Could be interesting: The Metagenomics MVP Challenge v1.0

Source: NIST Challenge — CosmosID – Exploring the Universe of Microbes This could be interesting.  NIST & COSMOS ID and ABRF are conducting a metagenomic sequencing methods challenge. From their site: When using metagenomic methods to assess the content of a complex microbial sample, there are many steps in the measurement process where bias might …

Wanted – recommended service providers for microbial sequencing (genomes, rRNA, metagenomes, etc)

In January 2014 I wrote this post about “microbiome” sequencing services. I have gotten many outside requests for the following information — what places (companies, Universities, government agencies, etc) provide contract services for rRNA PCR and sequencing? Source: Request — Information on Places that do rRNA sequencing as a service — microBEnet: the microbiology of the …

New paper of interest on “Phylotags” – High-resolution phylogenetic microbial community profiling

This seems like it could be of interest to microbial community researchers: The ISME Journal – High-resolution phylogenetic microbial community profiling Abstract (with bolding by me) Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more …

Evolution of DNA Sequencing

Last week I had the opportunity to present a lecture on the history of DNA sequencing in Jonathan Eisen’s EVE 161 Microbial Phylogenomics course. This lecture uses Elaine Mardis’ excellent review papers on the next generation sequencing methods as a guide (and required reading). You can see videos of both Dr. Mardis and Dr. Eisen presenting lectures on this topic. …

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 …

IBM and Mars kick off new food-supply sequencing project

IBM and Mars put out a joint press release today announcing a new effort to use metagenomics to study microorganisms in the food supply chain. The new initiative, called the Sequencing the Food Supply Chain Consortium (SFSC), will use metagenomics and metatranscriptomics to establish what they call a “microbial baseline” that can later be used …

Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project: Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 1(3):e00172-13. doi:10.1128/genomeA.00172-13. Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. strain UCD-THP (phylum …