Notes from the Biomass

The Nobel Prize in Medicine 2005 is awarded to the Australian scientists J. Robin Warren and Barry J. Marshall for the discovery of Helicobacter pylori.

Marshall infected himself with the bug to prove Koch's postulate, creating a lasting impression on me (and giving me the cramps really). It was also one of the first bacteria that we fully sequenced because there was little known about it 10 years ago. The Helicobacter field received copious amounts of grant money after the initial discovery, making it one of the research fields of bacteriology in the late 90s.

Genomic sequencing of prokaryotes is now in a stage where it's no longer sufficient just to sequence the genome of a prokaryote with some relevance for publication in a good journal. You will have to come up with novel insights and either an interesting bug (getting rarer...) or sequence a bunch of related genomes. The latter was performed by a group at TIGR on Group B Streptococci, reporting that sequencing a few strains are not sufficient to represent all strains in the species.

From the abstract:
Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.


Dr Ferfried Gutfind from the Barbara Cartland Center for Positivistic Genomics says: "The massive sequencing of six strains is a beautifully analyzed, yielding the surprising conclusion that species diversity in some niches will not be covered ever by traditional sequencing approaches. Even "classical" meta-genomics won't help to cover the sequence space in these organisms."
However, Noland Works, chairman of "Bioinformatics students against basically everything" concludes: "Yeah, roight, after sequencing six strains theses guys say that they need to sequence way more species to ever reach their goal in a contributed paper to PNAS. Sounds like setting up publications for references if you ask me." (I won't.)

See also the note in The Scientist.