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 …

microBEnet journal club: MetaBAT for reconstructing single genomes from complex microbial communities

    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 …

Simple & elegant solution to a big problem in DNA based microbial diversity studies

A new preprint has come out in PeerJ that presents a simple yet elegant solution to one of the bigger problems in DNA based microbial diversity studies.  The authors (Wenke Smets, Jonathan W Leff, Mark A Bradford, Rebecca L McCulley, Sarah Lebeer, Noah Fierer) show how one can use the addition of an internal standard …

How to choose a metagenomic sequencing strategy – input wanted

So … what goes around comes around.  In 2003 and 2004, I spent a lot of time discussing and arguing with people about what would be the best strategy for making and sequencing Sanger libraries for metagenomic sequencing for the  Sargasso Sea metagenome study coordinated by the Venter Institute (I worked at TIGR at the time and …

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 …