Showing posts with label metagenomics. Show all posts
Showing posts with label metagenomics. Show all posts

Friday, February 3, 2012

trying to understand a microbe that can't be cultivated

BioTechniques - Seawater Microbe’s DNA Demystified

A theme that I put out there all the time in my class relates to how we have been discovering over the years how we often don't even know that the microbes that are most dominant in a system exist, much less what they're doing. In this article, the authors run a metagenomic study - sequencing all the DNA that's in a sample of water they take from some surface seawater. They knew that something noncultivatible dominates that but did not have it in culture. From the metagenomic DNA they were able to sew together all the sequences that presumably came from that dominant organism thereby giving them the genomic data that they could analyze. With that data they could analyze what capabilities that microbe has - metabolic pathways, motility, ability to deal with light, etc. Very fascinating. This kind of approach will become increasing important in the next years

did I mention that the group they studied make up 50% of the microbes in the ocean? And can't be cultivated? That's wild that it could be that important in the system yet we can't cultivate it. It would be like trying to talk about the trees on Elon's campus but not being able to see the oaks....

Here's the link to the original article

http://www.sciencemag.org/content/335/6068/587.abstract


Wednesday, July 6, 2011

Isolation of a cellulase enzyme capable with optimal temp of 109 deg C

http://newscenter.berkeley.edu/2011/07/05/hot-springs-microbe-yields-record-breaking-heat-tolerant-enzyme/

highlights: 

  • Isolated from a hot spring
  • an archaea
  • metagenomics later used to implicate a few other archaea as well

Friday, June 24, 2011

tidbits from the metagenome

tidbits from June'11 issue of Microbe

- "metagenomic analysis suggests fourth domain within tree of life"

- gut microbiome contains 3.3 million genes!! Humans have ~20-30K so as the article points out human genes account for less that 1% of the gene types that are active in the body.