The document provides an overview of bacterial taxonomy, outlining the classification, nomenclature, and identification of organisms. It traces the historical development of taxonomic systems, including the contributions of various scientists, and introduces the five kingdom classification system. Problems in taxonomy, such as the classification of bacteria based on their characteristics and the use of numerical taxonomy for accuracy, are also discussed.

1. BACTERIAL TAXONOMY
COLLEGE OF MEDICINE AND ALLIED HEALTH SCIENCES
FACULTY OF MEDICAL LABORATORY SCIENCE AND DIAGNOSTICS
BSc, YEAR 2
LECTURER - ZEIN SOUMA

2. TAXONOMY
– Comes from the Greek word
taxis – arrangement;
nomos - rules
– Is a science of organismal classification
– It is a system that creates an universal name for
an organism
– Presents a reference point to classify organisms
– Taxonomy is made up of
i. classification
ii. nomenclature and
iii. identification

3. TAXONOMY
• Classification is the arrangement of
organisms into groups (taxa) according to
similarities and evolutionary connections
• Nomenclature is a branch that is involved
in the processing of naming a taxonomical
group according to a series of rules
• Identification determines taxa for organism
that were isolated

4. THE HISTORY OF TAXONOMY
• 1735 Plant and animal Kingdom
• 1857 Fungus and bacteria classified under plant
kingdom
• 1866 bacteria, protozoa, algae, and fungi makes up
the Kingdom Protista
• 1937 "Prokaryote" terminology used for organisms
without nucleus
• 1961 cells with non membrane nucleoplasm are
Prokaryote
• 1959 Kingdom Fungi
• 1968 Prokaryote Kingdom suggested
• 1978 Two types of prokaryotic cells found
Table 5.1

5. TAXONOMY
• Systematic or phylogeny
- Is the study of the evolutionary history of an
organism
• All Species Inventory (2001-2025)
– Was formed to identify all species on Earth
• Binomial Nomenclature – was proposed by Carolus
Linnaeus in the18 Century. This system introduced
• Genus
• Specific epithet
• Strain – is the subgroup of species
• Strain can be written as a name, nomber or an alphabet
• There are several rules that need to be observed in
writing a scientific name (see Table 5.2)

6. Carolus Linnaeus

7. Scientific Name
Scientific binomial Source of Genus
name
Source of
Specific epithet
Klebsiella pneumoniae Honors Edwin Klebs The disease
Pfiesteria piscicida Honors Lois Pfiester Disease in fish
Salmonella
typhimurium
Honors Daniel
Salmon
Stupor (typh-) in
mice (muri-)
Streptococcus pyogenes Chains of cells
(strepto-)
Forms pus (pyo-)
Penicillium notatum Tuftlike (penicill-) Spores spread in
wind (nota)
Trypanosoma cruzi Corkscrew-like
(trypano-, borer;
soma-body)
Honors Oswaldo
Cruz
Table 5.2

8. Taxonomic key
• Linnaeus suggested a taxonomical hierarchy
• All organisms that are from the same species are classified under
one genus
• Genus with the same traits will be classified into the same family
and the list goes on
• He classified all living organisms under two kingdoms, animal and
plant
Figure 5.1 The classification of human, dog, wolf and bacterium

9. DICHOTOMOUSKEYS
• The taxonomy keys are
used to identify
characteristics of an
organism
• We hope that the
classification of organisms
can be conducted based
on phylogenic connections
and evolutionary ties
between organism.
Figure 5.2 The dichotomous key generated
for classification of main bacterial groups

10. Problems in taxonomy
• Problems that crop up in taxonomy studies are
i. To determine members in a species
ii.To identify members of a kingdom and
kingdoms that are in a domain
• In an advanced organism such as plants and
animals, classification is conducted according to
the ability to reproduce, morphology and
geography
• genetic transfer and changes in morphology can
not be used in the classification of bacteria

11. Problems in taxonomy
• Bacteria is classified according to
i. chemical reaction
ii. Chemical composition
iii. Cell structure
iv. Genetic characteristic and
v. Immunological characteristic

12. Development since LINNAEUS
• 1866- Ernst H.Haeckel created the third kingdom
PROTISTA – which contains algae,
protozoa,bacteria,fungi and sponge
• 1956- Lynn Marguilis and H.F Copeland
introduced the 4 kingdoms classification scheme
for prokaryote and eukaryote
• i. Monera – inclu. all prokaryotes i.e. true
bacteria and blue green algae
ii. Protoctista- all eukaryotes as algae, fungi
and protozoa
iii. Plantae- all green plants
iv. Animalia – all animals created from zygotes

13. Development since LINNAEUS
• R.H. Whittaker does not accept the theory of
endosymbiosis for eukaryotic and prokaryotic
diversity
• Suggested a means of classification according
to the dietary requirements
• 1969- Whittaker suggested the division of
Protoctista to Prostista and Fungi

14. 5 Kingdom Classification System
• From Whittaker and other
taxonomist suggestion
and observations the 5
Kingdom classification
system was formed
• All prokaryotes were
classified as Monera – no
cells nucleus
• Unicellular Eukaryotes
with nucleus were
classified as Protista
Figure 5.3 The 5 Kingdom Classification
See Table 5.3 for characteristic
of all 5 kingdoms

15. Table 5.3 Characteristics of the 5kingdom classification

16. Kingdom Monera
• All prokaryotes including
eubacteria, cyanobacteria
and archaebacteria
Kingdom Monera
characteristics:
• Unicellular; no nuclei, no
membranous organelles
• DNA contains little or no
protein
• Binary fission
Rajah 5.4 Ahli kingdom Monera

17. Kingdom Monera
Type of organisms:
• Eubacteria is important in the area of health
science
• Cyanobacteria are important in maintaining
balance in environment
• Archaebacteria are primitive prokaryotic
organism that have formed adaptation to
extreme environments
* Methanogen
* Termoacidophiles
* Halophiles

18. KINGDOM PROTISTA
• Is unicellular; contains
nucleus with
membrane
• Lives in freshwater,
sea water and also in
soil
Figure 5.5 Member of the Kingdom Protista

19. • Members are mostly
multicellular with
some that are
unicellular
• Obtains nutrients via
absorption
• Produces spores
Figure 5.6 Members of the Fungal Kingdom
KINGDOM FUNGI

20. • Are animals that are
produced by zygote
formation
• Members are
macroscopic or
microscopic
• Includes many types
of animals including
Helminths and
Arthropods
Figure 5.7 Members of the Animal Kingdom
KINGDOM ANIMALIA

21. PROCESS OF PROKAROTIC
EVOLUTION
Figure 5.8 Evolutionary Model since the
identification of archaebacteria
Carl Woese, G.E.Fox 1970s
• The proof that was obtained
from research on
Archaebacteria and
stromatolites suggested that
there are three branches to
the “tree of life’ that was
produced in “Age of
Microorganism”
• Each of this branch
produces a different group
of organism
Tree of life

22. PROCESS OF PROKAROTIC
EVOLUTION
• 1977- T.Cavalier suggested that the archaebacteria
emerged after the eubacteria as a result of evolution of the
Gram positive bacteria that are actinomycetes
• 1988- J.A.Lake proposed a two branch model; one branch
produces the eubacteria and 2 groups of archaebacteria
and the other branch is divided into eukaryote and one
group of archaebacteria
• 1990- Woese suggested the domain category
Domain is above the kingdom
The three branch theory was not received by all.

23. THREE DOMAIN THEORY OF WOESE
• Before the three domain theory was proposed by Woese in 1998;
there were 3 views held by taxonomist
• 1st
view- from a general ancestor it branched out to bacteria and
archae, and the archae branched into eukaryote
• 2nd
view –all three domains existed together and this allowed for
the exchange of genetic content between all – universal genetic
code
• 3rd
view – there are 4 domains and the members of the 4th domain
that produced the eukaryote; this domain has become extinct

24. ENDOSYMBIOSIS THEORY
Figure 5.9

25. THREE DOMAIN THEORY OF WOESE
Figure 5.10
This diagram explains the three domain theory of Woese

26. THE DIFFERENCES BETWEEN BACTERIA, ARCHAE AND
EUKARYOTE
Table 5.4 Three Domain

27. WOESE’S THREE DOMAINS
Kingdom
Monera
All eucaryotes
Table 5.11

28. Figure 5.12 – The Shrub of life
Proposed by W Ford Doolittle
Has more than one ancestor
The interlinked and
intertwined
interactions show
that there is a lateral
gene transfer
between genomes

29. Lateral gene transfer
The different colored line that comes from different ancestors shows that
there is lateral gene transfer from one cell to another. When genes from
different sources are united, a new cell with ancestral diversity will be
Generated.
Figure 5.13

30. Three Domain System
Table5.5

31. Figure 5.14 Evolution Tree Generated
through Numerical Taxonomy
• Numerical Taxonomy – more
traits observed in an organism
will increase the accuracy by
which the similarities between
organism is determined
• When two organism have 90%
similarities in all traits that are
observed therefore both
organisms can be assumed to
be in the same species
Figure 5.14

32. NUMERICAL IDENTIFICATION
Figure 5.15

33. Genetic Homology
• Can be studied by :
i. studying the base composition
ii. Sequencing of DNA and RNA
iii. Through the hybridization of DNA
iv. Studying protein profile

34. • DNA base composition
– Guanine + cytosine
mol % (GC)
• DNA fingerprinting
– Electrophoresis of
restriction enzyme
digested product
• rRNA sequencing
• Polymerase Chain
Reaction (PCR)
Base composition, fingerprinting and PCR

35. Acid nucleic hybridization:DNA probes
Figure 5.16

36. Acid nucleic hybridization: DNA Chip
Figure 5.17

37. Western Blotting
Figure 5.18

38. Other methods used

39. • The difference in the
flow of electric between
species
• Cells are stained
selectively with
Antibodies and
fluorescent stain
Flow cytometry

40. • antiserum mixture
that is known with
unknown bacteria
– Agglutination slide
– ELISA
– Western blot
Serology
Figure 5.19

41. Phage Typing
Figure 5.20

42. Table 5.6

43. Differential evolution
• When a group of organism that are
connected is identified, it is presumed
that both have the same ancestor and
any differences observed is present
due to differential evolution
(divergent evolution)
• Divergent evolution happens when a
subgroup of organism have
experienced mutation where the two
organisms are differentiated into two
groups.
• Eubacteria can produce Gram
positive and Gram negative
Figure 5.21 divergent evolution

44. Characteristics used in classifying
bacteria
Table 5.7

45. Biochemical Test used in identification and
classification of bacteria
Table 5.8

46. Characteristics of bacteria that have
medical importance
Table 5.9

47. Characteristics of bacteria that have medical
importance
Table 5.10