systematics of bacteria

1. Unit II
Bacterial Systematics
Dr. Nidhi Verma
Department of Microbiology
RLAC, University of Delhi

2. 1. Taxonomy/Systematics:
In simple words, The science for studying classification is called Taxonomy (Greek: taxis =
arrangement; nomos = law) AND is further divided into three working groups: Classification,
Identification and Nomenclature.
Taxonomy is the branch of science dealing with naming, grouping of organisms on the basis of
the degree of similarity and arranging them in an order on the basis of their evolutionary
relationship.
Classification : placing organisms within groups with members exhibiting similarities (structure,
physiological or evolutionary relatedness). These groups are termed as taxa (s. taxon)
Nomenclature is assigning of scientific names to taxonomic groups in accordance with accepted
rules.
Identification is the practical side of taxonomy, the process of determining if a particular
isolate belongs to a recognized taxon.
The term systematics sometimes is referred synonymously with taxonomy. While, taxonomy is
plainly referred to identification, classification and naming of organisms; systematics is the
evolutionary history of organisms through time. Systematics, in other words, is used to
understand the evolutionary history of life on Earth.

3. Three types of Systematics/Taxonomy
1. Evolutionary Systematics : Grouping organisms that resemble ancestors
2. Numerical Taxonomy : Used mathematical models to group organisms according to
overall similarities
3. Phylogenetic Classification System : Groups reflect genetic similarity and
evolutionary relatedness.
• The importance of taxonomy has been ever increasing.
• In 2000, a project called “All Species Inventory” was started (http://www.all-
species.org/).
• Aim : to identify and record every species of life by 2025.
• Very challenging; till now 1.5 million species- identified
• Estimated number of species: between 7 to 100 million.
• For This mind boggling number : importance of cataloguing the species in a proper
and scientific way.

4. • Thus taxonomy is important for
(i) effective communication among scientists about the identity of a particular microbe
(ii) catalogue a large number of species in a systematic manner,
(iii) help in predictions and further research about a particular isolate if little is known
about it and it shows some similarities with microbes of particular group

5. • One of the oldest classification systems, called a Natural classification, arranges
organisms into groups whose members share many characteristics and reflects as
much as possible the biological nature of organisms.
• The Swedish botanist Carl von Linné, or Carolus Linnaeus as he often is called,
developed the first natural classification, based largely on anatomical characteristics.
• It had merits over previously employed artificial systems because knowledge of an
organism’s position in the scheme provided information about many of its properties.
For example, classification of humans as mammals denotes that they have hair,
self-regulating body temperature, and milk-producing mammary glands in the
female.

6. Phenetic Classification
• For a very long time, microbial taxonomists relied exclusively on a
phenetic system, which groups organisms together based on the mutual
similarity of their phenotypic characteristics.
• This classification system succeeded in bringing order to biological
diversity and clarified the function of morphological structures. For
example, because motility and flagella are always associated in particular
microorganisms, it is reasonable to suppose that flagella are involved in at
least some types of motility.
• Although phenetic studies can reveal possible evolutionary relationships,
they are not dependent on phylogenetic analysis.
• They compare many traits without assuming that any features are more
phylogenetically important than others—that is, unweighted traits are
employed in estimating general similarity.

7. Phylogenetic Classification
With the publication in 1859 of Darwin’s On the Origin of Species, biologists began
developing phylogenetic or phyletic classification systems that sought to compare
organisms on the basis of evolutionary relationships.
The term phylogeny (Greek phylon, tribe or race, and genesis, generation or origin) refers
to the evolutionary development of a species.
microbiologists could not effectively employ phylogenetic classification systems, primarily
because of the lack of a good fossil record.
When Woese and Fox proposed using rRNA nucleotide sequences to assess evolutionary
relationships among microorganisms.
The validity of this approach is now widely accepted and there are currently over 200,000
different 16S and 18S rRNA sequences in the international databases GenBank and the
Ribosomal Database Project (RDP-II).
the power of rRNA as a phylogenetic and taxonomic tool rests on the features of the rRNA
molecule that make it a good indicator of evolutionary history and the ever-increasing size
of the rRNA sequence database.

8. Genotypic Classification
• There are currently many ways in which the genotype of a microbe can be evaluated
in taxonomic terms.
• In general, genotypic classification seeks to compare the genetic similarity between
organisms. Individual genes or whole genomes can be compared.
• Since the 1970s, it has been widely accepted that procaryotes whose genomes are at
least 70% homologous belong to the same species.
• Unfortunately, this 70% threshold value was established to avoid disrupting existing
species assignments; it is not based on theoretical considerations of species identity.
Fortunately, the genetic data obtained using newer molecular approaches usually
concur with these older assignments.

9. 2. Binomial nomenclature
• Why needed?
• For millions of organisms, common names - lead to misunderstanding as different names are
used for same organism in different places.
• a naming system –introduced : termed “scientific nomenclature”.
• Every organism is given a binomial latin name and was first described by Carolus Linnaeus.
• In binomial nomenclature, name of every organismis composed of two parts: first is called
generic name representing the taxon –Genus to which it belongs.
• which is followed by the second part is called -Species.
• A taxon is a group organisms considered by taxonomists to form a related unit.
• The generic name always starts with capital letter and specific name always with small letter.
• These scientific names are used uniformly regardless of regions/countries or languages, and
two different organisms can not posses same scientific name.
• For example; humans are assigned scientific name as Homo sapiens.
• Always italicized (Homo sapiens), where genus name starts with a capital letter.
• Abbreviated as H. Sapiens

10. The nomenclature of organisms is governed by a set of rules framed by International
Codes of Nomenclature.
•There are different codes of nomenclature for different groups of organisms for
example, naming of bacteria, animals and plants is governed by International Code for
Nomenclature for Bacteria (ICNB), International Code of Zoological Nomenclature
(ICZN) and International Code of Botanical Nomenclature (ICBN), International
Code of Nomenclature for algae, fungi, and plants (ICN) respectively.
•The scientific name of an organism, when cited in any text, is always mentioned as in
italics or underlined fontstyle.

11. Signature Sequences
• The rRNAs from small ribosomal subunits (16S
from bacterial and archaeal cells and 18S from
eukaryotes) have become the molecules of
choice for inferring microbial phylogenies and
making taxonomic assignments at the genus
level. The small subunit rRNAs (SSU rRNAs) are
widely applicable in studies of microbial
evolution, relatedness, and genus identification
for several important reasons (figure 19.2).

12. importance
• they play the same role in all microorganisms.
• ribosomes are absolutely necessary for survival and
ribosomes cannot function without SSU rRNAs, the genes
encoding these rRNAs cannot tolerate large mutations.
Thus these genes change very slowly with time.
• rRNA genes are rarely subject to horizontal gene transfer,
an important factor in comparing sequences for
phylogenetic purposes.
• The utility of SSU rRNAs is extended by the presence of
certain sequences within SSU rRNA genes that are variable
among organisms as well as other regions that are quite
similar which enable comparison between closely related
microbes, whereas the stable sequences allow the
comparison of distantly related microorganisms.

13. oligonucleotide signature sequences
• These are short, conserved nucleotide
sequences that are specific for
phylogenetically defined groups of organisms.
• Thus the signature sequences found in
bacterial rRNAs are rarely or never found in
archaeal rRNAs and vice versa. Likewise, the
18S rRNA of eukaryotes bears signature
sequences that are specific to the domain
Eukarya.

14. multilocus sequence analysis (MLSA)
• For many applications, identification to levels
below species is required. Typically genes that
evolve more quickly than those that encode rRNA
must be analyzed.
• The technique called multilocus sequence
analysis (MLSA) compares the sequences of
several conserved housekeeping genes .At least 5
genes are examined to avoid misleading results
that can arise through horizontal gene transfer.

15. • Because many different versions, or alleles, of
each gene can exist, the finding that two
microbial isolates share the same alleles for
multiple genes is strong evidence that the two
strains are closely related, perhaps even the
same strain.
• MLSA is now often performed from whole
genome sequences, where it is termed
wgMLSA. The availability of wgMLSA data
enables extended gene-by gene comparison

16. RFLP- restriction fragment length
polymorphism
• Originally developed to analyze human DNA, SNP
analysis targets specific regions because they are
normally conserved, so single base pair differences
reveal evolutionary change. SNP analysis shares
features with analysis of restriction fragment length
polymorphism (RFLP).
• This technique identifies differences in restriction
endonuclease digestion patterns, which reflect
individual base pair changes. When this analysis is
applied to the gene encoding the SSU rRNA, it is
termed ribotyping. With the advent of WGS, these
techniques are increasingly performed in silico.

17. FAME
• Among the more useful biochemical characteristics used in microbial
taxonomy are bacterial fatty acids, which can be analyzed using a
technique called fatty acid methyl ester (FAME) analysis.
• A fatty acid profile reveals differences in chain length, degree of
saturation, branched chains, and hydroxyl groups. Microbes of the
same species will have identical fatty acid profiles, provided they are
grown under the same conditions; this limits FAME analysis to only
those microbes that can be grown in pure culture.
• Finally, because the identification of a species is done by comparing
the results of the unknown microbe in question with the FAME profile
of other, known microbes, identification is only possible if the species
in question has been previously analyzed. Nonetheless, FAME analysis
is particularly important in public health, food, and water
microbiology. In these applications, microbiologists seek to identify
specific pathogens.