microbiome
mikethemadbiologist | July 21, 2010Since I'm at a Human Microbiome Project meeting, and don't have time to write, I thought this post from the archives of Mad Biologist was appropriate:
A while ago, I talked about some things biologists should learn, and the glaring omission was mathematical fluency. I bring this up because one of the things the Mad Biologist does is work on the Human Microbiome Project (between that, and fighting evil, we are very busy...). The part of the Human Microbiome Project ('HMP') that I'm involved with is a consortium of four sequencing centers and an informatics center, whose goal is to sequence…
mikethemadbiologist | June 16, 2010Yes, you read the title correctly--I'll get to that in a bit. Nicholas Wade's article about the Human Genome Project (HGP), "A Decade Later, Genetic Map Yields Few New Cures" has been getting a lot of play. Thankfully, ScienceBlogling Orac summed up perfectly my thoughts about both the science and hype surrounding the HGP, so I don't have to. But this post by Mike Mandel has been getting some play:
My nomination for the most significant economic event of the past decade: The failure of the Human Genome Project to thus far deliver medically significant results.
I dunno: the collapse of…
mikethemadbiologist | May 3, 2010For those who haven't heard rightwing extremist Virginia Attorney General Ken Cuccinelli has subpoenaed all of the documents related to climatologist Michael Mann's state-funded research while Mann was at the University of Virginia (italics mine):
In papers sent to UVA April 23, Cuccinelli's office commands the university to produce a sweeping swath of documents relating to Mann's receipt of nearly half a million dollars in state grant-funded climate research conducted while Mann-- now director of the Earth System Science Center at Penn State-- was at UVA between 1999 and 2005.
If Cuccinelli…
edyong | March 3, 2010You are outnumbered by a factor of 10 to one, by forces you cannot see. Your body has around ten trillion cells, but it's also home to a hundred trillion bacteria. For every gene in your genome, there are 100 bacterial ones. Most of these are found the dark, dank environment of your bowel but their incredible diversity is being brought to the surface. Say hello to the gut metagenome.
Together with a team of international scientists, Junjie Qin and Ruiqiang Li from BGI-Shenzen had the unenviable task of studying the bacteria from the faeces of 124 Europeans. They used a formidable and…
mikethemadbiologist | January 19, 2010Since I'm on-route to a Human Microbiome Project meeting (uncharacteristically, it's being held in a climate-friendly location--Houston; last year, it was held in Boston. In January.), reviewing this paper about the GEBA project, the Genomic Encyclopedia of Bacteria and Archaea, seemed appropriate. Sequencing bacterial genomes not only tells us a lot about the biology of the organisms sequenced, including their function, potential ecology, and evolution, but it also has a far more pragmatic use too.
As we try to understand microbial communities using DNA sequencing, including those microbes…
mikethemadbiologist | January 11, 2010It turns your bacteria Jewish*. Seriously, the strong finding of this article was completely ignored. Anyway....
A recent paper describes the effect of circumsion on the bacteria that live on the penis. The authors swabbed uncircumsized and circumsized penises, and then PCR amplified the 16S rRNA gene which is found in all bacteria, and can be used as a 'barcode' to identify bacteria. This article has received a lot of attention because of this speculation in the discussion (italics mine):
The observed decrease in anaerobic bacteria after circumcision may be related to the elimination of…
mikethemadbiologist | June 7, 2009I realize that the typical format for blogging is to find something that pisses you off and then rant about it, but I actually like the recent workshop report by NHGRI, "The Future of DNA Sequencing at the National Human Genome Research Institute." (pdf file) While I'll have more to say about the report overall, I liked the section about the Human Microbiome Project (the goal of the HMP is to use sequencing technologies to understand how the microbes that live on us and in us affect health and disease).
I was happy to see that NHGRI still thinks that it has a role in funding the HMP. It's…
edyong | May 28, 2009It's a diverse melting-pot of different groups, with hundreds of different cultures living together in harmony, many sticking to their own preferred areas. No, not London, New York or any other cosmopolitan city; I'm talking about your skin. It may all look the same to you, but to the bacteria living on it, it's an entire realm of diverse habitats.
From a microscopic perspective, the hairy, moist surface of your armpits is worlds apart from the smooth, dry skin of your forearms. Even though they are separated by mere inches, these patches of skin are as different to their microscopic…
mikethemadbiologist | October 7, 2008I'm not certain you can have all four. Let's start at the beginning.
Just to review, one way to examine the human microbiome--the organisms that live on and in us--is extract the DNA from a biological sample (usually something from a person that is slimy, stinky, or both, such as feces or a nasal swab), and then amplify, using PCR, the 16S rRNA gene. 16S is found in all archaea and eubacteria, and can serve as a barcode that can be used to identify microbes*. This approach means you don't have to culture the bacteria and count things on agar plates (assuming they can be cultured in the…