analysis
Bacteria rule!
The start of a new era in bacterial microbiology?
Molecular biology and molecular needed for its maximal exploitation. For away from relative youth. Indeed, the cur-
genetics now the fastest growing example, the molecular basis of the stand- rent membership reflects the golden years of
research fields and a billion-dollar indus- ard blue white colour test for identifying microbial molecular biology from the
try started in the 1960s and 1970s with insertions in commonly used bacterial 1960s to the early 1980s. It was with this
biochemists and microbiologists working plasmids is rarely properly understood, as background, plus the fact that the explo-
on bacteria and their viruses. The basic is the need to use these plasmids in the sion in bacterial genome data is finally
knowledge on macromolecular process- appropriate strains. attracting the much needed interest in
ing and its control, as well as the breaking bacteria, that some 50 bacteriologists
of the genetic code, all came from work gathered in Heidelberg last November to
It has become even clearer that
on these easily propagated and analysed discuss the future of bacterial microbiology.
bacteria are excellent model
organisms, particularly Escherichia coli Julien Davies from Vancouver, Canada,
organisms for studying cellular
and its viruses. The development of reminded us in the keynote lecture that
processes that are common in
recombinant DNA technology in the early the 1030 bacteria inhabiting Earth account
prokaryotes as well as eukaryotes
1970s was rooted in studies of bacterial for some 50% of the biomass carbon and
restriction modification systems and of 90% of the biomass nitrogen phosphorus.
autonomously replicating viruses and There may be as many as 108 different
plasmids. Transfection and transformation The decrease in basic research on bacterial species. Less than 1% of them
techniques to reintroduce manipulated bacterial molecular biology has occurred are identified and even fewer are culti-
DNA completed the basic toolbox at the very time when it has become even vated. Bacteria are responsible for most
needed for in vitro recombinant DNA clearer that bacteria are excellent model biotransformations and they exhibit the
research. Further refinement of recom- organisms for studying cellular processes most diverse range of metabolic processes.
binant DNA techniques, together with that are common in prokaryotes as well as They are intimately involved with human
new biochemical analysis methods, then eukaryotes. These include DNA replication health and disease, as well as being indis-
enabled biologists to expand their and its control, DNA repair, recombination pensable for life as we know it on this planet.
research into the realm of eukaryotic and transcription, protein synthesis and Genome sequence programmes have
organisms. cellular protein processing. With growing already provided 37 complete bacterial
knowledge, biologists also realized that genome sequences, with 117 prokaryota
Consequently, many scientists interested
the parallels between these systems in and 10 archaea in progress. This growing
in the study of basic molecular biology
processes left bacteria as their experimen- bacteria and their eukaryotic counterparts resource is facilitating an understanding of
are closer than thought before. the biology of specific bacteria and provides
tal organism and concentrated their work
There has also been a decline in basic invaluable material for population and
on eukaryotes, from simple ones such as
research to explore a bacterium s own evolutionary biologists. Comparison of
yeast to complex metazoans and plants.
unique biology, whether to decipher the eubacterial and archaeal sequences
This change in focus has had outstanding
successes, scientifically as well as econo- networks of intracellular physiological underlines the mosaic natures of geno-
mically. Indeed, many advances in medi-
cal research and the advent of promising
Few of the best young scientists decide to study microbiology because
therapies for a lot of ailments would not
eukaryotes seem to be more attractive and promising in terms of
have been possible without extensive
scientific funding and economic rewards
studies of eukaryotic cells and complex
organisms. But at the same time, the level
processes, the ways in which microbes mes, demonstrates the importance of
of research in basic bacterial molecular
excrete molecules, or sense, signal and horizontal gene transfer and provides fur-
biology has reduced drastically over the
interact with other cells. This is not to say ther insight into the origin of eukaryotes.
past 25 years. This compromises research
that there are no excellent laboratories in Remarkably, some bacteria encode as
and teaching expertise in those areas of
all of these areas, but the overall coverage many genes as simple eukaryotes.
microbial molecular biology that are at
the very basis of recombinant DNA tech- in Europe is rather  patchy . Also, few of The scientific presentations covered a
the best young scientists decide to study broad range of topics in microbiological
niques used for studies of eukaryotic
microbiology because eukaryotes seem to research, as the following brief summary
systems. This has been brought home to
be more attractive and promising in terms of shows. Erik Boye from Oslo and Dusko
this correspondent several times, when he
scientific funding and economic rewards. Ehrlich from Jouy-en-Josas in France
has been an examiner of PhD theses on
This reduction in activity in microbial focused on macromolecular processing in
eukaryote topics. I have often found that a
candidate knows little about the proper- research is mirrored by EMBO membership; the context of the whole cell, while
ties of a particular bacterial strain although microbiologists represent <"10% of Antonella Covacci from Siena, Italy,
the members, their age profile is skewed Pascale Cossart from Paris and David
plasmid combination, or the conditions
© 2001 European Molecular Biology Organization EMBO reports vol. 2 | no. 3 | 2001 175
analysis
Holden from London illuminated the bacteria hold an enormous potential for laboratories and that, given the prospects
complexities of bacterial pathogenicity. their use as biosensors and for facilitating for future funding, it may be difficult to
The  New Microbiology , the fusion of bioremediation. To understand interactions rebuild the critical mass necessary to stay
genomics and classical bacterial molecular of microorganisms with their environment ahead scientifically. In the future, we
biology, was represented by Ray Dixon or their host during pathological processes, therefore not only need  cutting edge
from Norwich, UK, who spoke about we must also refine the study of specific research, but must also increase the
bacterial physiology and signalling and gene expression and physiology under cer- visibility of bacterial research in regard to
the broader scientific and political com-
munities. Such an undertaking, most
Genomics might rejuvenate microbiology as scientists who have not
participants agreed, could already be
been trained as bacteriologists enter the field and make large impacts
achieved by raising the profile of micro-
with their functional or population-evolutionary biology research
biology when teaching biology students.
There were pleas to support outstanding
Victor de Lorenzo, Madrid, who gave his tain conditions. This research will also prove young microbiologists by getting them
presentation about exploring the absolute to be useful for scientists who bridge prokary- elected to EMBO membership. There was
microbial genome to identify useful ote and eukaryote biology, in order to study
organisms for bioremediation. Also, Nigel the interactions and consequences of bacte-
Many of us remained concerned
Saunders, Oxford, updated us on the rial interactions with plant and animal cells.
that Europe may have too few
current state of genome sequencing and The final discussions about the future of
how the information from these microbial research in Europe were lively microbial laboratories and that it
sequences can be  mined and exploited. and engaging. The participants debated
may be difficult to rebuild the
Miro Radman from Paris explained how whether shortages of funding are limiting
critical mass necessary to stay
evolutionary success in bacteria adapting microbial research and inhibiting young
ahead scientifically
to changing environmental conditions is people from entering the field. But it
promoted by increases in mutation rate. became clear through the meeting that
The underlying theme of most presenta- there appears to be no specific bias also a suggestion that a European micro-
tions was the emphasis on the importance of against microbiology. In those few coun- biology academy, such as the American
multidisciplinary integrated approaches tries that provide sufficient funding for the Society of Microbiology, might help focus
to research. The value of hypothesis- life sciences, no reduction in funds for on problems typical for microbiology and
driven research was stressed time and high-quality bacterial research was per- act as a lobbying group for future support.
again, as was the importance of maxi- ceived. And in those European countries We hope that the positive discussions in
mising the benefit of powerful databases where research funds are very limited and Heidelberg will provide the necessary
provided by genome sequences and their not designed for medium- or long-term impetus to do so and to organize further
expression patterns. The speakers also support of projects, no overt prejudice meetings and workshops that will address
pointed out relationships between the against microbiology as a discipline can the  New Microbiology .
reductionist approaches of structural and be observed. Inevitably, there was a
molecular biology, and the holistic debate about the funding of coordinated
approaches that come from technology- European efforts and infrastructure in
driven genomics and proteomics, protein genomics, gene expression and gene
modelling and the integrated use of genet- function analysis. Most participants felt
ics and cell biology. It was argued, with that the EC could, and should, play a
some justification, that genomics is more important role through the Frame-
indeed rejuvenating microbiology, as work Programmes. Properly funded and
scientists who have not been trained as coordinated activities in these areas are in
bacteriologists enter the field and make fact essential to make the best use of the
large impacts with their functional or emerging database information.
David Sherratt
population-evolutionary biology research. Most participants left Heidelberg
Some general messages about future reassured that there are exciting things
The author is the Iveagh Professor of Microbiology
directions of bacterial research emerged happening in bacterial research. This
in the Division of Molecular Genetics, Department
from the scientific discussion. Clearly, most excitement is renewing, or appears to be
of Biochemistry, University of Oxford.
E-mail: [e-mail]
microbial diversity remains to be explored, renewing, the interest of young scientists
and if we want to understand and exploit to pursue a career in this field. Never-
the capacities of biomolecule transforma- theless, many of us remained concerned
DOI: 10.1093/embo-reports/kve057
tions, bacteria are the key resource. Thus, that Europe may have too few microbial
176 EMBO reports vol. 2 | no. 3 | 2001 © 2001 European Molecular Biology Organization