Tag Archives: bacteria

A short list of tools for shotgun metagenomics

We are currently finalizing our work on the analysis of metagenomes for soils taken from the Etosha National Park, Namibia. These soils were interesting since Zebra blood containing the nasty bug Bacillus anthracis had poured into it. Our aim was … Continue reading

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How many PCR cycles should I use to create an amplicon library?

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 … Continue reading

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My antibiotics addiction means trouble for you!

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 … Continue reading

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Installing phiSpy on my macbook.

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 … Continue reading

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Is improvement possible? Quality control of a Illumina Nextera dataset for the novo genome assembly

In my current postdoc I work on genome analysis of multiple thermophilic bacteria belonging to the phylum Thermotogae. The data for such analyses comes from DNA shotgun sequencing. A technique were DNA chains are broken up in many small pieces … Continue reading

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The microbial communities of inactive Oslofjord pockmark sediments – Part 2

My previous blog post I ended with the main activity of microbes in marine sediments: the breakdown of organic matter deposited from the water column. The sedimentation rate at which organic matter is deposited at the sea bed is dependent … Continue reading

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The microbial communities of inactive Oslofjord pockmark sediments – Part 1

Last Friday I added another article to my publication list. The publication was in the PLOS ONE journal and caries the title: Linking microbiology and Geology: inactive pockmarks affect sediment microbial communities structure. I am very happy with this publication, … Continue reading

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