I just wrote a small tool to help infer phylogeny from genome data. It’s called quickCOAT (quick Concatenated Ortholog Alignment Tree). You can download it from the quickCOAT Github page and try it out for yourself. quickCOAT works by taking a set of genomes (that is, protein sequences from each genome), using blastp to determine single-copy orthologs within that genome … Continue reading Genome phylogeny using concatenated protein alignments made easy: quickCOAT
Cable bacteria were first discovered back in 2012, and although they’re quite narrowly defined phylogenetically, we’ve referred to them as “cable bacteria” rather than a proper scientific name. Names have now been proposed in a recent publication: D. Trojan, L. Schreiber, JT Bjerg, A. Bøggild, T Yang, KU Kjeldsen, A Schramm, (2016). A taxonomic framework for cable … Continue reading Cable bacteria now have a name: genera Electrothrix and Electronema
Those of us working with genes and genomes from uncultivated organisms have been trapped in a weird nameless limbo for a long time. To give a microorganism a proper latin name you had to have it in pure culture, with few exceptions. However, just because a strain isn’t in culture it doesn’t mean we don’t … Continue reading Choosing good working names for your bugs can really help
Since we started cultivation-independent analysis of microbial DNA, there’s been an explosion in the number of phyla (or “candidate phyla”, “phylum-level groupings”, etc.). We’ve found a lot of microbes whose 16S rRNA genes, or other marker genes, do not cluster within established phyla, and therefore we create new phyla to accommodate them. This creates a … Continue reading New “tree of life” paper suggests a more rational way to define phyla
Once upon a time, scientific papers used to be available on real paper, and only on real paper. I’m lucky enough to have started doing science in the era of digital publication, but recently I’ve started to suspect that we’re vastly under-utilising the potential of digital publication. Our papers are still PDFs, i.e. static on-screen … Continue reading Dynamic plots could be really useful for science – sediment cell count/age/TOC example
When I first started dabbling in bioinformatics in 2007, I was advised to use either Mac OS X or Linux. Linux had a powerful command line, so it was simple and trivial to do stuff like `fgrep -c “>” filename.fasta` to find the number of sequences in a fasta file, or `fgrep “>” | cut … Continue reading Did Windows just become a much better option for bioinformatics?
The Center for Geomicrobiology at Aarhus University in Denmark (where I work) is now on Twitter and Facebook. These accounts will mostly be used to let the world know when we publish a paper, but occasionally for other news too. Twitter: @centerfgeomicro Facebook: Center for Geomicrobiology So follow us on Twitter or Like us on … Continue reading Center for Geomicrobiology is now on Twitter and Facebook
There are many well characterized organohalide-respiring bacteria from the phylum Chloroflexi, especially from within the class Dehalococcoidia, like Dehalococcoides mccartyi. The question has always been what context this trait of obligate organohalide respiration (and the genes encoding the necessary reductive dehalogenases) evolved in – we’ve often looked to ocean sediment, as the ocean is where … Continue reading Finally, a reductive dehalogenase in a marine deep-subsurface Chloroflexi genome
A while back I wrote a blog post about metabolic partitioning in anaerobic environments, and wondering why we hadn’t found a methanogen capable of using more complex compounds, like amino acids or sugars, as catabolic substrates rather than relying on other fermenters as a middle-man to serve up hydrogen, acetate, or a few other selected compounds … Continue reading Could this be the universal methanogen?
The idea of posting “preprints”, or un-reviewed, unpublished manuscripts ahead of normal review and publication, has been gaining popularity recently (although it’s been around for a long time in other fields, like physics). Especially now that we have a preprint server dedicated to biology, there’s people saying that publishing preprints can help science be disseminated … Continue reading Why I don’t think I should submit preprints