Zit microbiomes

Can't help but love the title, eh? So these researchers did microbial analysis both of skin from clear-skinned students and skin from acne-ridden students. The main bacterium Proprionibacteium acne was present on both but when they did genomic analysis they were able to detect strain-level differences. What was different about the two?

P. acne on acne-ridden students: contained "gene islands" associated with skin issues. A "gene island" is a series of genes in the genome that are in the same segment, associated with some particular process, and are often times thought to have entered the genome via some kind of genetic event.

P. acne on healthy skinned-students had genes that had something to do with viral blocking (the secondary source I was reading was not very detailed on this)

current students will find the last couple of paragraphs in the secondary summary articel at Biotechniques to be interesting. Read it and see if you can see Koch's Postulates popping up

Here's the primary resource if anyone wants to follow up on this

Fitz-Gibbon et al. Journal of Investigative Dermatology aop, (2013) | doi:10.1038/jid.2013.21.

Megavirus chilensis takes current award for biggest virus

From Oct 10, 2011 issue of PNAS

http://www.pnas.org/content/early/2011/10/04/1110889108.abstract

isolated from the sea near Chile, somewhat related to the prior record-holder Mimivirus, contains 1120 protein-coding genes, 1.26 Mbp of DNA, and size of ~0.2-0.3 uM

(image from geekosystem.com)

next generation sequencing strikes again

A while back I noted a "proof-of-concept" study where researchers took a problematic strain of E. coli from an outbreak, pumped out the genomic sequence and analysis in a few days and were able to make great strides in understanding the nature of why this particular strain was a problem.

The same research group have now applied that to Klebsiella pneumoniae Oxa-48 - a bacterial strain responsible for hospital infections in the Netherlands. This really seems to support the importance of DNA technology advances and how genomic level information will be used in the future.

New tech sequences bacterial genome in 2 hrs

http://www.iontorrent.com/technology-how-does-it-work-more/

How it works (if you're into this kind of thing): 

many miniwells, each with strand of DNA (stands that you want to sequence) anchored. Wash specific nucleotide (ex. dATP) over the slide. If that specific nucleotide gets incorporated, sensors detect the release of H+ ions from the reaction which lets you know "yep, that was an A". Generates 100 bp length reads - of course it's 1.4 million of them. They sequenced bacterial genomes (5x-10x coverage) in 2 hours with just 6 hours of prep time for each sample. 

Interestingly enough, they also sequenced Gordon Moore's genome as a test. He's the guy who developed Moore's Law which describes how technology doubles. His genome coast $50K to do but they think that this technology will advance quickly to get close to that target $1000 genome that everyone talks about. Not sure how much the bacterial genomes cost each

Link to the Nature summary

Evidence of ancient antibiotic resistance genes in bacteria

"Researchers Find Antibiotic Resistance in Ancient DNA"

link to NYTimes article

Highlights

• researchers isolated and sequenced DNA from bacteria in 30,000 yr old permafrost
• by comparing the gene sequences to current databases they were able to identify some of the ancient genes as genes involved in antibiotic resistance

for current Micro students - so given that 30,000 years precedes human use of antibiotics (considerably I might add), why did those bacteria have antibiotic resistance genes? (let me know if you think you have an answer...you'll find out later this semester but it's an interesting one to think about in the meanwhile.)

whole genome sequencing of E.coli in outbreak

Article in Genome Technology this month: (click to see it)

stresses the power of the genomics age. Check out this timeline:
- received sample on May 30
- completed genome sequencings on June 1
- Genomes assembled and submitted to NCBI by June 2

Findings
- that E. coli was a new strain
- that E. coli had many antibiotic resistance genes

concept of "Genomic epidemiology"discussed

Another part of this article looks at MRSA and genomic sequencing of 63 isolates - identifying 6700 SNP (single nucleotide polymorphisms) that accounted for the variability seen and related to the microevolutionary changes being seen.

E. coli outbreak resources from NY Times

http://topics.nytimes.com/topics/reference/timestopics/subjects/e/e_coli_bacteria/index.html