The Bioinformatics Blog

• MEGAN MEtaGenome ANalyzer. A stand-alone metagenome analysis tool.
• Metagenomics and Our Microbial Planet A website on metagenomics and the vital role of microbes on Earth from the National Academies.
• The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet A report released by the National Research Council in March 2007. Also, see the Report In Brief.
• IMG/M The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI.
• CAMERA Cyberinfrastructure for Metagenomics, data repository and tools for metagenomics research.
• A good overview of metagenomics from the Science Creative Quarterly
• list of Metagenome Projects from genomesonline.org
• MG-RAST publicly available, free, metagenomics annotation pipeline and repository for pyrosequences, Sanger sequences, and other sequence approaches.
• Human microbiome project
• MetaHIT official website for the EU-funded project : Metagenomics of the Human Intestinal Tract
• Annotathon Bioinformatics Training Through Metagenomic Sequence Annotation
• Metagenomics Metagenomics research and applications

With IBM tossing it’s hat into the ring of “next-next-generation” sequencing, I’m starting to get lost as to which generation is which. For the moment, I’m sort of lumping things together, while I wait to see how the field plays out. In my mind, first generation is anything that requires chain termination, Second generation is chemical based pyrosequencing, and third generation is single molecule sequencing based on a nano-scale mechanical process. It’s a crude divide, but it seems to have some consistency.

At any rate, I decided I’d collect a few videos to illustrate each one. For Sanger, there are a LOT of videos, many of which are quite excellent, but I only wanted one. (Sorry if I didn’t pick yours.) For second and third generation DNA sequencing videos, the selection kind of flattens out, and two of them come from corporate sites, rather than youtube – which seems to be the general consensus repository of technology videos.

Personally, I find it interesting to see how each group is selling themselves. You’ll notice some videos press heavily on the technology, while others focus on the workflow.

As an aside, I also find it interesting to look for places where the illustrations don’t make sense… there’s a lovely place in the 454 video where two strands of DNA split from each other on the bead, leaving the two full strands and a complete primer sequence… mysterious! (Yes, I do enjoy looking for inconsistencies when I go to the movies.)

Ok, get out your popcorn.

First Generation:
Sanger Entry: Link

Second Generation:
Pyrosequencing Entry: Link

Read more…

There was an article on probiotics in the New York Times today. By Tara Parker-Pope it addresses some important issues rarely covered in the press about probiotics (see Well – Probiotics – Looking Underneath the Yogurt Label – NYTimes.com).

On the one hand, the article does a decent job of pointing out that there is great strain to strain variation among microbes labelled as probiotics. In this regard there is a great quote by Gregor Reid:

Lactobacillus is just the bacterium,” said Gregor Reid, director of the Canadian Research and Development Center for Probiotics. “To say a product contains Lactobacillus is like saying you’re bringing George Clooney to a party. It may be the actor, or it may be an 85-year-old guy from Atlanta who just happens to be named George Clooney. With probiotics, there are strain-to-strain differences.”

Read more…

Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read – an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor – To Fight Cancer, Know the Enemy – NYTimes.com)

This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.

First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.

Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.

Read more…

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing