Minion

Some updates

Time flies and I have been very bad in updating this page. The last post is almost two years old and a lot of things have happened. I have for instance temporary left Sweden and I am now located in Boston since some months. This will hopefully lead to some new collaboration and interesting projects. New sequencing methods have also emerged and I have probably left the era of 454 and Ion torrent behind me. Most of my sequencing is now done using Illumina (HiSeq/MiSeq) and Pacbio.

Phylogeny of Francisella

Updated phylogeny of the Francisella genus

We have recently published an updated Francisella genus based on whole genome sequencing data [1]. Prior to our study, relatively few strains of Francisella had been genome-sequenced and previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F.

Ion torrent data finally arrived...

I ordered some Ion torrent data early this spring because I was curios to get some fast sequencing of novel Francisella strains, in addition to sequence our reference strain. Unfortunately, it wasn't that fast and the regular Illumina Hiseq 2000 sequences arrive much faster (around 2½ months).

The nice outcome is that I now have an old Sanger reference sequence, Illumina 100bp pair-end reads and Ion torrent 150bp reads from the same strain, I will try to get the comparisons post here once they are ready after the vacation.

Cod

Francisella species in Norwegian coastal and fresh waters

We recently published an article reporting the diversity and distribution of Francisella species in Norwegian coastal and fresh waters [1]. In total, samples were obtained from 149 and 64 seawater and freshwater sites. Francisella-related bacteria were identified in approximately 30% of seawater sampled sites, mainly in southern Norway, although a single positive sample was identified in the far north of the country. No PCR positives were identified from the freshwater sources.