Bakteriologi I: Taxonomy,

Structure, and Function

E. Hagni Wardoyo
Mataram, 28 Oktober 2015

Classification Systems
Taxonomy:
Classification of living organisms into groups

Phylogenetic Classification System:

Groups reflect genetic similarity and evolutionary relatedness

Phenetic Classification System:

Groups do not necessarily reflect genetic similarity or
evolutionary relatedness. Instead, groups are based on
convenient, observable characteristics.

Levels of Classification
Taxon:
A group or level of classification
Hierarchical; broad divisions are divided up into smaller
divisions:

Kingdom (Not used by most bacteriologists)

Phylum (Called Division by botanists)
Class
Order
Family
Genus (plural: Genera)
Species (Both singular & plural)

Definition of Species
The basic unit of taxonomy, representing a specific,
recognized type of organism
For sexually reproducing organisms, a fundamental
definition of species has been reproductive
compatibility
This definition fails for many microbial species
(including bacteria), because they do not reproduce
sexually

Definition of Species
Definition of species in microbiology:
Classic definition: A collection of microbial strains that share
many properties and differ significantly from other groups of
strains
Species are identified by comparison with known type
strains: well-characterized pure cultures; references for the
identification of unknowns
There are several collections of type strains, including the
American Type Culture Collection (ATCC)

Definition of Species
Definition of species in microbiology (cont.):
Strain:
A population of microbes descended from a single individual or pure
culture
Different strains represent genetic variability within a species
Biovars: Strains that differ in biochemical or physiological differences
Morphovars: Strains that vary in morphology
Serovars: Stains that vary in their antigenic properties

Nomenclature
Scientific name (Systematic Name)
Binomial System of Nomenclature
Genus name + species name

Italicized or underlined
Genus name is capitalized and may be abbreviated
Species name is never abbreviated
A genus name may be used alone to indicate a genus group; a species
name is never used alone
eg: Bacillus subtilis
B. subtilis

Nomenclature
Common or descriptive names
(trivial names)
Names for organisms that may be in common usage, but are
not taxonomic names
eg: tubercle bacillus
(Mycobacterium tuberculosis)
meningococcus
(Neiserria meningitidis)
Group A streptococcus
(Streptococcus pyogenes)

Useful Properties in Classification

Colony morphology
Cell shape & arrangement
Cell wall structure (Gram staining)
Special cellular structures
Biochemical characteristics

Useful
Properties in
Classification

Microbial Phylogeny
Bergeys Manual of Systematic Bacteriology
In 1927, David Bergey & colleagues published Bergeys
Manual of Determinative Bacteriology, a manual that grouped
bacteria into phenetic groups, used in identification of
unknowns. It is now in its 9th edition.
In 1984, a more detailed work entitled Bergeys Manual of
Systematic Bacteriology was published, still primarily phenetic
in its classification.

Microbial Phylogeny
Bergeys Manual of Systematic Bacteriology
Publication of the second edition of Bergeys Manual of
Systematic Bacteriology was begun in 2001.
The 2nd edition gives the most up-to-date phylogenic
classification of prokaryotic organisms, including both
eubacteria and archaea.
When it is completed, it will consist of 5 volumes.
The classification in Bergeys Manual is accepted by most
microbiologists as the best consensus for prokaryotic
taxonomy.

Microbial Phylogeny
Domains
Based on the research of Woese and others in the
1980s and 1990s, most biologists divide all living
organisms into 3 domains:
Domain Archaea
Domain Bacteria
Domain Eucarya

rRNA sequence data suggests that Archaea &

Eucarya may share a more recent common ancestor
with each other than with Bacteria

Microbial Phylogeny
Domains (cont.)
Many microbiologists reject the kingdom designation.
Each domain is divided into phyla, phyla into classes. etc.
There is often great metabolic and ecological diversity among
the members of a group, perhaps reflecting parallel evolution
of such things as fermentation pathways, photosynthetic
pathways, etc.

The Three-Domain System

Figure 10.1

Microbial Phylogeny
Phylogeny of domain Bacteria
The 2nd edition of Bergeys Manual of Systematic Bacteriology
divides domain Bacteria into 23 phyla. Nine of the more
notable phyla are described here.
Phylum Aquiflexa
The earliest deepest branch of the Bacteria
Contains genera Aquiflex and Hydrogenobacter that can obtain energy
from hydrogen via chemolithotrophic pathways

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Cyanobacteria
Oxygenic photosynthetic bacteria

Phylum Chlorobi
The green sulfur bacteria
Anoxygenic photosynthesis
Includes genus Chlorobium

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria
The largest group of gram-negative bacteria
Extremely complex group, with over 400 genera and 1300 named species
All major nutritional types are represented: phototrophy, heterotrophy, and
several types of chemolithotrophy
Sometimes called the purple bacteria, although very few are purple; the
term refers to a hypothetical purple photosynthetic bacterium from which
the group is believed to have evolved

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria (cont.)
Divided into 5 classes: Alphaproteobacteria, Betaproteobacteria,
Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria (cont.)
Significant groups and genera include:
Photosynthetic genera such as Rhodospirillum (a purple non-sulfur
bacterium) and Chromatium (a purple sulfur bacterium)
Sulfur chemolithotrophs, genera Thiobacillus and Beggiatoa
Nitrogen chemolithotrophs (nitrifying bacteria), genera Nitrobacter and
Nitrosomonas
Other chemolithotrophs, genera Alcaligenes, Methylobacilllus,
Burkholderia

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria (cont.)
Significant groups and genera include:
The family Enterobacteriaceae, the gram-negative enteric bacteria,
which includes genera Escherichia, Proteus, Enterobacter, Klebsiella,
Salmonella, Shigella, Serratia, and others
The family Pseudomonadaceae, which includes genus Pseudomonas
and related genera
Other medically important Proteobacteria include genera Haemophilus,
Vibrio, Camphylobacter, Helicobacter, Rickessia, Brucella

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Firmicutes
Low G + C gram-positive bacteria
Divided into 3 classes
Class I Clostridia; includes genera Clostridium and
Desulfotomaculatum, and others
Class II Mollicutes; bacteria in this class cannot make peptidoglycan
and lack cell walls; includes genera Mycoplasma, Ureaplasma, and
others
Class III Bacilli; includes genera Bacillus, Lactobacillus, Streptococcus,
Lactococcus, Geobacillus, Enterococcus, Listeria, Staphylococcus, and
others

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Actinobacteria
High G + C gram-positive bacteria
Includes genera Actinomyces, Streptomyces, Corynebacterium,
Micrococcus, Mycobacterium, Propionibacterium

Phylum Chlamidiae
Small phylum containing the genus Chlamydia

Microbial Phylogeny
Phylogeny of domain Bacteria (cont.)
Phylum Spirochaetes
The spirochaetes
Characterized by flexible, helical cells with a modified outer membrane (the
outer sheath) and modified flagella (axial filaments) located within the
outer sheath
Important pathogenic genera include Treponema, Borrelia, and Leptospira

Phylum Bacteroidetes
Includes genera Bacteroides, Flavobacterium, Flexibacter, and Cytophyga;
Flexibacter and Cytophyga are motile by means of gliding motility

Bacteria: Structure and

function

Morphology of bacteria
1. Shapes (cocci, rod, spiral)
2. Staining (Gram positive, Gram negative, Acid-fast,
Special staining)
3. Size

Shapes

Image source: http://thumbs.dreamstime.com/z/types-bacteria-commoninfecting-human-vector-illustration-classified-groups-according-to-their-basicshapes-spherical-34700241.jpg

Staining
Microbial cytoplasm is transparent it is necessary to
stain microorganisms
Microbial with motility direct observation w/out
staining wet mount
A small sample of microorganisms is placed on a slide
and permitted to air dry the smear is heat fixed by
quickly passing it over a flame Heat fixing kills
the organism, adhere to slide and permits them to
accept the stain

Simple stain techniques

Use basic dyes such as crystal violet or methylene blue
Nigrosin or Congo red, acidic negatively charged
dyes gather around the cells leaving the cells clear
and unstained the negative stain technique

Differential stain techniques

Distinguishes two kinds of organisms
Gram stain
Acid fast stain

Gram stain technique

Differentiate: Grampositive bacteria and Gramnegative
bacteria.
4 dyes: Crystal violet, iodine, alcohol and safranin
Firstly crystal violet is applied, then mordant iodine,
then the slide is washed with alcohol (in this step Gram
positive bacteria retain the crystalviolet iodine stain;
Gramnegative bacteria lose the stain) the last dye will
subsequently stain Gram negative while Gram positive
resist to it
Grampositive bacteria appear blue or purple
Gramnegative bacteria appear red

Gram stain technique

http://image.slidesharecdn.com/gramstaining131103063701-phpapp01/95/gram-staining-6638.jpg?cb=1384912330

Acidfast technique
differentiates species of Mycobacterium from other
bacteria
3 dyes: carbol fuchsin, acid alcohol, methylene blue
Heat or a lipid solvent is used to carry carbolfuchsin,
into the cells. Then the cells are washed with a dilute
acidalcohol solution. Mycobacterium species resist the
effect of the acidalcohol and retain the carbolfuchsin
stain (bright red). Other bacteria lose the stain and take
on the subsequent methylene blue stain (blue).

Acidfast technique

https://s3.amazonaws.com/classconnection/450/fla
shcards/7787450/jpg/acid_fast_steps-

Other staining
identify various bacterial structures of importance:
flagella, capsule etc
special stain technique: identify spores
Malachite green is used with heat to force the stain into the
cells and give them color. A counterstain, safranin, is then
used to give color to the nonsporeforming bacteria. At the end
of the procedure, spores stain green and other cells stain red.

Organisms unable/difficult to stain

with Gram stain
Mycobaterium spp
Chlamydia spp
Ricketsia
Haemophillus spp

Cell wall structure Gram + and bacteria

http://www.majordifferences.com/2013/10/differenc
e-gram-positive-vs-gram_2.html#.Vi6k2G5_ekh

Clinical importance of Gram Stain

The Gram stain is used to provide preliminary
information concerning the type of organisms present
directly from clinical specimens or from growth on
culture plates
This stain is used to identify the presence of
microorganisms in normally sterile body fluids
(cerebrospinal fluid, synovial fluid, pleural fluid,
peritoneal fluid).
It is used to screen sputum specimens to establish
acceptability for bacterial culture (<25 squamous
http://www.mayomedicallaboratories.com/testepithelial cells
per field is considered an acceptable
catalog/Clinical+and+Interpretive/8078
specimen for culture) and may reveal the causative

Gram positive bacteria

Fewer pathogen than Gram negative bacteria
Important human pathogen:

Staphylococcus aureus
Staphylococcus epidermidis
Staphylococcus saprophyticus
Streptococcus pneumonia
Streptococcus pyogenes
Streptococcus agalactiae
Enterococci
Bacillus anthracis
Clostridium tetanii
Clostridium botulinum
Clostridium perfringens
Clostridium difficile
Listeria monocytogenes

Gram negative bacteria

E. coli
Acinetobacter baumanii
Pseudomonas aeruginosa
Klebsiella pneumoniae
Klebsiella oxytoca
Neisseria gonorrhoeae
Enterobacter aerogenes
Enterobacter cloacae
Serratia marcescens
Morganella morgagni
Eikenella corrodens
Francisella tularensis

Size of bacteria

Microbial nutrition and

growth

Sumber Carbon
1. AUTROTROPHS
Organisme yang menggunakan karbon
anorganic (CO2) sebagai sumber karbon
dan bahan pembentuk senyawa organik
2. HETEROTROPHS
Mengkatabolisme molekul organik yang
tereduksi (seperti protein, KH, asam
amino dan asam lemak) yang didapat
dari organisme lain

 PHOTOTROPHS
Organisme yang menggunakan cahaya sebagai sumber
energi untuk proses anabolisme, intraselular transport
dan pergerakan
CHEMOTROPHS
Mendapatkan energi dari reaksi redoks yang
melibatkan senyawa organik dan anorganik

OKSIGEN
Oksigen sangat esensial pada kelompok aerob obligat
sebagai akseptor elektron akhir pada rantai transport
elektron, yang akan menghasilkan sebagian besar ATP
Pada obligat anaerob, oksigen menjadi sangat toksik

 Fakultatif anaerob
Bakteri aerob yang dapat mempertahankan
kehidupannya melalui proses fermentasi atau respirasi
anaerob, meskipun metabolismenya mengalami
penurunan
Cth : E.coli

 Anaerob aerotoleran
Tidak menjalani metabolisme aerob, tetapi mentoleransi
oksigen dengan memiliki sedikit enzim yang dapat
mendetoksifikasi bentuk toksik dari oksigen
Cth : Lactobacillus

 Mikroaerofilik
Bakteri aerob yang membutuhkan oksigen dengan
kadar 2-10%.
Mikroaerofilik ini akan rusak oleh kadar oksigen atmosfir
21% karena keterbatasannya dalam mendetoksi
hidrogen peroksida dan radikal superoksida
Cth : Helicobacter pylori

5 Kelompok mikroba :
1. Obligat aerob
2. Obligat anaerob
3. Fakultatif anaerob
4. Anaerob aerotoleran
5. Mikroaerofilik
Kebutuhan mikroba akan oksigen dapat
diidentifikasi dengan melihat
pertumbuhannya pada medium yang
mengandung gradiasi oksogen dari
permukaan sampai ke dasar tabung

NITROGEN
Elemen penting lain dalam pertumbuhan mikroba adalah
nitrogen
Banyak terdapat pada senyawa organik
Komposisinya 14% pada sel mikroba
Nitrogen sering merupakan nutrisi yang membatasi
pertumbuhan pada banyak organisme, karena tidak adanya
bahan untuk membentuk protein dan nukleotida
Organisme bisa mendapatkan nitrogen dari nutrisi organik
maupun anorganik

BAHAN KIMIA LAIN

Karbon, hidrogen, oksigen dan nitrogen menyusun lebih
dari 95% sel
Sisanya : fosfor, sulfur, kalsium, mangan, magnesium,
copper, zat besi, dan beberapa elemen lain
Beberapa mikroorganisme memerlukan asupan
senyawa organik yang tidak dapat dihasilkannya sendiri
yang disebut growth factor

References
Paul De Vos, George M. Garrity, Dorothy Jones, Noel R.
Krieg, Wolfgang Ludwig, Fred A. Rainey et al. BERGEYS
MANUAL OF Systematic Bacteriology, 2nd Ed, Vol 3, The
Firmicutes. Springer, Atlanta, 2009
Don J. Brenner, Noel R. Krieg, James T. Staley (Editors)
BERGEYS MANUAL OF Systematic Bacteriology, 2nd Ed,
Vol 2, The Proteobacteria
JK Sthruthers, RP Westran. Clinical Bacteriology. ASM
Press Washington, 2003