Research in Microbiology 161 (2010) 430e438

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Microbial systematics and taxonomy: relevance for a microbial commons

Edward R.B. Moore a,b,*, Sashka A. Mihaylova c, Peter Vandamme d, Micah I. Krichevsky e,
Lenie Dijkshoorn f
a
Culture Collection University of Gothenburg (CCUG), Department of Clinical Bacteriology, Sahlgrenska University Hospital, PO Box 7193, 402 34
Göteborg, Sweden
b
Department of Infectious Disease, The Sahlgrenska Academy of the University of Gothenburg, PO Box 7193, 402 34 Göteborg, Sweden
c
Department of Microbiology, Virology and Medical Genetics, University of Medicine, Kliment Ohridski1, 5800 Pleven, Bulgaria
d
Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
e
Bionomics International, 3023 Kramer Street, Wheaton, MD 20852, USA
f
Department of Infectious Diseases C5-P, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands

Received 28 March 2010; accepted 11 May 2010

Available online 1 June 2010

Abstract

The issues of microbial taxonomy and potential interactions with a microbial commons are discussed, with emphasis on three components:
characterization; classification; and nomenclature. The current state of technology and the spectrum of methods that are used for phenotypic and
genotypic characterization of prokaryotes, classification at different taxonomic levels and points of prokaryote nomenclature are reviewed. While
all taxonomic ranks comprise a cohesive systematic framework for microorganisms, the prokaryotic genus and species provide the “working
unit” of taxonomy. Since 2004, the number of validly published genera and species has increased by approximately 50%. Extensive development
of technology will continue to enable ever higher resolution characterization and more refined classification of microorganisms. Characterization
and classification at the species level may be most relevant for bacterial taxonomy, although reproducible differentiation at the strain level will
probably prove to be more relevant for a microbial commons. A dynamic microbial taxonomy, albeit with well-founded and stable guidelines for
defining microorganisms, provides an efficient organizational system for dealing with the enormous spectrum of microbial diversity.
Ó 2010 Elsevier Masson SAS. All rights reserved.

Keywords: Taxonomy; Characterization; Classification; Nomenclature; Microbial commons

1. Introduction essential for furthering developments in academic, medical and

Advances in science arise as new developments to the insight
of previous generations by, in the words of Sir Isaac Newton,
“standing on the shoulders of giants”. Access to information and
biological resources, including microbiological materials, is
* Corresponding author. Culture Collection University of Gothenburg
(CCUG), Department of Clinical Bacteriology, Sahlgrenska University
Hospital, The Sahlgrenska Academy of the University of Gothenburg, PO Box
7193, 402 34 Göteborg, Sweden. Tel.: þ46 31 342 4696; fax: þ46 31 829 617.
E-mail addresses: erbmoore@ccug.se (E.R.B. Moore), sashkam@yahoo.
com (S.A. Mihaylova), peter.vandamme@UGent.be (P. Vandamme),
micahkr@verizon.net (M.I. Krichevsky), l.dijkshoorn@lumc.nl (L. Dijkshoorn).
biotechnological research. Restrictions imposed on the acqui-
sition, use or distribution of biological materials are counter-
productive, limiting possibilities and effectively impeding
scientific progress. A microbial commons approach with respect
to information relating to the processing and archiving of
reference microorganisms is increasingly recognized to play an
integral role in ensuring the availability of strains for repro-
ducible application. In turn, an effective microbial commons
relies upon the quality and reliability of the resources and
information on materials being exchanged.
The reliability of microbial strain material is dependent upon
established taxonomy in place for microorganisms. Microbial
taxonomy may be defined as the study of the diversity of

0923-2508/$ - see front matter Ó 2010 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.resmic.2010.05.007
 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438 431

microorganisms with the aim of organizing and prioritizing in an ultimately, cost, in handling of microorganisms. Thus, the
orderly manner (Trüper, 1991). The “species”, assigned to simple act of imparting a taxonomic designation to a microbial
a “genus”, in a binomial combination, is considered to be the strain may have far-reaching effects. For example, the shipment
basic unit of microbial taxonomy, although the definition as well of strains in a particular risk category may require more stringent
as the concept of a bacterial or prokaryotic species are topics of and expensive containment, as well as specialized courier
debate among microbiologists. Often regarded as having little protocols. The listings in Table 1 also demonstrate that there is
practical importance, the influence of microbial taxonomy, currently little coordination between national agencies respon-
however, extends to all branches of microbiology. Attaching sible for deciding risk group classifications. This lack of coor-
a name to a microbial strain imparts assumptions and implica- dination is due, in part, to a traditional lack of appreciation of the
tions associated with that organism. The most direct example of taxonomy of microorganisms.
such an impact can be seen in the field of infectious disease, in Tindall et al. (2010) has proposed a view of taxonomy as
which identification of an isolate from a patient sample leads to relying on three elements: characterization; classification; and
implications associated with pathogenicity, contagion risk, nomenclature; with each element being dependent upon the
diagnoses, treatment and strategies for prevention of spread and others. Evaluation of these three elements of microbial
eradication. Microorganisms have long been recognized as taxonomy, in turn, is necessary for an effective microbial
possessing inherent risks according to their taxonomic classifi- commons. This review provides an overview of prokaryotic
cations. Table 1 lists the number of prokaryotic species and taxonomy and its relevance for a microbial commons and
genera classified into the risk group categories of different highlights some of the issues facing the interactions of
countries. Risk group categorization of an isolate is based on its taxonomy and a commons.
taxonomic classification and has consequences on how the
organism is handled in the laboratory, what protective measures 2. Characterization of prokaryotes
must be taken to ensure the safety of clinical personnel and how
the strain may be disseminated to the scientific community. The Characterization of a prokaryote strain (i.e. a “population”,
identification of a clinical isolate and its associated risks impact derived from a clonal variant, obtained from a given specimen)
the patient and, potentially, other patients and medical personnel may be argued to be the key element in microbial taxonomy
that come into contact with the source. In biotechnology (Tindall et al., 2010). Certainly, novel microorganisms should
research, the allocation of a microorganism to a risk group will be analyzed and described comprehensively, with the objective
have further implications regarding the effort, safety and, of providing as complete a picture as possible of the dis-
tinguishing traits of organisms, ultimately enabling reliable
Table 1 classifications and identifications. Prokaryote characterization
Comparison of the numbers of genera and species in the risk group classifi-
may follow two basic modes of analyses, i.e. characterization
cations of different countries.
of phenotypic traits and characterization of genotypic traits.
Risk group 2 Risk group 3
Phenotypic traits are the observable characteristics that result
No. of genera No. of species No. of genera No. of species from the expression of genes of an organism. Genotypic traits
Australia 55 76 10 10 of an organism are those within its genetic material, the
New Zealand 55 76 10 10 genome. The Ad Hoc Committee for the Re-evaluation of the
Canada 35 69 10 12
Species Definition in Bacteriology (Stackebrandt et al., 2002)
Chinaa 63 145 7 9
EU 56 122 13 25 and, more recently, Tindall et al. (2010) have described the
Belgium 123 557 14 39 methods and rationale that should be considered for compre-
Bulgaria 54 121 12 28 hensive characterization of prokaryotes.
Germany 208 969 13 31
Sweden 54 122 12 28
2.1. Phenotypic characterization
UK 60 127 13 31
USA 41 84 9 22
Phenotypic characterizations have formed the traditional
Risk group 1: no or very low individual and community risk; a microorganism
that is unlikely to cause human or animal disease. bases of microbial description and characterization. Pheno-
Risk group 2: moderate individual risk, low community risk; a potentially typic characteristics are useful or, in some cases, essential for
pathogenic microorganism that is unlikely to be a serious hazard to laboratory differentiation of taxa at the highest levels, i.e. phylum, class,
workers, the community, livestock or the environment. order, family, etc., as well as at the lowest levels, i.e. species
Risk group 3: high individual risk, low community risk; a pathogenic micro-
and subspecies (strains, varieties, types, etc.) (Fig. 1). The
organism that usually causes serious human or animal disease but does not
ordinarily spread from one infected individual to another; effective treatment methods employed have included descriptions of such features
and preventative measures are available. as growth conditions, aerobic, anaerobic or CO2 requirements,
Risk group 4: high individual and community risk; a pathogen that usually the components of media upon which organisms are able to
causes serious human or animal disease and that can be readily transmitted grow and colony and cell morphology. Colony characteristics
from one individual to another, directly or indirectly; effective treatment and
are culture traits often able to be observed directly, i.e. shape,
preventative measures are not usually available.
a
China risk group classification is inverted, i.e. China RG2 ¼ EU RG3, size, elevation, color, texture, opacity, appearance of margins,
China RG3 ¼ EU RG2; numbers in table are according to EU definition of risk emulsifability, as well as features of growth, such as motility
groups. on solid surfaces, production of extracolonial pigments or,
432 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
Fig. 1. Methodologies for the characterization of prokaryotes and the approximate respective taxonomic levels of resolution.The figure was modified from
Vandamme et al. (1996).
even the odor. Usually, such traits of a prokaryote strain are the
first characteristics to be recognized and recorded. The
problem, of course, is that the limited number of visible traits
does not afford unique descriptions for each of the millions of
prokaryotes. Furthermore, such characteristics are not neces-
sarily correlated with the evolutionary relationships of
prokaryotes, to the point that one is not able to extrapolate that
strains exhibiting different morphological features are also
more disparate genotypically than strains exhibiting similar
features. However, the experienced microbiologist is able to
use the information of growth requirements and colony
morphology, taking into account the origins of samples as well
as clinical and ecological information, as the starting points
for further characterization. Prokaryote cell shape and size, as
well as features such as formation of prosthecae, branching,
endospores, presence and insertion of flagellae, etc., are
determined by light and electron microscopy. Staining char-
acteristics of cells differentiate prokaryotes based on cell wall
or cell membrane structure. The Gram stain (Gram, 1884) is
one of the most common tests to be employed in character-
izing a bacterium. Again, although useful for initial descrip-
tions, the results of such characterizations are limited in their
value for definitive classifications of prokaryotes. Such anal-
yses are generally employed as initial tests, with the results
being interpreted for defining subsequent and more definitive
analyses.
Physiological testing generates profiles of characteristic
reactions for the utilization of substrates or other features that
provide information about the basic metabolic activities of
prokaryotes (Bochner, 2003). Various commercial test panels
have been developed which have proven to be useful for the
automation and standardization of these tests. The limitations
of such protocols lie in the limited range of taxa for which
standardized test panels may be applied and often the lack of
correlation of results with phylogenetic relationships among
bacteria. However, the protocols utilizing physiological test
panels are sensitive and are often effective for discriminating
the least differentiable bacterial taxa. The limitations in
reproducibility can be overcome, at least partly, through
effective standardization of protocols with reliable controls.
Chemical characterization (“chemotaxonomy”) exploits
differences in the structural components of prokaryote cells, i.
e. the cell wall, the cell membrane or the cytoplasm. Useful
differences may be detected in cell peptidoglycan, teichoic
acids, mycolic acids, fatty acids, polar lipids, respiratory lip-
oquinones, pigments and polyamines (Tindall et al., 2010).
The protocols for analyzing such cellular features enable
systematic differentiations that often correlate with the
evolutionary relationships of prokaryote taxa, although a given
protocol may exhibit varying degrees of resolution for
members of different taxa. The limitations to such protocols
are an evident lack of resolution at the lower taxonomic levels,
i.e. below the genus (Fig. 1). However, the strength of such
methods is that many of them are able to define higher taxa in
ways that physiological and biochemical testing cannot, e.g.,
the presence of ether-linked lipids with isoprenoid side-chains
linked to glycerol at positions 2 and 3 unambiguously distin-
guishes the Archaea (pers. comm., B.J. Tindall).
All methods targeting phenotypic characteristics of
prokaryotes suffer from differing degrees of reproducibility
 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
and comparability of results obtained by different laboratories.
However, one should recognize that reproducibility is
a potential problem for any method that measures quantitative
degrees of expression. Rigorous standardization is required, as
well as the establishment of comprehensive databases for the
relevant characteristics. An important point to appreciate
regarding phenotypic analyses is that trends in substrate
utilization or end-product accumulation or production of
specific chemotaxonomic traits generally are stable and reli-
able, even if absolute values change with differing conditions.
2.2. Genotypic characterization
The last half-century has witnessed an “explosion” in the
development and application of DNA-based analyses for the
characterization of microorganisms. The first genotypic
methodology employed in a systematic manner utilized the
ratio of guanine and cytosine nucleosides within the total
genomic DNA, i.e. %G þ C content (Marmur and Doty, 1962).
Although this methodology provides limited taxonomic reso-
lution (Fig. 1), it is still considered to be an important protocol
for characterizing the overall nature of the genomic DNA of an
organism. The G þ C contents of prokaryotes are recom-
mended for higher taxonomic level classification (Wayne
et al., 1987). As a general rule, organisms exhibiting
genomic DNA G þ C contents of more than 10% difference
will belong to different genera.
DNAeDNA hybridization (DDH) of genomic DNA
(Johnson and Ordal, 1968) is recognized to be the genotypic
“gold standard” for the comparison of prokaryotes. A DDH
similarity of approximately 70% serves as the recommended
demarcation for defining bacterial species (Wayne et al.,
1987). However, DDH protocols are considered to be
a tedious and complicated methodology with inherently large
degrees of error. Few laboratories have this method installed as
routine and the necessity for alternative methods for eluci-
dating prokaryotic species has been expressed (Stackebrandt
et al., 2002). The best possibility to date of an alternative
method for replacing DDH as the genotypic “gold standard”
for defining prokaryotic species appears to be the genome
Average Nucleotide Index (ANI) (Kostantinidis and Tiedje,
2005; Goris et al., 2007), derived from multiple-loci
sequence analyses. ANIs calculated from pair-wise genome
comparisons correlate exceedingly well with DDH results.
Richter and Rosselló-Móra (2009) demonstrated that complete
genome sequence determinations are not necessarily essential
for reliable comparisons of prokaryotes, but rather, random
sequencing with approximately 20% coverage is adequate for
purposes of taxonomic analyses.
Methods exploiting applications of DNA fragment profiling
or “fingerprinting”, generally based on characteristic variation
in genomic restriction sites, insertions and deletions, DNA
sequence repeats or microsatellites, single nucleotide poly-
morphisms (SNPs) or other sequence variations distributed
throughout prokaryote genomes, have been developed and
applied for rapid, high-resolution differentiation of some taxa.
For example, grouping by amplified fragment length
433
polymorphism (AFLP) analysis has been found to correlate
with grouping by DDH of species of the genera Xanthomonas
(Rademaker et al., 2000) and Acinetobacter (Janssen et al.,
1997). AFLP has also been shown to be a powerful method
for the delineation of novel species (Nemec et al., 2001).
Initially employed as more rapid and less expensive alterna-
tives to DNA sequencing, such methods may eventually prove
obsolete as the capacity and efficiency of DNA sequencing
continue to improve.
DNA sequence-based determinations and analyses have
rapidly become the “methods of choice” among prokaryotic
systematists, offering the highest level of resolution and
differentiation of the targets of analysis, i.e. the level of reso-
lution, by definition, at single nucleotide differentiation. With
the application of targeted PCR amplification and sequencing of
ribosomal RNA (rRNA) genes, particularly the small subunit or
16S rRNA genes (Medlin et al., 1988), phylogenetic relation-
ships of bacteria are able to be estimated rapidly, reliably and
with reproducibility in different laboratories. However, since
different laboratories may use different amplification and
sequencing protocols, different alignments with various mask-
ing practices and algorithms for cluster analyses, etc., different
results may be obtained for the same organism. Thus, although
DNA sequence-based methodologies offer the potential for
analyzing and exchanging information on a static target, the lack
of standardization for many genotypic methods is a current
limitation. Furthermore, although touted initially as the method
that would provide the basis for revising microbial taxonomy
and providing definitive identifications, rRNA gene sequence
analysis has come to be recognized as offering limited species-
level differentiation (Fig. 1). More recently, gene sequencing,
targeting selected “housekeeping” genes (i.e. genes of
conserved enzymes essential for cellular function), as well as
combinations of gene targets in “multilocus” analyses, offer
opportunities for exploiting the varying degrees of conservation
contained within genomes for elucidating prokaryotic taxa at
increasingly higher levels of resolution (Bishop et al., 2009;
Maiden et al., 1998). Thus, multilocus sequence analysis
(MLSA) and multilocus sequence typing (MLST) provide
analytical methods for the differentiation and characterization
of prokaryotes at the species and strain levels, respectively
(Fig. 1). However, to date, no consensus has been established for
the particular targets of analyses for particular taxa.
With the increasing speed and the decreasing costs of DNA
sequencing within recent years, the ability to cover complete
genomes of prokaryotes, as well as other microorganisms, has
resulted in a dramatic expansion in the number of sequences
available as references (Margulies et al., 2005). Currently, more
than 2400 prokaryote genome sequencing projects have been
completed or are in the process of being completed [Genomes
OnLine Database (GOLD), v. 2.0; http://www.genomesonline.
org]. The United States Department of Energy (DOE), via the
GEBA (Genomic Encyclopedia of Bacteria and Archaea)
project, has initiated an effort at determining of the genome
sequences of the type strains of all prokaryote species (http://
www.jgi.doe.gov/programs/GEBA). More than twenty years
ago, Wayne et al. (1987), proposed that “. the complete
434 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
deoxyribonucleic acid (DNA) sequence would be the reference
standard to determine (prokaryotic) phylogeny and that
phylogeny should determine taxonomy.” To date, the formerly
implausible possibility of using entire genomes in direct
comparison for characterization and taxonomy is becoming
a reality with the recent introduction of “next-generation”
sequencing technology, and the question of whether complete
genome sequence determinations will be routinely used for
comparative analyses is being discussed by microbiologists. In
such a scenario, the exponentially increasing amount of genome
sequence data will ensure that the most reliable “biomarkers”
will be identified and defined for taxonomic characterization.
Furthermore, the definitive characteristics of any organism at the
strain level would be available through a microbial commons.
2.3. Polyphasic characterization
Polyphasic characterization or polyphasic taxonomy inte-
grates multiple analyses, usually including both phenotypic
and genotypic data, to attain consensus classifications. The
term “polyphasic taxonomy” was first coined by Colwell
(1968) and the concept and details have been reviewed by
Vandamme et al. (1996). An overview view of various
methods and the approximate taxonomic levels of information
obtainable are shown in Fig. 1. The choice of methods varies
depending on the organism of study and according to the level
of resolution desired. The ultimate aim is to apply as much
information as possible to obtain the most comprehensive
characterization possible.
Generally, phenotypic and genotypic characterizations are
carried out for the purposes of classifying microorganisms
taxonomically, for the identification of species and for strain
differentiation studies. The particular methods applied will
vary depending upon the organism of study and the results of
initial testing. Thus, although polyphasic characterizations
may be used ultimately for definitive classifications of
prokaryotes, the usual practice in the past two decades has
come to rely predominantly upon comparative 16S rRNA gene
sequence analyses for primary characterization. The results of
the 16S rRNA gene sequence analyses enable initial phylo-
genetic placements, which have served to define the extent of
further analyses that may be necessary for confirming classi-
fications. It should be pointed out that most microbial
systematists insist upon more comprehensive analyses for
classification and identification of prokaryotes. Thus, poly-
phasic characterizations provide effective strategies for
analyzing microorganisms, although the specific set of
analytical methods will vary with respect to the microbe being
analysed.
3. Classification of prokaryotes
Classification may be defined as the arrangement of
organisms into categories (taxa) on the basis of similarities or
relationships (Brenner et al., 2001). Comprehensive charac-
terizations of prokaryotic strains enable their recognition
within a hierarchical framework of the diversity of
microorganisms that have been validly or effectively pub-
lished (Tindall et al., 2010). Validation, i.e. valid publication
of names of prokaryotes, follows the guidelines of the
“Bacteriological Code, 1990 Revision” (Lapage, et al., 1992;
Tindall et al., 2006), albeit, there is no “official” classifica-
tion of prokaryotes. However, among the most widely
accepted classifications are probably those presented in
Bergey’s Manual series, overseen by Bergey’s Manual Trust
(http://ww.bergeys.org). The first volume of the most recent
edition was published in 2001 and subsequent volumes have
followed; to date, the complete edition has not yet been
published. The time required to publish such comprehensive
references means that the information contained in them will
often not be current. Addressing this problem, the internet
website, “Taxonomic Outline of the Bacteria and Archaea”
(TOBA) was established and maintains a resource for up-to-
date classifications (http://www.taxonomicoutline.org). The
classification schemes of Bergey’s Manual and the TOBA
resource have been established primarily on the basis of
phylogenetic relationships elucidated through comparative
16S rRNA gene sequence analyses.
Kluyver and van Niel (1936) recognized the arbitrary
nature of bacterial classification of that time, more than 70
years ago. They insisted that a “scientific foundation” of
bacterial classification should be based upon the “natural
relationships” of the organisms. Later, genomic DNA mol%
G þ C contents and DDH similarities were able to provide
genotypic insight into the evolutionary relationships of
bacteria. Although phylogeny may be inferred through anal-
yses of phenotypic characterisitics, in recent years, the use of
16S rRNA gene sequence analyses has come to be accepted as
the primary means for estimating prokaryotic phylogenetic
relationships. As a point of interest, it should be pointed out
that early phenotypic-based classifications have correlated
amazingly well with newer genotypic-based classifications.
The “Living Tree Project” (Yarza et al., 2008) has estab-
lished a reference base of prokaryotic relationships, derived
from a dynamic database that compiles and curates the 16S
rRNA gene sequence data for the type strains of all prokaryote
species for which sequences are available (http://www.arb-
silva.de/projects/living-tree). The most recent release
(September, 2009) included 7710 sequences. The Living Tree
Project has highlighted the limitations in the sequence data
available in the public databases. A surprisingly low
percentage (i.e. less than 50%) of 16S rRNA gene sequences
archived in GenBank and EMBL are considered to be of
quality that can be used for reliable phylogenetic reconstruc-
tions. Much of the sequence data are too short or they include
too many ambiguously identified nucleotide positions. The
Living Tree Project is pushing an ongoing effort to generate
quality sequences for the 16S rRNA genes of the type strains
of all validly published species.
3.1. Classification ranks of prokaryotes
The classification ranks of prokaryotes follow the general
scheme of Carl Linnaeus (Carl von Linné) for systematic
 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
classification of the natural world, proposed in his Systema
Naturae in 1735. The Linnaean system of taxonomy has since
been complimented with the highest taxonomic rank for
prokaryotes, called a “domain”. All prokaryotes are placed
within the domains Bacteria or Archaea. Successively lower
ranks follow as non-overlapping subsets of the domain:
“phylum”; “class”, “order”, “family”, “genus”, “species” and
“subspecies” (Brenner et al., 2001). The “phylum”, “family”
and “subspecies” ranks, as well as “suborder” and “subclass”,
sometimes used for classification of prokaryotes, were added
to the original Linnaean classification scheme. Table 2 pres-
ents an overview of the increase in the number of prokaryotic
classification ranks since 2004. Although the higher taxo-
nomic ranks are useful for appreciating the overall relation-
ships of bacteria, the “working classification” relies on the
genus and species binomial ranks. The number of validly
published genera has increased by 51% since 2004; the
number of species has increased by 48% in the same time
period (Table 2).
3.2. The prokaryote species
The species represents the basic unit in taxonomy. One
definition of a prokaryotic species, i.e. “a category that
circumscribes a (preferably) genomically coherent group of
individual isolates/strains sharing a high degree of similarity in
(many) independent features, comparatively tested under
highly standardized conditions” (Rosselló-Móra and Amann,
2001), has received the acknowledgement of the Ad Hoc
Committee for the Re-evaluation of the Species Definition in
Bacteriology (Stackebrandt et al., 2002). Although there may
be some disagreement within the microbiology community
regarding whether a concept of “prokaryotic species” is
legitimate, i.e. in comparison with species of higher organ-
isms, the reality is that recognition of prokaryotic species
provides a framework enabling microbiologists to formulate
assumptions regarding the characteristics of strains with which
they are working and that have been identified. Conceivably,
the same framework could also be arranged according to
numerical “bar codes” or other organization. However,
microbiologists, since they are biologists as well, adopted the
Table 2
Classification ranks of the prokaryotes and the increase in the number of
validly published taxa during the last five years.
Rank Year
2004 2007
Domain 2 2
Phylum 26 27
Class 50 44
Order 94 97
Family 244 260
Genus 1253 1553
Species 6747 8233
315 344 498
Data obtained from TOBA (www.taxonomicoutline.org) and the list of
prokaryotic names with standing in nomenclature (www.bacterio.cict.fr).
435
organizational system applied to higher organisms and the
practice has been perpetuated, although not without some
resistance from some corners. Essentially, the application of
a prokaryotic species concept is merely one mechanism for
applying a systematic categorization to a complex system, for
organizational purposes.
3.3. Subspecific classification of prokaryotes
Within species of prokaryotes, subspecies may be differ-
entiated which typically are genotypically closely related
organisms exhibiting some phenotypic heterogeneity, although
allowable genotypic variation also can be recognized. The
subspecies is the lowest, official rank in prokaryotic taxonomy
(Brenner et al., 2001). The subspecific “variety” (in practice,
also referred to as “type”) is based on selected traits and has no
official rank. Besides characterizations used to determine the
taxonomic position of an organism, it may, in fact, be more
relevant for purposes of a microbial commons to categorize
microorganisms according to their individual biological
characteristics. Such characteristics define microbial strains
with respect to their activities as characteristic members of
diverse ecosystems, as plant symbionts, as active members of
the human or rumen microbiome, as the key factors in
fermentation and probiotic processes, as essential biodegra-
dation and biological control agents, as producers of toxins or
antibiotics and as the agents of human, animal or plant disease,
to name a few. These and other expressed characteristics are
the traits that attract academic and biotechnological research
and drive the interest in the exchange and distribution of
materials. Such features may be species-dependent or they
may be relegated to subsets within a species, such as strains or
varieties (types). Currently, definitions for these species
subsets are not applied to prokaryotes in a systematic fashion.
For the purposes of a microbial commons, these issues should
be clarified. Tools for the unambiguous classification of
organisms characterized at the sub-species level will be
increasingly important, given their relevance in particular
fields, as well as for culture collections, biological resource
centers and for a microbial commons.
3.4. The importance of type strains
The “nomenclatural type” of a prokaryotic species is
designated when the new species is described and submitted
for validation. “A type strain is made up of living cultures of
an organism which are descended from a strain designated as
2010 the nomenclatural type. The strain should be maintained in
2 pure culture and should agree closely in its characters with
27 those in the original description.” This is the designation of
75 “type strain” as described in the “Bacteriological Code”. The
123
procedures have been formalized and the guidelines and
279
1886 proposals for designating and making type material available
9994 to the scientific community have been described recently
(Tindall and Garrity, 2008). In theory, the type strain should be
the “representative” strain of the species. That is, with respect
to the phenotypic or genotypic variation among the strains of
436 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
a species, the type strain would be expected to hold a central
position within the range of the diversity of the species. This
may be the case for some prokaryotic species, although, in
practice, the type strain is more often, simply, the first strain of
the species to be isolated, characterized and described for
publication and validation of the species name. Thus, the type
strain for some species may actually come to represent
outlying subspecific lineages.
A critical point with respect to type strains and the
description of new prokaryotic species names is outlined in
Recommendation 30a of the Bacteriological Code, i.e. “Before
publication of the name of a new species, a culture of the type
strain . should be deposited in at least one of the permanently
established culture collections from which it would be readily
available.” This policy was expanded with the proposed rule
change, i.e. “In the case of species or subspecies the culture
collection numbers of at least two publicly accessible service
collections in different countries where a subculture of the
type strain has been deposited must be indicated” (De Vos and
Trüper, 2000). The two public strain collections receiving new
type material for purposes of validation should be associated
with the World Federation of Culture Collections (WFCC). A
listing of WFCC strain collections may be found at http://
wdcm.nig.ac.jp/wfcc/. Type strains of validly published
species receive collection-particular accession numbers with
a capitalized and superscript “T” designation, e.g., ATCC
12600T (American Type Culture Collection) and CCUG 1800T
(Culture Collection University of Gothenburg) are both type
and equivalent strains of Staphlyococcus aureus. It is impor-
tant to note that the type strains in different strain collections
are, in fact, subcultures of the same strains. A valuable tool for
searching for strain designations is the StrainInfo website
(Dawyndt et al., 2005; http://www.straininfo.net). This search
tool networks to the catalogues of more than 60 strain
collections worldwide, i.e. those that have active internet
pages.
The value of type strains of prokaryote species, for
purposes of taxonomic studies, is in the reference such
material provides for comparison and description of new
species. Strains with restricted access, e.g. patent strains
should not serve as type strains (Tindall et al., 2006). All
relevant type strains of related species must be included as
comparison in studies classifying new species of a genus or in
elucidating new bacterial strains. Unfortunately, through time
many type strains have been lost. Particularly, type strains that
were deposited in only one collection, i.e. before 2001 (De Vos
and Trüper, 2000) are considered to be “at risk”. The WFCC
and the European Culture Collection Organization (ECCO:
www.ecosite.org) have designated as a priority the effort to
identify type strains that are archived in one collection and to
try to distribute those strains to at least one other collection.
Further issues facing WFCC and ECCO collections are the
variation in authentication protocols. Some collections operate
under a strict Quality Management (QM) system, e.g., ISO,
etc., while others do not. Such variation among collections
may result in discrepancies in equivalent strains, etc. The lack
of standardization among collections could have consequences
leading to virtual monopolies by some collections and corre-
sponding decreases in the distribution of microbial strains.
Such effects would be deleterious to the “spirit” of the
microbial commons.
4. Nomenclature of prokaryotes
Nomenclature involves the assignment of names to the
taxonomic units which have been characterized and classified.
While characterizations and, to some degree, classifications of
prokaryotes follow recommendations or loose guidelines, the
naming of prokaryotic species follows a precise set of rules
defined in the “Bacteriological Code”. The name of
a prokaryote taxon is considered to be valid only after meeting
the requirements of the “Code”, as reviewed and published in
the International Journal of Systematic and Evolutionary
Microbiology (IJSEM) (ijs.sgmjournals.org). The key element,
as indicated by Tindall et al. (2006), is the system of valid
publication of a name, which effectively “registers” that name.
Prokaryotes are designated by Latin names, in italics, with the
genus name capitalized and the species written in small case,
e.g. Escherichia coli. For describing the origin or etymology
of prokaryotic names, reference is made to the review, “How
to name a prokaryote? Etymological considerations, proposals
and practical advice in prokaryote nomenclature” (Trüper,
1999).
4.1. Establishment of prokaryote names
Until 1980, numerous bacterial names were in circulation,
including many synonyms. In 1980 the “Approved List of
Bacterial Names” was published (Skerman et al., 1980),
consolidating the names of taxa that were considered to be
adequately described and for which a type, neotype or other
reference strain was available, finally comprising a listing of
2335 names that were acknowledged to be “validly pub-
lished”. Names published prior to 1980 but not included in
the “Approved List” had no further standing in nomenclature.
Since 1980, the names of new taxa are considered to be
validly published only after peer review and publication in
the IJSEM, the official journal of the International
Committee on Systematics of Prokaryotes (ICSP). Names of
taxa published in other scientific journals are regarded to be
“effectively published”, so long as they are not validated in
the IJSEM. In such cases, the names are written in quota-
tions, e.g. “Acinetobacter equinus”. The list of validly pub-
lished prokaryote names is monitored continuously and is
compiled on the internet (http://www.bacterio.cict.fr)
(Euzéby, 1997). This internet tool provides an invaluable
resource for the current status of the nomenclature of all
validly published prokaryotes as new analyses require
restructuring of the taxonomy.
The absolute diversity of prokaryotes or number of species
is unknown and the theoretical approach is an ongoing topic of
study (Curtis et al., 2002). Many (most) species are (yet) to be
isolated, although cultivation-independent molecular tech-
niques have demonstrated the existence of a number of these.
 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438
These organisms are classified into “candidate” species in
“candidate” genera. The number of new species descriptions
in IJSEM is recent years increased dramatically (Table 2),
particularly those species detected in the environment, i.e.
outside human or animal.
Sneath (1977) has calculated that approximately 25, pref-
erably, but not less than 10 strains are necessary for describing
a new species, i.e. so that the variation of the species is well
defined. More recently, a minimum of five strains in the
description of new species was proposed (Christensen et al.,
2001), although this proposal has not been adopted by
IJSEM. The policy of describing species on the basis of
“single strains” has become established, with the underlying
justification that an organism recognized as new possesses
a unique position within prokaryotic diversity and the new
species should be recorded so that it is established as a refer-
ence. It should be noted that the description of the pathogen
for Whipple’s disease, Tropheryma whipplei, was based on
a single isolate.
4.2. Nomenclatural changes
The rules of the Bacteriological Code indicate that the
species name in new combinations with a new genus should
remain in place, e.g. Pseudomonas maltophilia was reclas-
sified in the existing genus Xanthomonas, which led to the
novel recombination, Xanthomonas maltophilia sp. nov.
Subsequently, X. maltophilia was reclassified in a novel
genus, Stenotrophomonas, as the novel recombination,
Stenotrophomonas maltophilia comb. nov.
Sometimes, despite the rules of the Bacteriological Code,
name designation is decided pragmatically. This is the case
of classifications for special purposes, with certain charac-
teristics when it is deemed that taxonomic principles should
be overruled. Well-known examples are the artificial divi-
sion of Escherichia coli and Shigella dysenteriae, because
of the particular pathogenicity of S. dysenteriae. Similarly,
the classification and naming of Salmonella species is an
example wherein the taxonomy and public health relevance
are at odds (Brenner et al., 2000). Since 1930, serological
typing has been the basis for Salmonella classification. More
than 2400 serotypes (serovars) have been described within
the genus, whereby serotyping formed the basis of species
designations. However, DDH has shown that only two
species can be distinguished within the genus Salmonella,
S. enterica and S. bongori. S. enterica includes six
subspecies and more than 1400 serotypes and has warm-
blooded animals as habitat. The valid name for what
previously was designated as S. typhi is now S. enterica
subsp. enterica serovar. Typhi (Tindall et al., 2005). The
CDC and the WHO, for practical reasons and visibility for
physicians, maintained its own Salmonella nomenclature, i.e.
S. enterica ser. Typhi.
Changes in microbial taxonomy have impacts on medical
microbiology because the visibility of certain organisms may
be lost. A recent example is the change in the name of
Streptococcus bovis, a species associated with colon
437
carcinoma, to Streptococcus gallolyticus, a name that not
every physician will recognize (van’t Wout and Bijlmer,
2005). Such problems in this respect can be prevented by
reporting the new name, followed by the old name in brackets,
e.g. Streptococcus gallolyticus [Streptococcus bovis].
However, it is important also to maintain the databases of
commercial identification systems with the nomenclatural
changes and additions of new species. It is also important that
quality authentication protocols be used by strain collections
for confirming strain deposits. Such strains should be
authenticated according to reliable characterization criteria
and classification schemes.
5. Conclusions
The classification of microorganisms is continuously
changing as a result of progressive developments of analyses.
Unlike the case in earlier years, prokaryote taxonomy has
developed into a discipline with a diversity of techniques
used to analyze organisms. Although invaluable for charac-
terizing prokaryotes and determining their classifications,
many of the methodologies used for such analyses may, in
fact, not be practical for the issues of relating prokaryote
taxonomy to a microbial commons. Among the critical issues
facing strain collections and biological resource centers for
interfacing with a global microbial commons are the ques-
tions of overall effort and resources in maintaining the strain
data, as well as the biomaterial. The current methodologies
employed for analyzing prokaryote strains are simply too
slow and require too much manpower and effort to be truly
effective. Furthermore, as stated previously, the most
important aspects of biomaterial and documented informa-
tion, for purposes of a microbial commons are probably at
the strain level. Fortunately, new technologies employing
extremely rapid and inexpensive species-level identification
using MALDI-TOF mass spectrometry (MS) (http://www.
anagnostec.eu), and RAMAN spectroscopy (http://www.
riverd.com) for high-resolution strain typing are currently
available, although, to date, not widely used. Such advances,
together with the development of a reliable replacement for
the DDH protocol, are the means for establishing effective
interactions between prokaryote taxonomy and a microbial
commons.
Acknowledgements
The authors acknowledge Ramon Rosselló-Móra and Paul
DeVos for their critical reviews of the manuscript and Brian
Tindall for his expertise, insight and discussions on micro-
bial systematics and taxonomy. Thanks go to: Hans H. Yu,
Science Policy Directorate, Health Canada, Linda Deitch,
Occupational Health and Safety, University of Wollongong
and Wang Lei, Office of Laboratory Management, China
Centers for Disease Control for their help in compiling
information on the National Risk Group classifications of
microorganisms.
438 E.R.B. Moore et al. / Research in Microbiology 161 (2010) 430e438

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