One of my side projects deals with the gut microbiota of Atlantic Cod (Gadus morhua). In 2014 we published a pilot experiment on this where we sequenced the 16S rRNA to get a taxonomical overview of the microbial gut content of 11 Cod specimens caught in the Oslofjord, Norway.
The Cod in the pilot experiment were wild fish and we had not really an idea what we would find. So it was a bit of a surprise that these 11 fish had only a few species of bacteria in common in their gut. Most species belonged to the order Vibrionales and Bacteriodales. Continue reading
Posted in High-throughput Sequencing, Microbes
Tagged amplicon, bacteria, high-throughput, Illumina, microbial community, microbiology, Oslofjord, paired-end, PCR, publication, Quality control, sequencing
The statement that antibiotics are addictive is of course nonsense, but my experiences with this type of medicine gives me often a different feeling. I will explain why… and get rid of some frustration on the way…
I got my first antibiotics treatment when I was three years old to get rid of a urinary tract infection (UTI). That is now almost 40 years ago. Since then I have had an antibiotics treatment at least once a year to treat chronic or acute infections of the areas connected to my urinary tract system. Continue reading
At the moment I am processing quite a few bacterial genome assemblies that I created for various Thermotogae species.
I am comparing assemblies created by CLC, Velvet and the latest SPAdes assembler with REAPR. Both CLC and Velvet were set to only keep contigs larger than 500 bp, but for SPAdes I have not found that restriction. In addition, I did not specify what the coverage cut-off should be in order to keep or thrash low coverage contigs. Continue reading
The reason for this post is that in my current project I need to identify prophages in Thermotogales genomes. Prophages are phages /virusses that are integrated into the genome of their host, in our case Bacteria. To check if our genome sequences have prophages in I ran two phage finding tools on our selection of genomes: prophinder and PHAST. Both tools gave me different answers for my set of genomes.
With that in mind I decided to test one of the newer tools to identify prophages in bacterial genomes, phiSpy. Here I describe how I installed it on my macbook and how I tested that phiSpy works.
Posted in Genomics & more, Microbes, software
Tagged awk, bacteria, bacteriophage, biopython, canopy, commandline, gcc, genome, genomics, grep, installation, Mac osx 10.6.8, macbook, phage, prophage, python, R-statistics, software, Thermotogae
This photo was taken in the Vigeland park, Oslo on the 7th of june, 2013.
It is one of my favourites due to the high contrast, the sun radiating in the trees and the long shadows in the foreground. The walking woman makes the image more interesting, and when I stood in the lane, I just had to wait until somebody would come walking into the lane for me to capture the moment. I actually had several different shots, but Continue reading
November 3, 2014
Tagged B&W, black & white, Camera Canon EOS 60D, Focal Length, light, Oslo, Photography, shadow, sun, trees, Vigeland park, woman
Today I am writing a rant here since I am quite fed up.
Removing the tags and graffiti.
Street art by an unknown artist found in Oslo.
Photo by: Thomas H.A. Haverkamp
The reason for this post is the following: A paper on which I am a co-author was recently accepted for publication in the journal BMC bioinformatics, after being rejected in BMC genomics since our paper was not suitable for that journal. It’s a bioinformatics tools to analyze big blast files, so that is not bad at all. Such news is wonderful, and as a young scientist these are the moments you work for.
So what is making me fed up? Continue reading
In my current postdoc I work on genome analysis of multiple thermophilic bacteria belonging to the phylum Thermotogae.
Electron micrograph of a typical Thermotogae bacterium: Thermotoga maritima. Thermotogae cells (dark structure) are surrounded by a membrane called a “toga”, which is the light circle around the cell. Figure by
The data for such analyses comes from DNA shotgun sequencing. A technique were DNA chains are broken up in many small pieces and with sophisticated algorithms the original sequence is retrieved on our computers. In a perfect world we can combine the shotgun sequences into a complete genome sequence without any holes. But as we know, the world is not perfect. Many issues prevent us from creating the original genome sequence of our bug of interest. This blog is an example of what stops us. Continue reading
Posted in Genomics & more, High-throughput Sequencing
Tagged assembly, bacteria, bad data, CLC assembler, E. coli, fastqc, genome, high-throughput, Illumina, MiSeq, paired-end, preqc, Quality control, Rubbish, sequencing, Thermotoga maritima, Thermotogae