Another important paper: microbiome studies “strongly influenced by sample processing & PCR primers”

Another paper on how sample processing (and in this case PCR primer choice) can influence microbiome studies.  And another one that is definitely worth looking at: 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice. Microbiome 2015, 3:26 doi:10.1186/s40168-015-0087-4 by Alan W. Walker, Jennifer C. Martin, …

Important paper on how biases in DNA extraction can shape inferences from metagenomics (re spore formers)

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: …

Anvi’o: a new platform to work with metagenomic data

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 …

Empiricist League #16 meeting at Union Hall on The Hidden DNA of NYC

OK this looks like it will be really really interesting.  Laurie Garrett sent me a link to this announcment about a meeting of the Empiricist League in New York: What are the 15,000 microscopic lifeforms that live on the subway? How disgusting are the contaminants in the Gowanus Canal? Can we use technology to stop …

Microbiome informed design – air quality, avoiding filtering, and lichens

This is one of those stories / articles / posts that simultaneously fascinates me and freaks me out a bit and for which I fluctuate wildly between those two points of view: bioME – RSA Human By Nature Entry on Behance By Candice de Aguiar Her basic design idea here is to allow for more microbial diversity …

Interesting and important new paper: Microbial composition of purified waters 

There is an interesting and potentially important new paper out from Caitlin Proctor, Marc Edwards and Amy Pruden: Microbial composition of purified waters and implications for regrowth control in municipal water systems in Environmental Science: Water Research & Technology.  The abstract is below: