December Mothur Workshop, part 2

Here are my notes from day 2 of the Mothur workshop taught by Pat Schloss (pdschloss at gmail.com) in December 2015. For those who are interested in learning to use Mothur for microbiome studies, Pat will be teaching another one in February. Mothur is better for bacterial characterization than eukaryotes because the sequences are aligned before OTU clustering. This …

December Mothur Workshop, part 1

Pat Schloss (pdschloss at gmail.com) offers excellent workshops on the Mothur software for analyzing 16S rRNA data for bacteria. He’s just announced the next one (February 8 to 10, 2016 near the Detroit airport). I had the pleasure of attending the December workshop. A diverse and international group attended the workshop, with many folks who are interested in the human microbiome. …

The Making of MetAnnotate

Blog post prepared jointly by Andrew Doxey (@acdoxey) and Josh Neufeld (@joshdneufeld) The “aquariome” Back in 2013, as part of a project assessing aquarium microbial communities and their role in nutrient cycling, Laura Sauder (graduate student in the Neufeld lab) sequenced a shotgun metagenomic library from a freshwater aquarium biofilter that was installed on this …

Important paper: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. For anyone interested in rRNA studies of microbial communities, ancient microbiomes, or analysis of samples with small amounts of DNA this …

Wrap up of talk by Norm Pace on “Metagenomics and the Tree of Life”

Norm Pace gave a talk at UC Davis yesterday on “Metagenomics and the Tree of Life”. I and a few other people posted live Tweets from the talk which I have compiled together via the Storify system.  This “Storify” is embedded below. In addition, Lisa Cohen, who was at the talk posted her notes which …

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 …