Research in Microbiology 159 (2008) 74e80
www.elsevier.com/locate/resmic
In a world of microbes, where should microbiology stand?
1. Introduction
Microbes and their viruses have always dominated the bio-
sphere and will continue to do so. However, this reality has
been recognized only recently, even by microbiologists. As
a consequence, the place of microbiology has not been cor-
rectly estimated. In particular, the microbial world has for
a long time been largely ignored by evolutionists, who have
focused on macrobes (plants and animals). This has changed
in recent decades, thanks to the application of methodological
and conceptual advances from molecular biology to microbiol-
ogy. The universal tree of life turns out to be overpopulated by
microbes and engulfed in an ocean of microbial viruses. We
have thus experienced an ongoing revolution in our vision of
the biosphere and its evolution, which is not yet fully appreci-
ated. Old anthropomorphic prejudices and misleading termi-
nologies still resist and prevent us from fully realizing the
potential of this new vision. At the onset of a new century,
120 years after the opening of the first Institute originally
entirely devoted to microbie (and 120 years after the crea-
tion of its first journal), it is a good time to rethink the place
of microbiology in the life sciences and to face its bright future
with optimism.
Life probably appeared on our planet sometime between
the end of the late heavy bombardment (e.g. 3.9 Gy ago)
and the oldest known bona fide microfossils (2.7 Gy) [15].
For the first two to three billion years, life was only microbial,
since macrobes (large animals, fungi and plants visible to the
naked eye) only appeared 600 million years ago. Microbes
(archaea, bacteria, unicellular eukaryotes) and viruses infect-
ing them, still dominate the present biosphere. On one hand,
microbial organisms are far more numerous than macrobial
ones by several orders of magnitude. On the other, plants
thrive thanks to their association with endosymbiotic cyano-
bacteria (chloroplasts) and all eukaryotic macrobes rely on
the original symbiosis of one of their ancestors with an a-
proteobacterium (the progenitor of mitochondria). The origin
of macrobes themselves can probably be linked to the large
rise in oxygen in the atmosphere triggered by microbial life,
and macrobes today are the hosts of large microbial communi-
ties that are essential for their survival (there are more bacteria
than human cells in our body). Finally, microbial life will sur-
vive all catastrophic events that may possibly jeopardize the
fate of our planet (from meteorite bombardment to nuclear
0923-2508/$ - see front matter 2007 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.resmic.2007.12.001
winter) until sun expansion will finally destroy Earth itself.
Save the planet is not a slogan for microbes, since they
can adapt perfectly well to all human activities and the Earth
would be perfectly fine with a microbial-only biosphere.
As a consequence of their antiquity and continuous domi-
nance, microbes and their viruses have evolved and diversified
much more than macrobes (as exemplified by the variety of
microbial metabolisms) and are the most abundant living enti-
ties by several orders of magnitude [45]. If science were to
reflect reality in the absence of any human prejudice, 99%
of biology would thus be microbiology, whereas plants and
animals would be principally considered as a strange (albeit
very interesting) epiphenomenon. Of course, being macrobes
ourselves, and science being a human activity, things do not
work that way. For a long time, our vision of the living world
was restricted to the animal/plant dichotomy, and microbes,
once discovered, were first considered themselves as curiosi-
ties. Annoying curiosities for sure, once it became apparent
that some of these little creatures were responsible for major
plagues throughout human history and are still ready to kill
us in every corner of a hospital.
2. Microbiology and molecular biology: a complex
love affair
Microbiology (formerly microbie), as a new quarter in biol-
ogy, started brilliantly in the nineteenth century, when Pasteur
and a number of other great scientists identified several mi-
crobes at the origin of important life-threatening diseases
and major natural processes useful for our well-being
(making wine, for instance). However, for a long time, our an-
thropocentric view of the world prevented us from fully
realizing what was going on. When I first had a lecture on bac-
teria in 1969 at the University of Paris 7, it was taught in the
course of botany! Because they had cell walls, bacteria were
considered tiny plants, and biology was still dominated by
the old macrobial dichotomy (zoology versus botany). Two
years later, in the new course of molecular biology, I finally
learnt that bacteria are not plants after all, but prokaryo-
tesdthe ancestors of eukaryotes [38,39]. The newly designed
eukaryote/prokaryote dichotomy based on cellular structure
became the modern and fashionable view (compared to the
five kingdoms of Whittaker and previous classifications that
were based on the structure of organisms) [46]. We were
 P. Forterre / Research in Microbiology 159 (2008) 74e80
finally more closely related to plants than plants were to bac-
teria, and prokaryotes (bacteria and cyanobacteria) now occu-
pied half of the classification landscape (instead of one fifth in
the Whittaker scheme). This was a revolution in our concep-
tion of the world that emerged right away at the turn of the
last century from the new concepts in cellular and molecular
biology [38,39]. These new concepts themselves owed a
profound debt to microbiology, since the study of microbesd
especially fungi, bacteria and their virusesdas model systems
paved the way for the emergence of molecular biology. This
could have led to a re-evaluation of the status of microbiology
as a (the) major discipline in biology. However, for many of
the early leaders in molecular biology, the study of microbes
was only a first obligatory step before jumping to more serious
tasks, such as the understanding of brain functions or cancer
development (something obviously critical for macrobes of
our kind). As a consequence, microbiology was often un-
officially but forcefully considered as a second-rate science,
mainly interesting from an applied perspective (microbes be-
ing tools for biotechnology or as agents of infectious diseases).
The situation could have been even worse, since it was even at
one point considered that microbes were not a threat anymore
(for instance when the US Surgeon General William H Stewart
announced in 1969 that its time to close the book of infec-
tious diseases, the war against pestilence is over [41].
For a long time, microbiology was thus not taught as a dis-
cipline of its own at most universities and was still a minor
component of biological departments around the world (with
few exceptions, such as, of course, the Institut Pasteur). In
particular, microbiology was nearly completely forgotten by
evolutionists (and vice-versa, evolution was sidelined by mi-
crobiologists). Considering that, according to the famous aph-
orism of Theodosius Dobzhansky, nothing in Biology makes
sense, except in the light of evolution [9], one could have
concluded at that time that Nothing makes sense in microbi-
ology. However, this was not realized by most leaders of the
molecular biology revolution, because the concept of proka-
ryotes apparently makes some sense in the evolutionary land-
scape by claiming that bacteria, with their primitive nucleus
(this is what prokaryote means), preceded eukaryotes (with
their true nucleus) and were most likely monophyletic [39].
This suggested that the last common ancestor of all living or-
ganisms was a small primitive bacterium lacking a cell wall,
very similar to a Mycoplasma [44]. Although fashionable at
that time (as was the prokaryote concept itself), this view
was clearly biased by anthropocentric prejudices that evolu-
tion goes from simple to complex (i.e. from bacteria to hu-
mans) and that bacteria are all the same just because they
are so different from usdeukaryotes (somewhat reminiscent
of racial prejudice!). It is significant that biologists were for
a long time reluctant to consider as bacteria groups such as cy-
anobacteria or streptomycetes that did not fit with the view of
bacterial morphology as either unicellular bacilli or cocci.
Fortunately, repaying its debt to microbes, molecular biol-
ogy finally exerted a critical impact on the development of
microbiology, thanks to the pioneering work of Sanger and
colleagues, who designed efficient tools to read the genetic
75
text imprinted in proteins, RNA and eventually DNA, and to
the visionary insight of Pauling and Zuckerkandl, who realized
that the genetic text is a record of evolutionary history [50].
Pasteur and Darwin thus finally met 30 years ago when Carl
Woese and his colleagues of the Urbana school, using the
Sanger strategy to characterize 16S rRNA molecules, pub-
lished in the November 1977 issue of PNAS their analyses
of rRNA oligonucleotide catalogues that surprisingly chal-
lenged the prokaryote/eukaryote dichotomy. They found that
some prokaryotesdthe methanogenic bacteriadare no
more related to other bacteria than they are to eukaryotes,
challenging the idea that all bacteria belong to a single line
of descent [47]. The reconstruction of a universal tree based
on 16/18S rRNA finally revealed the reality behind the sur-
face, with macrobes representing only the tips of two tiny
branches (one for plants, one for animals and fungi) at the
top of the eukaryotic bush, itself comprising only one-third
of global cellular biodiversity (see Fig. 1 in the paper by
Lopez-Garcia and Moreira in this issue [26]).
Archaea turned out to be a gold mine for microbiologists
and molecular biologists alike. The elaboration of the archaeal
concept is directly linked to the discovery of hyperthermo-
philes and, together with the PCR gold rush, it triggered
a hunt for extremophiles that led us to re-evaluate the limits
of Earth habitability [40]. Further work on Archaea revealed
more surprises; not only are these prokaryotes strikingly
different from the Escherichia coli standard model system,
but, upon closer inspection at the molecular level, they are
much more similar to us (eukaryotes) than they are to bacteria
[29]. This has already led to several major discoveries that are
relevant for our own biology. For instance, the search for the
archaeal type II DNA topoisomerase led, unexpectedly, to
the discovery of the protein that triggers meiotic recombina-
tion in eukaryotes [2]. For a very recent example, two papers
in Science report, in August 2007, the resolution of complexes
between replication origins and the archaeal replication initia-
tor, shedding light on the highly similar mechanism of the eu-
karyotic origin of replication complex (ORC) [10,20]. Besides
the archaeal saga, 16S rRNA comparison had many other con-
sequences for our view of early evolution. An early significant
observation was that mycoplasmas are not primitive bacteria
after all, but former Gram-positive bacteria that lost their
cell wall in the distant past [49]. Evolution thus can go from
complex to simple, even for microbes. The recently discovered
genus Nanoarchaea is very likely another example of such
a reductive evolution [5]. Could it be that both archaea and
bacteria evolved by reduction from a more complex microbial
ancestor (more akin to eukaryotic microbes) [16,34]? This is
indeed suggested by a recent comparative proteomic analysis
[24].
The diversity of microbial phenotypes, including unusual
morphological features, is now finally recognized. In particu-
lar, the discovery of bacterial groups with intracellular mem-
branes (Planctomycetales, Poribacteria) including a nuclear
envelope (Gemmata obscuriglobus) has even more strongly
challenged the prokaryote/eukaryote terminology [18]. Is it
politically correct for us to consider that we have the true
76 P. Forterre / Research in Microbiology 159 (2008) 74e80
nucleus after all, and that the nucleus of Gemmata is false (or
primitive)? For a fascinating story involving unusual bacteria
that experienced tremendous morphological changes, I recom-
mend the paper by Rosati and co-workers on the epixenosome
(a bacterial ectosymbiont of a eukaryotic microbe): your con-
cept of a bacterium will never be the same [32].
The 16S/18S rRNA has been for the last thirty years the
Rosetta stone of microbial evolution and the main descriptor
of biodiversity. The spectacular rise of molecular microbial
ecology, as a byproduct of the PCR revolution, has further
enlarged the microbial world to unexpected borders (see the
chapter by Lopez-Garcia and Moreira in this issue [26]). Not
only do microbes dominate the universal rRNA tree of organ-
isms that we have been able to grow in the laboratory, but this
tree is itself a pale reflection of a much larger tree of rRNA
including the microbes that we have not yet been able to
cultivate [22]. The discovery of phylotypes corresponding to
new groups of Archaea, Bacteria and Eukarya dramatically il-
lustrates what remains to be known of the microbial world
(both in terms of quantity and quality). In particular, new
phyla of bacteria have been discovered at an amazing rate,
with between 50 and 100 phyla now recognized (versus
around 10 in 1987 and 23 in the 2001 edition of Bergeys Man-
ual) [12,19]. Some of these phyla are probably as diverse, and
exhibit the same level of evolutionary divergence, as Proteo-
bacteria. More than half of them have currently no cultivated
representative. A few species of these new groups of Bacteria
and Archaea have been successfully put into culture these last
two years, leading to very important discoveries (such as the
major role of ammonium oxidizing archaea in the global nitro-
gen cycle) [23,25,26]. This is now leading to a re-evaluation of
the importance of cultivation, itself dependent on a profound
understanding of microbial physiology and of the involvement
of microbes in geochemical cycles [26].
The general shape of the tree of life, with three distinct do-
mains and the overwhelming dominance of microbes, has been
validated by all comparative analyses performed since the be-
ginning of the genomic era, and the existence of a huge hidden
world of unknown microbes has been confirmed by the first
metagenomic analyses [12,26]. A big challenge now will be
to sort out the phylogenetic relationships between the various
phyla and/or divisions identified by 16/18S rRNA analyses
inside each cellular domain. It has sometimes been argued
that this is impossible because the history of species has
been blurred by extensive lateral gene transfers. However, in
the case of Archaea at least, phylogenetic analyses have dem-
onstrated the existence of a core of genes whose phylogeny
retraces the history of the organisms [4]. It can be hoped
that similar types of analyses will finally reveal deep branch-
ing topology in Bacteria and Eukarya as well. Comparative
analysis of gene content and careful polarization of indels
(insertionedeletion) in core genes (not affected by gene trans-
fers) could complement the use of traditional phylogenetic
analyses to test parts of the trees that are not well resolved,
or to solve contradictions between different trees. All these
strategies require the analysis of complete genome sequences,
which means that it will be essential in the next few years to
complete the catalogue of complete genomes to cover all divi-
sions, phyla, subphyla, etc. detected by environmental rRNA
sequencing, if we hope to truly understand the evolution of
microbes (i.e. 99% of life). The availability of a robust species
tree is indeed a prerequisite to analyzing the evolution of all
metabolic pathways and molecular structures that appeared in
the course of cellular evolution and shaped modern organisms.
3. The viral ocean, a new playground for microbiologists
A final touch to this picture was added when it was realized
that not only is the universal tree dominated by microbes, but
also that this tree itself is immersed in an ocean of microbial
viruses (viruses infecting microbes) [1]. Ecological studies
focusing on viruses started to accumulate 20 years ago and
showed that viruses are about 10 times more abundant than
cells in marine environments [3,42]. This is probably true
for other environments as well, since all cellular organisms
can be the targets of multiple viruses. In agreement with these
assumptions, metagenomic analyses now reveal that viral
genes are more abundant than cellular ones in the genosphere
[11]. At the same time, structural studies of capsid proteins
and comparative viral genomics have shown that viruses are
extremely ancient, since homologous features are shared by
viruses infecting different cellular domains, suggesting that vi-
ruses were already there at the time of LUCA [1,14]. It is
therefore logical to assume that viruses have always coexisted
with cellular organisms (probably ever since outnumbering
cellular organisms). If this is true, the overall bidirectional
gene flow between cells and viruses should have been quanti-
tatively in favor of transfers from viruses to cells. This logi-
cally implies that viruses have played a major role in
biological evolution, transferring molecular novelties, first in-
vented in the viral world, into the cellular world [14]. It seems
quite clear now, for instance, that bacteria acquire their arsenal
of toxins and other pathogenicity factors mainly from inte-
grated viruses [6]. This has again been recently exemplified
by similarities between the type VI secretion system of Vibrio
cholerae and the tail-spike protein complex of the bacteriovirus
T4 [36]. Not only can viruses provide extra features of selec-
tive advantage for cellular organisms, but they can introduce
dramatic changes in their basic fabric, as illustrated by the viral
origin of mitochondrial transcription and the replication appa-
ratus [13]. As a consequence, viruses have been introduced as
key players in several recent evolutionary scenarios, from the
origin of DNA to the origin of the eukaryotic nucleus [7,14].
The recognition that viruses are major components of the bio-
sphere and should be taken into account in any evolutionary
scenario has finally completed the Woesian revolution by uni-
fying the living world into a single evolutionary picture.
4. Whats in a name?
Microbiology, as the science of microbes and their viruses,
obviously covers the most profound and relevant aspects of
biology. As expected from what we know of human history
(the interplay of revolutions and counterrevolutions), this has
 P. Forterre / Research in Microbiology 159 (2008) 74e80
not been fully realized by fellow macrobiologists and even by
most of us (microbiologists). Misleading anthropocentric con-
ceptions and old terminologies continue to be pervasive in bi-
ology. To start with a minor example, it is amazing that most
bacteriologists and nearly all molecular biologists are still
happy to define their favorite bacterium as Gram-negative,
even though this does not make sense, since 21 out of the
23 phyla of bacteria now recognized in Bergeys Manual are
composed of Gram-negative bacteria [19]! More troublesome,
in many scientific papers and comments in prestigious jour-
nals, molecular biologists and biochemists continue to speak
of lower and higher eukaryotes, a notion that directly re-
fer to the Scala natura of Aristotle! This is probably why
the universal tree of life is still rooted in the bacterial branch
in most textbooks, despite the absence of robust support [16],
simply because traits common to Archaea and Eukaryotes are
considered by definition to be higher features compared to
bacterial ones. We (eukaryotes) are indeed strange creatures,
with our incredible spliceosome machinery, nuclear pore gi-
gantic complex and other features whose origins remain mys-
terious, but this does not imply that these features have
evolved more recently than operons (making gene regulation
so much easier) or bacterial DNA gyrases (such a fascinating
enzyme that can couple the intracellular ATP/ADP ratio to the
activated state of DNA). Specific eukaryotic features could
also be primitive traits, remnants of evolutionary scenarios
that we simply cannot imagine at present. Unfortunately, the
general acceptance of the prokaryote first concept still
biases most work on the nature of LUCA, the rooting of the
tree of life, and the origin of eukaryotic features.
The prokaryote/eukaryote terminology itself continues to
be currently used and even strongly defended by some biolo-
gists (see the recent debate in Nature between Norman Pace,
who suggested abandoning this nomenclature, and his oppo-
nents [28,30]). In my opinion, the term prokaryote is indeed
misleading since, for many biologists, it is still synonymous
with bacteria (as previously noticed by Norman Pace, a chapter
on prokaryotic transcription in most textbooks will generally
mean transcription in bacteria [30]). This situation is worsened
by the continuous use of the term archaebacteria which
fools people into thinking of Archaea as some kind of strange
bacteria [48]. As a consequence, bacterial traits are sometimes
wrongly attributed to Archaea as well, or Archaea are simply
ignored in prokaryotic molecular biology. A strange situa-
tion occurs in particular with archaeal viruses, which are often
labeled as bacteriophages in textbooks and/or described
under the headline bacterial viruses just because any virus
that infects a non-eukaryote is considered to be a bacterio-
phage (this is one of the reasons I prefer to use here the
term bacteriovirus instead of bacteriophage).
Besides the force of habit and our natural preference for
dichotomies, the eukaryote/prokaryote nomenclature still
resists (and is even making a kind of comeback) for various
reasons which are interesting to list here. First, it is favored
by recent evolutionary scenarios that restore the traditional
gradist view of evolution (prokaryotic firstdeukaryote after)
by explaining the origin of eukaryotes via the association of
77
a bacterium and an archaeon ([27] and references therein). Re-
ciprocally, these scenarios are accepted partly because they fit
the old prejudice, although they require ad hoc (to me highly
unlikely) explanations for the origin of the many eukaryotic
features lacking in Archaea and Bacteria (such as the spliceo-
some and nuclear pores) and, more generally, to explain the
transformation of two domains into a third one (for in depth
critical analysis of fusion scenarios, see Ref [33]). Second,
in the genomic and post-genomic era, the eukaryote/prokary-
ote nomenclature fits well with recent trends favoring global
approaches in biology that seem modern compared to the
reductionism of the last decade. Although focusing exclusively
on reductionist approaches has its own limitation, one should
not forget that this approach was essential to dig into the es-
sence of organisms and to identify the structure of the univer-
sal tree by focusing on the ribosome. Global approaches
performed without a critical view have the negative conse-
quence of maintaining the biologists focus on the superficial
similarities that exist between the structure of the archaeal
and bacterial genomes, without asking whether these features
are primitive due to convergent evolution or if they correspond
to real synapomorphies (shared derived traits) between
Archaea and Bacteria. The term prokaryote misleads us again
on that issue by suggesting that the question has been solved
and that these traits are primitive in the first place. They might
be, but we still have to get convincing evidences for it, which
is presently not the case.
5. The pro and cons of model organisms
There is more at work than nomenclature behind the resis-
tances to an evolution-oriented view of the biosphere. Indeed,
30 years after the Woesian revolution, the vast majority of
bacteriologists continue to work on a very small number of
models belonging to only two phyla (Proteobacteria and
Firmicutes, Gram-negatives versus Gram-positives) among
the 50 or so bacterial phyla recognized today. Similarly,
most eukaryote model organisms belong to only two of the
eight major eukaryotic divisions, the Opistokonts (animals
and fungi) and the Viridiplantae (plant), with other divisions
that only include microbes still being largely ignored. The sit-
uation is slightly better with archaeal studies since, from the
beginning, scientists working on Archaea (embracing the
Woesian revolution) have been more prone to appreciating
the biodiversity of this domain.
The study of viruses also still suffers from our ancient
vision of the living world, even amplified by the fact that,
for most biologists today (except virologists!), viruses are
only viewed as providing tool kits for genetic manipulations.
Although the situation is slowly improving (for instance,
with a recent interest in cyanoviruses), most bacterioviruses
studied at the molecular level are still those infecting some
genera of Proteobacteria and Firmicutes. We still have no
idea of the nature of viruses infecting the majority of archaeal,
bacterial or eukaryotic phyla (or divisions). Head-and-tail
bacteriophages (Caudavirales) are often assumed to repre-
sent all prokaryotic viruses, whereas human viruses are
78 P. Forterre / Research in Microbiology 159 (2008) 74e80
assumed to represent all eukaryotic viruses. The discovery of
the amazing morphological diversity of viruses infecting a sin-
gle order of hyperthermophilic archaea (Sulfolobales) [35] and
the isolation of the giant Mimivirus [37] (with a genome two
times bigger than that of a Mycoplasma) clearly tell us that
more surprises are ahead for those who will meet the challenge
of searching for new viruses infecting poorly studied groups of
cellular organisms.
The focus on model organisms has been essential for the
development of biology and will still be determinant in the
future, but this trend has to be balanced by an exhaustive
exploration of biodiversity (i.e. both by increasing the number
and diversity of model organisms from an evolutionary per-
spective and by the systematic screening of everything out
there). There is a risk that the current trend toward system
biology will again shift the pendulum towards models at
the expense of diversity. On one hand, this could help to again
place some microbes on top of the biologists agenda (models
will first have to be very simpledthus microbial), but on the
other, this could again lead some biologists to forget the real
living world.
Surely it will take time for institutions and individuals to
shift their research programs in line with scientific break-
throughs, and the fact that most known human pathogens
belong to Proteobacteria and Firmicutes is playing a role,
but the persistence of the old view of the microbial world
among biologists is not only due to the weight of the past
or of medical microbiology, but likely to the failure of
even new generations of microbiologists to fully grasp evolu-
tionary concepts. The teaching of microbiology has probably
had much to do with this situation, since the new concepts
are only slowly replacing the old view in scientific programs.
In particular, the study of evolution (not to mention microbial
evolution) has been absent in most biology curricula. I never
heard of Darwin during my studies in biochemistry, genetics
or molecular biology at the University of Paris in the early
1970s and I suspect that this is still the case in too many pla-
ces. The impact that physicists had on the birth of molecular
biology probably played a role in this context by slowing
down the diffusion of new evolutionary concepts in biology,
since students in physics and chemistry are usually even
more ignorant of basic aspects of the Darwinian theory
than students in biology. Since physicists will probably
play an increasing role in the development of biology in
this century by bringing new concepts and methodology,
the risk exists that these positive trends will be accompanied
by a negative one, a continuous underestimation of the im-
portance of evolution in biology. This pleads for the intro-
duction of Darwinism in the program of physics and
chemistry. Ironically, the new surge of creationist theories
could have a positive impact by forcing biochemists, geneti-
cists and microbiologists to think more about evolution [31].
Many of them still consider living organisms as machines (or
systems) to be deciphered by logical thinking. It should be
realized that such mechanistic views could pave the way
for Intelligent Design (searching for the intelligent engi-
neer), and that living organisms and all structures therein
are historical entities that have been shaped by natural selec-
tion and complex historical pathways which can only be un-
derstood via the prism of evolution.
6. Future prospects
Microbiology is on the rise. The number of papers dealing
with microbes and published in Nature and Science has in-
creased these last few years, with emphasis on geo-microbiology
and metagenomic studies. Alas, microbiology might finally
benefit from media headlines once the actual prophecies about
the end of the antibiotic era and the emergence of new patho-
gens proves to be true. As stated recently by Julian Davies,
Microbes have the last word, which is not surprising in
a world dominated by microbes [8]. The growing threat of
pathogenic microbes will again shift microbiology towards
the medical side, but will also force microbiologists to explore
new avenues. Dramatic advances have been made in our
knowledge of the mechanisms of pathogenicity, thanks again
to molecular biology (see the chapter by Philippe Sansonetti
in this issue), but they still have to produce new treatments
in many cases. The rediscovery of phage therapy is a good
example of what should be done. Alongside many historical,
physiological and practical reasons [21], phage therapy was
partly forgotten because the diversity and dominance of bac-
terioviruses has been largely underestimated. Now that envi-
ronmental microbiologists have demonstrated that viruses
control the ecology of bacterial systems in the environment
[42], it remains to be realized that the human body is also
an environment for concluding that bacterioviruses are indeed
our best allies against pathogenic bacteria [43]. Considering
the human body as an environment (a very complex and inter-
esting one) should also help to join together environmental mi-
crobiologists and medical microbiologists in the search for
unknown pathogens among the plethora of not yet cultivable
organisms that live with us or could invade us (a notre insu,
[17]). It might be that not only rare diseases in search of
a cause but also major new plagues (the obesity pandemic,
for instance) could be related to a microbial agent or to a com-
bination of microbial agents (commensal and pathogenic)
living in delicate equilibrium [17].
However, although focusing primarily on applied microbi-
ology is rational in anthropocentric terms, scientists and
decision-makers in science should be aware that anthropocen-
tric approaches can be misleading over the long term in sci-
ence programs (the Earth is not flat after all). Research
programs driven by pure curiosity and our desire to finally un-
derstand the world in which we are living as it is (and not as
we think it is) should be the major incentives in microbiology,
as in all other scientific disciplines. If this is understood, we
will be able to face with optimism the bright future of micro-
biology. The vast reservoir of new molecular mechanisms,
new metabolisms and/or fascinating new structures hidden in
the microbial world is enormous, and will reward future gen-
erations of microbiologists with great discoveries. We can only
hope that microbiology will in the end finally be recognized,
 P. Forterre / Research in Microbiology 159 (2008) 74e80
and will occupy the place it rightfully deserves in a world of
microbes.
Acknowledgments and apologies
I am grateful to Claudine Elmerich for the invitation to
write this paper and to David Prangishvili and Simonetta Gri-
baldo for critical reading of several versions of the manuscript.
This is a very personal view of the place of microbiology in
science, and I had to omit some very important aspects of
this discipline for no good reason (for instance, all modern
studies dealing with the location of microbes in space instead
of timed biogeographydor in a communityd biofilms). I
also apologize for a highly biased selection of references
and probably some important omissions.
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