High throughput full length 16S sequencing

Microbial ecology has benefited enormously from the development of high throughput sequencing technologies, driving the discovery of massive diversity in environments from the ocean to the human body.  Where sequencing of less than one hundred 16S rRNA genes from several samples used to be common place with cloning and Sanger sequencing, we can now generate tens …

Gates Foundation seeking proposals on Characterizing and Tracking Antimicrobial Resistance

This seems like a really good opportunity for some interesting and critically important microbial diversity work: Novel Approaches to Characterizing and Tracking the Global Burden of Antimicrobial Resistance | Grand Challenges This link is to a call for proposals from the Bill and Melinda Gates Foundation on Antimicrobial Resistance.  Specifically they write: We are soliciting …

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 …