Bacterial taxonomy & classification

This presentation is based on basics taxonomy and bacterial classificaiton

1. Taxonomy & Bacterial
Classification
By: Dr. MohammedAzim Bagban
Assistant Professor

2. Why do we classify?
•Classification puts organisms into groups by looking
at characteristics (traits) they share.

3. Taxonomy
•Classifying living things
into groups based on
their body structures
(anatomy), DNA or
other traits.

4. Carolus Linneaus
•Swedish botanist, lived
1707-1778
•Invented binomial
nomenclature, the 2-
word naming system we
still use today to classify
organisms
•Called “the father of
taxonomy.”

5. Binomial Nomenclature
•Gives a unique 2-word, Latin, scientific
name to all living things
•Genus is capitalized; species is not; both
are italicized
•Examples: Homo sapiens = human
Felis domesticus = cat
Panthera tigris = tiger

6. Hierarchical arrangement:

1.Domain
2.Kingdom
3.Phylum
4.Class
5.Order
6.Family
7.Genus
8.Species
Binomial name or
Scientific Name

7. 8 taxa of classification
DOMAIN

8. “Trick” to remember the 8 taxa of
classification:
•Dumb
•King
•Phillip
•Came
•Over
•For
•Grape
•Soda

9. History


Carolus
Linnaeus
1735
Ernst
Haeckel
1866
Edourd
Chatton
1925
Herbert
Copeland
1938
R. H.
Whittaker
1969
Carl
Woese et
al.
1990
Cavalier-
Smith
1998
[


2015
2
kingdoms
3
kingdoms
2 empires
4
kingdoms
5
kingdoms
3 domains
2
empires, 6
kingdoms
2
empires, 7
kingdoms
(not
treated)
Protista
Prokaryot
a
Monera Monera
Bacteria
Bacteria
Bacteria
Archaea Archaea
Eukaryot
a
Protoctist
a
Protista
Eucarya
Protozoa Protozoa
Chromist
a
Chromist
a
Vegetabili
a
Plantae Plantae
Plantae Plantae Plantae
Fungi Fungi Fungi
Animalia Animalia Animalia Animalia Animalia Animalia

10. Species
•Species is the
smallest, most
specific group in
classification
•Organisms in the
same species can
reproduce
together and their
offspring are
fertile.

11. Species Identification
•Characterized by Phenotypic, genotypic, and
phylogenetic criteria.
•Species of bacteria are identified by rRNA
sequencing rely on 16S RNA in which 95%
resembles in same species.
•Because of progressive increase in genomic data
the definition needs revision:
•“ A collection of organisms having same
sequence in their core housekeeping genes”.

12. Tool: Phylogeny
a “family tree” that classifies organisms by their
evolutionary history

13. Tool: Cladogram
•Shows older traits (bottom)
•Shows newer or “derived” traits (top)

14. Tool: Dichotomous Key
•Helps identify organisms
•Questions with 2 answer choices lead you through the key until
you find the correct organism

15. Strain
•In biology, a strain is a low-level taxonomic rank
used at the intraspecific level (within a species).
•When two clones of same species differ
genetically and express different characters are
called Strains.
•Arises because of mutation.
•Denoted by capital letters followed by some
numbers.
•E.g. Bacillus thuringensis AB3

16. Strain
•Several types:
1.Biovers: Variant of strain with different biochemical and
physiological character.
2.Morphover: Morphological varient
3.Serovar: Distinct antigenic properties.
4.Phagover: Differing in susceptibility & resistance towards
bacteriophages.

ATCC: American Type Culture Collection

17. Methods for classification of Bacteria
• Bacteria can be classified in many ways. The first
classification scheme was published in 1773 and
many more have appeared since.
•Science of microbiology has developed other
kind of classification but medically important
classification is as follows

18. Based on several major
properties
•Morphological
•Anatomical
•Staining
•Based on pathogenicity
•Based on relationship of host and organism
•Nutrition
•Environmental factors

19. Morphological characters
•Shape and size of the cell

20. •Based on Anatomical features:

23. Based on Staining
•(A) Gram stain:
•1) Gram positive: after the gram stain organism which occur
violet in colour.
•2) Gram negative: Which appear pink or red

•(B)Acid fast stain:
•1) Acid fast organism: after the ziehl – neelsen stain it will
show pink in colour
•2) Non acid fast organism: after this stain organism will appear
blue in colour

25. Physiological & Metabolic characteristics
I.Mode of Nutrition:






II.Physiological Characteristics:
Mode of
Nutrition
Autotrophic Heterotrophic Phototrophic Chemotrophic
Physiological
Characteristics
Growth Temp. pH
Oxygen
Requirement
Antibiotic
sensitivity

26. Biochemical Characteristics
•Catalase test
•Sugar Fermentation
•Gelatin Liquefaction
•Sugar Fermentation
•Indole Production
•Hydrogen sulfide production
•Mixed acid fermentation
•Nitrate reduction
•Urease production
•Utilization of specific nutrients

27. Molecular characteristics
•G + C content




•Estimated by determining the melting temperature of the
DNA
•Higher G + C gives a higher melting temperature
100%
TACG
CG
C)(GMol% 




28. Nucleic acid hybridization

•By mixing ssDNA from two different species and
determining the percentage of the DNA that can form
dsDNA hybrids
•The greater the percent hybridization, the closer the
species


•Genes for specific enzymes
•The nucleic acid sequence for the complete genome of
several species is now available
•5S and 16S rRNA (ribosomal RNA) sequences;
comparison of these sequences has been extensively
used to determine the phylogenetic relationships of
microbial groups


Nucleic acid sequencing

29. Bergey’s Manual of Systematic
Bacteriology
•In 1923, David Bergey & colleagues published
Bergey’s Manual of Determinative Bacteriology, a
manual that is used to classify bacteria based on
their structural and functional attributes by
arranging them into specific familial orders.
•In 1984, a more detailed work entitled Bergey’s
Manual of Systematic Bacteriology was
published, still primarily phenetic in its
classification.

30. Bergey’s Manual of Systematic Bacteriology
•The change in volume set to "Systematic
Bacteriology" came in a new contract in 1980,
whereupon the new style included "relationships
between organisms" and had "expanded scope"
overall. This new style was picked up for a four-
volume set that first began publishing in 1984.
The information in the volumes was separated
as:

31. •Volume 1 included information on all types of Gram-
negative bacteria that were considered to have "medical
and industrial importance.“
• Volume 2 included information on all types of Gram-
positive bacteria.
•Volume 3 deals with all of the remaining, slightly
different Gram-negative bacteria, along with the
Archaea.
•Volume 4 has information on filamentous actinomycetes
and other, similar bacteria.
Bergey’s Manual of Systematic Bacteriology
First Edition

32. •Volume 1 (2001): The Archaea and the deeply branching and
phototrophic Bacteria
•Volume 2 (2005): The Proteobacteria—divided into three
books:
•2A: Introductory essays
•2B: The Gammaproteobacteria
•2C: Other classes of Proteobacteria
•Volume 3 (2009): The Firmicutes
•Volume 4 (2011):
The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Aci
dobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmat
imonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae,
and Planctomycetes
•Volume 5 (in two parts) (2012): The Actinobacteria

Bergey’s Manual of Systematic Bacteriology
Second Edition

33. Bacterial cell size
•Bacteria are very minute in size ranging
from 0.2-8.0 µm.
•1 µm = 10
-3
mm = 10
-6
cm
•Some exceptional bacteria are found
below and above this range also.
•Some examples are shown below….
•

35. Shape of the Bacteria
•Three basic bacteria shapes are coccus
(spherical), bacillus (rod- shaped), and spiral
(twisted).

•Arrangement of cocci
•Cocci may be oval, elongated, or flattened on
one side. Cocci may remain attached after cell
division. These group characteristics are often
used to help identify certain cocci.

39. Bacilli
•Bacillus is a shape (rod shaped) and only divide across
their short axis there are fewer groupings.

41. Spiral bacteria

•Spiral bacteria have one or more twists.

42. Other shapes

43. Ultra structure of typical bacterial cell

44. Bacterial spores & Cysts
•Bacterial spores and cysts are the dormant
(functionally Inactive) structures of prokaryotes.
Endospore
•An endospore is a dormant, tough, and non-
reproductive structure produced by some
bacteria in the phylum Firmicutes.
•The name "endospore" is suggestive of a spore
or seed-like form (endo means within), but it is
not a true spore (i.e., not an offspring).

45. • Endospore formation is usually triggered by a
lack of nutrients, and usually occurs in gram-
positive bacteria.
•In endospore formation, the bacterium divides
within its cell wall, and one side then engulfs the
other.
•Endospores enable bacteria to lie dormant for
extended periods, even centuries. There are
many reports of spores remaining viable over
10,000 years, and revival of spores millions of
years old has been claimed.

46. •When the environment becomes more
favorable, the endospore can reactivate itself to
the vegetative state. Most types of bacteria
cannot change to the endospore form. Examples
of bacterial genera that can form endospores
include Bacillus and Clostridium.
•The endospore consists of the bacterium's DNA,
ribosomes and large amounts of dipicolinic acid.
Dipicolinic acid is a spore-specific chemical that
appears to help in the ability for endospores to
maintain dormancy. This chemical accounts for
up to 10% of the spore's dry weight.

47. •A stained preparation of the
cell Bacillus subtilis showing
endospores as green and
the vegetative cell as red
Phase-bright endospores
of Paenibacillus alvei imaged
with phase-contrast
microscopy

49. Shapes of spores
•The shape & position of the cell is characteristic of the
species.
•Spherical, oval or elongated in shape
•May be narrower or bulged than parent cell.

50. Position of the spore
 Terminal (located at one of the poles)
 Sub terminal or sub central(between center & one of
the poles)
Equatorial (central)

51. Structure of endospore
(Protoplast)

52. Exosporium
•Thin delicate covering of spore arises from
cell membrane.


•Thick layer consist of several layers of
proteins.
•Impermeable to toxic chemicals
•Contains enzymes for sporulation





Spore coat

53. •Structure more than half of spore volume.
•Less cross linked peptidoglycans
•High amount of calcium dipicolonate
•15% of the cellular dry weight


•Consist of core wall, cytoplasm, ribosome &
nucleiod.
•Water content is complex with protein.



Cortex
Spore core (Protoplast)

54. Sporogenesis

55. Germination
•Transformation of dormant spore into
vegetative cells called germination.
•Dormancy may be long but return to the
vegetative stage is very rapid involves
three stages:
•1. Activation
•2. Germination
•3. out growth

56. Activation
•Condition of the spores when nutrition
available
•It can be achieved by:
•Heat treatment (60°C- 70°C )
•Storage of suspension at room
temperature

57. Germination
•Rapture of spore coat.
•Loss of calcium dipicolonate and cortex
components.
•Increase in stainability.
•Loss of resistance to heat
•Release spore components
•Increase metabolic activity

58. Out growth
•Outgrowth follows germination and involves the
core of the endospore manufacturing new
chemical components and exiting the old spore
coat to develop into a fully functional vegetative
bacterial cell, which can divide to produce more
cells.