INTRODUCTION TO MICROBIAL TAXONOMY

What is Classification?

• Living organisms are grouped according to similar characteristics (classification), and each
organism is assigned a unique scientific name.
• Microbial classification is the process of organizing microorganisms into specific groups
based on shared characteristics. Its primary goal is to establish relationships and identify
microorganisms in a systematic and consistent manner.
• Classification is the organization of organisms into progressively more inclusive groups on
the basis of either phenotypic similarity or evolutionary relationship.
• A species is made up of one to several strains, and similar species are grouped into genera
(singular, genus). Similar genera are grouped into families, families into orders, orders into
classes, up to the domain, the highest level taxon.
• Such a “classical” bacterial organization, which is typified by the Bergey’s Manual of
Determinative Bacteriology, is based on metabolic, immunological, and structural
characteristics. Strains, for example, are all descended from the same organism, but differ in
an aspect such as the antigenic character of a surface molecule

key objectives of microbial classification:

• Understanding Evolutionary Relationships: By classifying microorganisms, scientists can

trace their evolutionary history and understand how different groups are related to each
other.
• Facilitating Communication: A standardized classification system provides a common
language for scientists to communicate about microorganisms, ensuring clarity and
consistency in research and discussions.
• Identifying and Diagnosing Pathogens: Accurate classification is crucial for identifying
disease-causing microorganisms, enabling timely diagnosis and treatment.
• Discovering New Species: Classification can lead to the discovery of new microbial species,
expanding our knowledge of biodiversity.
• Understanding Microbial Functions: By grouping microorganisms based on their shared
characteristics, scientists can better understand their roles in various ecosystems and their
potential applications in biotechnology and medicine.

In essence, microbial classification provides a framework for organizing and understanding the
vast diversity of microorganisms, enabling researchers to study and utilize these organisms more
effectively.

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 The Taxonomic Hierarchy

• Microbial classification is the process of organizing microorganisms into specific groups

based on shared characteristics. Its primary goal is to establish relationships and identify
microorganisms in a systematic and consistent manner.
• The classification of microbes involves placing them within hierarchical taxonomic levels.
• All organisms can be grouped into a series of subdivisions that make up the taxonomic
hierarchy.
• Microbes in each level or rank share a common set of specific features.
• The ranks are arranged in a nonoverlapping hierarchy so that each level includes not only
the traits that define the rank above it, but a new set of more restrictive traits.
• Classification of prokaryotes has long been based on the same hierarchical systems on
which Linnaeus (Linnaeus 1753) based his nomenclatural system applied initially to plants
and animals. These classifications are hierarchically organized into seven levels: kingdoms,
phyla, classes, orders, families, genera, and species.
➢ Just as a number of species make up a genus, related genera make up a family.
➢ A group of similar families constitutes an order, and a group of similar orders makes
up a class.
➢ Related classes, in turn, make up a phylum.
➢ All phyla that are related to each other make up a kingdom, and related kingdoms are
grouped into a domain.
• The highest rank is the domain, and all prokaryotes belong to either the Bacteria or the
Archaea. Within each domain, each microbe is assigned (in descending order) to a phylum,
class, order, family, genus, and species .
• Some prokaryotes are also given a subspecies designation.
• Thus, a particular organism (or species) has a genus name and specific epithet and
belongs to a family, order, class, and phylum.

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• Microbial groups at each level have a specific suffix indicative of that rank or level.

Rank Suffix Example

Phylum -ota Pseudomonadota

Class -ia Gammaproteobacteria

Order -ales Pseudomonadales

Suborder -ineae Pseudomonadineae

Family -aceae Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas aeruginosa

• The hierarchical system of the official nomenclature is as follows: (only the popular ones are
given)
o Phylum (or Division): at present, the phylum rank is not controlled by the
Prokaryotic Code.
o Class: The class is named after the type genus of the type order of the class.
o Order: The type of an order is one of the genera. The order name is named after the
type genus of the order. E.g. The order Pseudomonadales is named after the type
genus Pseudomonas.
o Family: In general, the family name is named after the type genus of the family, e.g.
The family Pseudomonadaceae is named after the type genus Pseudomonas.
o Genus
o Species
o Subspecies: Subspecies are created only when it is necessary. For example, an
important probiotic species, Lactobacillus delbrueckii contains six subspecies.

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Example: previous system

Example: updated system

Domain Bacteria Bacteria

Kingdom Pseudomonadati Bacillati
Phylum Pseudomonadota Bacillota
Class Gammaproteobacteria Bacilli
Order Enterobacterales Bacillales
Family Enterobacteriaceae Staphylococcaceae
Genus Escherichia Staphylococcus
Species Escherichia coli Staphylococcus aureus

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Taxonomic update

As the classification process is information-dependent, new technological advances providing

greater and more reliable information concerning microorganisms exert a significant impact on it.
Until mid-1980s, microbial classification was based primarily on phenotypic and chemotaxonomic
characteristics, which poorly correlated with evolutionary relationships. Thereafter, the introduction
of 16S rRNA sequence analysis for deciphering evolutionary relationships led to dramatic changes
in the classification of microorganisms (e.g., name change of Pseudomonas cepacia to
Burkholderia cepacia). Although analysis of 16S rRNA remains an important tool, it has limited
resolving ability. A far greater revolution in microbial taxonomy has recently been ushered in by
technological advancements enabling rapid and inexpensive whole-genome sequencing (WGS) of
microorganisms. WGSs are now available for the majority of validly named species and also large
numbers of uncultured and uncharacterized species/strains. These sequences provide an all-
encompassing resource for developing a reliable evolutionarily coherent classification of
prokaryotic organisms. Based on WGSs, phylogenetic trees can be constructed from a large
dataset of genes/proteins, exhibiting a high degree of resolution at different taxonomic levels.
These trees form the basis of the Genome Taxonomy Database, which has become an important
reference resource for the classification of prokaryotic organisms.
Taxonomy is not fixed. This means that it can change based on new information we gather about
living organisms.

Example: Proposal of Names for domains and kingdoms

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories
domain and kingdom. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati,
Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary
phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure,
including ‘diderms’ vs. ‘monoderms’, Gracilicutes vs. Firmicutes, ‘Negibacteria’ vs. ‘Unibacteria’,
‘Hydrobacteria’ vs. ‘Terrabacteria’, and ‘Hydrobacterida’ vs. ‘Terrabacterida’. The domain Archaea is
proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting
the previous division into ‘Euryarchaeota’, ‘DPANN superphylum’ and ‘TACK superphylum’.
Domain: Bacteria
Kingdom:
➢ Bacillati
➢ Fusobacteriati
➢ Pseudomonadati
➢ Thermotogati

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Domain: Archaea
Kingdom:
➢ Methanobacteriati
➢ Nanobdellati
➢ Thermoproteati

Ref: Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J
Syst Evol Microbiol. 2024 Jan;74(1). doi: 10.1099/ijsem.0.006242. PMID: 38252124.

Example: Changes in the bacterial phylum names

The newly adjusted rule (Rule 8) in the ICNP requires all formal rank names to be formed by the
addition of the suffix ” -ota” to the stem of the name of the designated type genus.

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Example: Pseudomonadota

• Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria.

The renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains
controversial among microbiologists, many of whom continue to use the earlier name
Proteobacteria, of long standing in the literature. The phylum Proteobacteria includes a
wide variety of pathogenic genera, such as
Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others. Others are free-living
(non-parasitic) and include many of the bacteria responsible for nitrogen fixation.
• The Pseudomonadota are divided into several classes. Pseudomonadota classes with validly
published names include some prominent genera: e.g.:

1. Acidithiobacillia: Acidithiobacillus, Thermithiobacillus

2. Alphaproteobacteria: Brucella, Rhizobium, Agrobacterium, Caulobacter, Rickettsia, Wolbac
hia, etc.
3. Betaproteobacteria: Bordetella, Ralstonia, Neisseria, Nitrosomonas, etc.
4. Gammaproteobacteria: Escherichia, Shigella, Salmonella, Yersinia, Buchnera, Haemophilus,
Vibrio, Pseudomonas, Pasteurella, etc.
5. Hydrogenphilia : Pelomicrobium
6. Magnetococcia : Magnetococcus marinus
7. Zetaproteobacteria: Mariprofundus

Example: Enterobacterales

• Enterobacterales is an order of facultatively anaerobic Gram-negative bacilli in the class

Gammaproteobacteria, containing some of the most frequently encountered pathogens in
the clinical microbiology laboratory. The family Enterobacteriaceae was created with a
single-type genus (Enterobacter). Groundbreaking work by scientists at the CDC in the
1980s—including expanded biochemical testing and morphologic, culture, and other
biochemical features, as well as percentage G + C content and DNA-DNA hybridization
studies—led to a seminal article published in the Journal of Clinical Microbiology describing
new bacterial species within the family Enterobacteriaceae.
• More recently, in 2016, Adeolu and colleagues utilized whole genome sequencing to
identify interrelationships within the order using core genome phylogeny. Based on this
work, the order Enterobacteriales—which was never validly published according to the
Code—was divided into 7 families comprising distinct clades of related genera based on

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 overall genome similarity, 4 multilocus sequence analysis proteins, and the identification of
conserved signature insertion/deletions.
• The order Enterobacterales contains >250 species. Multiple genera that were not sequenced
as part of this work were placed into one of the families based on 16S rRNA gene sequence
analysis; Plesiomonas was not assigned to any of the families in the revisions and remains
incertae sedis (Latin for “of uncertain placement”).
• From a practical standpoint, revisions to the higher-order levels of taxonomy as previously
discussed are not likely to have much impact on the identification and reporting of these
organisms when identified in clinical cultures as laboratories typically report organisms at
the level of genus and species.

(Ref: Change of Plans: Overview of Bacterial Taxonomy, Recent Changes of Medical Importance,
and Potential Areas of Impact Andrea M. Prinzi, and Nicholas M. Moore)

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More examples:

Old Name Revised Name Year of Clinical Significance

Revision
Clostridium difficile Clostridioides 2016 Antibiotic-associated colitis
difficile
Propionibacterium Cutibacterium acnes 2016 Normal microbiota of skin and mucosal
acnes surfaces. Associated with orthopaedic
infections involving hardware,
endovascular devices, and cerebrospinal
shunts.
Enterobacter Klebsiella aerogenes 2017 Isolated from blood, urine, sputum,
aerogenes wounds. Treatment with third-generation
cephalosporins can induce AmpC β-
lactamase production

The above represent just a few examples of how microbial taxonomy continues to change at a very
rapid rate in this era of molecular diagnostics including whole genome sequencing.