New directions in biofilm research

paul stoodley P.Stoodley at exeter.ac.uk
Sat Aug 29 04:39:36 EST 1998


Jan Kreft wrote:

> I believe biofilm research in the future should be more 
> quantitative. Quantitative analysis of biofilm structure; 
> beyond beautiful pictures! Quantitative work on 
> pheromones in biofilms.

> That's my $.02.

> Jan Kreft

> Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036
> Cardiff School of Biosciences Fax +44 1222 874305
> Cardiff University E-mail Kreft at cardiff.ac.uk
> PO Box 915, Cardiff CF1 3TL, UK

I quite agree that some kind of quantification of biofilm 
structure is required if we are really going to get a 
handle on the relationships between structure and the 
numerous variables which may influence structure. However, 
this is not a trivial matter. The problem is to find a 
parameter or set of parameters that can define a unique 
structure. When we consider biofilms we are looking at 
patterns made up of the cell clusters and the spaces that 
surrounded them (voids or channels). Some parameters such 
as percent cover or porosity may be useful for describing 
the accumulation process but contain no structural 
information. Fractal analysis seems to be the best bet but 
even then we can not construct a unique structure from the 
fractal dimension alone. To make matters worse when we do 
fractal or other pattern analyis we are using images that, 
because of imperfections in optical systems contain all 
sorts of artifacts. These can be from uneven illumination 
due to surfaces not being completely flat, light scatter 
from the surface, out of focus haze, differential light 
absorption through different thicknesses of biofilm, pH 
influences on fluorescence, photo-bleaching, variations in 
illumination intensity from 1 day to the next etc. etc.. 
Confocal microscopy and deconvolution programs can help 
reduce, but not eliminate these. Further, image anlysis 
requires that images are converted into binary - black and 
white. Fuzzy edges do not threshold well. Slight 
differences in threshold settings can give very different 
patterns and shape perimeter values of which fractal 
dimensions are very sensitive. Magnification will also 
influence how we see the structure. In my experience 
microscopists generally find structures that nicely fit 
into the field of view.

So to wrap up I think that the quantification of biofilm 
structure is a very difficult, but necessary, problem to 
overcome. It will require an interdisciplinary solution 
with components of math, image analysis, microscopic 
techniques, and microbiology. I am aware that a few groups 
have begun to tackle this problem and look foreward to 
seeing how thier work progresses. I also think that this is 
an area worthy of debate in the newsgroup. I should add 
that I am not actively involved in research in 
this area but am an interested onloooker.

Paul Stoodley.


----------------------
Paul Stoodley

Environmental         Tel: 01392 264348       
Microbiology          Fax: 01392 263700

Research              email: p.stoodley at exeter.ac.uk
Group
Exeter University

Biological Sciences
Hatherly Laboratories
Prince of Wales Road
Exeter EX4 4PS. UK.



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