol-driven methods, one used …
Here are the microbiology of the built environment papers that were already featured on my MicrobiomeDigest blog this week, all in one handy edition. The first paper is about dust, so Siouxsie & The Banshees – Cities In Dust would match perfectly. The ecology of microscopic life in household dust – Albert Barberán – Proceedings B …
A moderately new paper is out that is an excellent example of how biases in DNA extraction can have major impacts on inferences from culture independent DNA studies. The paper is in what I think is a generally non open access journal (Computational and Structural Biotechnology Journal) for fortunately has been made open access Source: …
Three weeks ago I stood in front of the 60 attendees of the STAMPS course and asked, “How many of you are currently working with shotgun metagenomes?” Ten to fifteen people raised their hands. In contrast, almost all had their hands in the air when I asked how many were expecting to work with shotgun …
I recently came across this detailed review “Metanalysis: Cleaning Hospital Room Surfaces to Prevent Health Care—Associated Infections” from the Annals of Internal Medicine. I think this is a fascinating topic because hospitals have to walk such a fine line with regards to microbes. On the one hand they want to avoid the probably counter-productive “kill …
There is an interesting paper out a few days ago in PeerJ: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. By Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang​. The key to what they do in the paper is summarized in Figure 1: The legend is below: There are three preprocessing steps before MetaBAT is …