Sunday, January 29, 2012

The controversy over H5N1 research

Ferret, photo by Mika Hiltunen
Since last November, the scientific community has been shaken by what the journal Science has called "a media storm" on H5N1 research. I don't really have an a priori opinion about the potential risks of this research – I am not a virologist, after all – but this is a fascinating controversy which is of importance for microbiologists in general. Science provides us with a special page archiving the news and commentaries related to these events

It all started with experiments on H5N1 avian influenza virus that were meant to study what mutations can increase its transmissibility in ferrets (commonly used as a model animal for influenza research). Two virologists in different countries – Ron Fouchier in the Netherlands and Yoshihiro Kawaoka in the USA/Japan – have managed to create H5N1 strains that are transmissible between ferrets (and thus, potentially, between human beings) and want to publish their independent results in Science (Fouchier) and Nature (Kawaoka). The question that these researchers are willing to answer is: can H5N1 cause a human pandemia, and if yes, what mutations would allow it to do so? Fouchier argues, for instance, that knowing the mutations will allow the researchers to look for them in the field, thus being proactive against the virus spread.

Saturday, January 21, 2012

Bacteria, Archaea, bacteria, or prokaryotes?

In this blog, I use the term ‘bacteria’ (with a lower case), as a generic term equivalent to prokaryotes (that is, Bacteria and Archaea). In this I follow the example of the Brock Biology of Microorganisms, a reference textbook in microbiology (and a wonderful read, by the way).
If you are not familiar with these denominations, here is a brief recap:

Thursday, January 19, 2012

How many bacteria out there?

At first sight, it seems a very difficult question to answer. How can we possibly estimate such a number? Well, William Whitman, David Coleman and William Wiebe - all from the University of Georgia, USA - have provided us with a very exciting proposition in a 1998 article published in the Proceedings of the National Academy of Sciences of the USA.

And the astonishing number is: ~5 x 1030 bacteria!


Our own 7,000,000,000 suddenly seem less impressive.
Whitman and his colleagues noted that the actual total number of bacterial cells had never been assessed, ‘because an estimation of the number of prokaryotes would seem to require endless cataloging of numerous habitats’. It certainly seemed to me that way, but they ended up with a convincing estimation after looking for representative habitats in both aqueous and terrestrial environments. What is striking is that many habitats that show very high densities of bacteria, such as, say, animals’ gut (up to 1011 per g of human colon), account for a negligible fraction of the total. The main crowd is apparently to be found in subsurface sediments and terrestrial subsurface (probably >95%). Hence, what is directly accessible to us (plants, animals, soil, oceans, lakes, etc.) represents a mere 5% of the total bacterial environment. Talking about the tip of the iceberg…