TDU (M. oxydans) info, and what lies ahead

The ominous clouds in the sky and the cool breeze in the air can only mean one thing – Summer is gone and it’s time to stop slacking off.  With that in mind, I thought I would update everyone on how my work on Microbacterium oxydans has progressed.  Now that the bioinformatics  work is more or less done, I’ve been putting all of the information together and trying to make it sound somewhat coherent.  I am currently halfway to the 500 word limit that the Journal of Bacteriology has imposed for genome announcements, so the end is definitely in sight but  more work still needs to be done.   It’s going to be interesting managing classes, this paper, and another project I’m working on (more on that later) but I’m optimistic that the paper will be completed within the next week or two.

M. oxydans infothat I’ve written about so far:

  • Microbacterium have been found in many human associated environments (blood, radioactive sites, food) and also act as plant pathogens in some cases. TDU was found in a toilet (thanks David!)
  • The a5 pipeline produced 1,131,749 paired end reads with an average length of 133 base pairs, giving 80.358 fold coverage after error checking and quality control were performed. The N50 value of the genome is 1,056,891 bp (this is a weighted median, denoting the contig size in which 50% of all bases are contained in contigs that size or greater). I still need to include scaffold and contig length information, such as median and mean values
  • The size of the genome is 3,746,321 bp comprised of 44 contigs in 8 scaffolds
  • RAST was used to automatically predict the genes present in the TDU sequence. The default RAST gene model was used to make these predictions.  The program predicted 3,667 coding regions and 357 subsystems.  I will probably go more in depth into this area of the paper
  • A phylogenetic tree of 16s sequences was created to confirm TDU as M. oxydans. I still need to include information about percent identity

Once this is all taken care of, I will be undertaking a new, independent project through the Provost’s Undergraduate Fellowship.  My proposed project will deal with milk pasteurization in regards to cheese safety and quality.  I will be creating cheeses using pasteurized cow’s milk and raw, unpasteurized cow’s milk and assessing the microbial content of the final products to see if there is a correlation between pasteurized milk and cheese safety.  I will look for and attempt to identify and quantify known cheese pathogens, such as E. coli, Salmonella, and Listeria monocytogenes.  The debate between raw milk and pasteurized milk has been ongoing, but with this study I can hopefully provide a little bit of insight into the controversy. Right now I’m writing my proposal (due in 3 weeks, yikes!) and doing hours of research to make sure I am prepared to undergo this project, but it’s still early and I have a lot to learn.

UPDATE (10/15) – So I was able to put some more time into the paper and it looks like I’ve gotten all of the information I need down. I’ll be sending it off to David so he can critique it

2 thoughts on “TDU (M. oxydans) info, and what lies ahead”

  1. Wow – that is a very big N50 which means the genome is in great shape. I note – I think the N50 means 50% of the DNA is in contigs of that size or bigger (not 50% of the contigs are bigger).


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: