PENDAHULUAN EVOLUSI DAN KERAGAMAN MIKROBA TINGKATAN TAKSONOMI SISTEM KLASIFIKASI KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI PENDUGAAN (ASSESSING) FILOGENI MIKROBA DIVISI UTAMA ORGANISME BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY GARIS BESAR FILOGE

(1)

I. PENDAHULUAN

II. EVOLUSI DAN KERAGAMAN MIKROBA

III. TINGKATAN TAKSONOMI

IV. SISTEM KLASIFIKASI

V. KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM

TAKSONOMI

VI. PENDUGAAN (ASSESSING) FILOGENI MIKROBA

VII. DIVISI UTAMA ORGANISME

VIII. BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY

IX. GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT

X. MENGENAL LEBIH DEKAT ANGGOTA DUNIA MIKROBA

(2)

A. ARCHAEA

B. BACTERIA

C. FUNGI

D. ALGAE

E. PROTOZOA

F. VIRUS

(3)

X. MENGENAL LEBIH DEKAT ANGGOTA DUNIA MIKROBA

A. ARCHAEA

1. PENDAHULUAN

The archaea are quite diverse, both in morphology and physiology

a. They may stain gram positive or gram negative

b. They may be spherical, rod-shaped, spiral, lobed, plate-shaped, irregularly shaped or pleomorphic

c. They may exist as single cells, aggregates or filaments

d. They may multiply by binary fission, budding, fragmentation, or other mechanisms e. They may be aerobic, facultatively anaerobic, or strictly anaerobic

f. Nutritionally, they range from chemilithoautotrophs to organotrophs

g. Some are mesophiles, while others are hyperthermophiles that can grow above 100°C h. They are often found in extreme aquatic and terrestrial habitats; recently, archaea

(4)

2. Archaeal Taxonomy-the new edition of Bergey’s Manual will divide the archaea

into two phyla:

a. Phylum: Crenarchaeota

b. Phylum: Euryarchaeota

Many are extremely thermophilic, acidophilic, and sulfur-dependent

1) Sulfur may be used as an electron acceptor in anaerobic respiration, or as an electron source by lithotrophs

2) Almost all are strict anaerobes

3) They grow in geothermally heated water or soils (solfatara) that contain elemental sulfur (sulfur-rich hot springs, waters surrounding submarine volcanic activity); some (e.g., Pyrodictum spp.) can grow quite well above the boiling point of water (optimum ± 105oC)

4) Some are organotrophic; others are lithotrophic

(5)

A. ARCHAEA

2. Archaeal Taxonomy-the new edition of Bergey’s Manual will divide the archaea

into two phyla:

b. Phylum: Crenarchaeota

1) The Methanogens

2) The Halobacteria

3) The Thermoplasms

(6)

A. ARCHAEA

B. BACTERIA

C. FUNGI

D. ALGAE

E. PROTOZOA

F. VIRUS

(7)

B. BAKTERIA



Most widely accepted taxonomic classification for

_{Most widely accepted taxonomic classification for}

bacteria is

Bergey’s Manual of Systematic

Bacteriology

.



5000 bacterial species identified, 3100 classified.



Bacteria are divided into four

divisions

(phyla)

(8)

 Each division is divided into _{Each division is divided into}sections_sections according to:_{according to:} – _{Gram stain reaction}_{Gram stain reaction}

– _{Cell shape}_{Cell shape}

– _{Cell arrangements}_{Cell arrangements} – _{Oxygen requirements}_{Oxygen requirements} – _Motility_Motility

– _{Nutritional and metabolic properties}_{Nutritional and metabolic properties}

(9)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

2. Gram-Positive Bacteria (Divisi II)

3. Wall-Less Bacteria (Divisi III)

(10)

a. Spirochetes

– Helical shape. Flexible.Helical shape. Flexible.

– Contain two or more axial filaments Contain two or more axial filaments (endoflagella(endoflagella).).

– Move in corkscrew pattern.Move in corkscrew pattern.

– Medically important members:Medically important members:

 Treponema pallidumTreponema pallidum: Syphilis: Syphilis

 Borrelia spp.:Borrelia spp.: Lyme disease, relapsing feverLyme disease, relapsing fever  LeptospiraLeptospira: Leptospirosis: Leptospirosis

Borrelia Burgdorferi

(11)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)-

lanjutan

b. Aerobic, Motile, Helical/Vibroid Gram-Negative Bacteria



Rigid helical shape or curved rods



Lack axial filaments (endoflagella); have polar flagella

_{Lack axial filaments (endoflagella); have polar flagella}

instead.



Most are harmless aquatic organisms

.



Genus

Azospirillum

fixes nitrogen in soil.



Genus

Bdellovibrio

attacks other bacteria.



Important pathogens include:

–

Campylobacter jejuni

:

Most common bacterial food-

Most common bacterial

food-borne intestinal disease in the United States (2 million

borne intestinal disease in the United States (2 million

cases/year). Associated with undercooked chicken.

–

Helicobacter pylori

_{Helicobacter pylori}

: Causes most gastric ulcers in

:

Causes most gastric ulcers in

humans.

(12)

c.

Gram-Negative Aerobic Rods and CocciGram-Negative Aerobic Rods and Cocci

Contains many medically significant groups (Genera). Contains many medically significant groups (Genera).

 PseudomonasPseudomonas:: Rods with polar flagella. Many secrete pigments in media. Rods with polar flagella. Many secrete pigments in media.

– Pseudomonas aeruginosa_{Pseudomonas aeruginosa}:: Urinary tract infections (UTIs), Urinary tract infections (UTIs),

septicemia, abcesses, burns, pulmonary infections in cystic fibrosis septicemia, abcesses, burns, pulmonary infections in cystic fibrosis patients, and meningitis.

patients, and meningitis.

 LegionellaLegionella:: Rods that live in natural waters. Frequently found in air Rods that live in natural waters. Frequently found in air

conditioning systems, humidifiers, showers, spas, and fountains. conditioning systems, humidifiers, showers, spas, and fountains.

– Legionella pneumophilaLegionella pneumophila:: Legionnaires’ disease (pneumonia, 1976) Legionnaires’ disease (pneumonia, 1976) and Pontiac fever.

and Pontiac fever.

 NeisseriaNeisseria:: Diplococci. Frequently found on human mucous membranes. Diplococci. Frequently found on human mucous membranes.

(13)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

-lanjutan



Genus Moraxella

Genus

Moraxella

:

Aerobic egg-shaped cocco-bacilli.

Moraxella lacunata

: Conjunctivitis.



Genus Brucella

Genus

Brucella

:

Small nonmotile coccobacilli.

All species are obligate parasites of mammals.

Cause brucellosis. Can survive phagocytosis.



Genus

Bordetella

:

Nonmotile rods. Virulent forms have

capsules.



Genus

Francisella

: Small pleomorphic bacteria.

Francisella tularensis

:

Tularemia



Genera

Rhizobium

and

Bradyrhizobium

:

Form nodules

on legume roots and fix nitrogen in soil.

(14)

d.

Facultative Anaerobic Gram-Negative Rods

Many cause diseases of gastrointestinal tract;

Contains three medically significant families.

1) Family Enterobacteriaceae (Enterics)



Inhabit intestinal tracts of animals.



Motile bacteria with peritrichous flagella or nonmotile.



Many have fimbriae for attachment to mucous membranes and sex

pili for exchange of DNA (antibiotic resistance genes)



Most ferment glucose and other sugars.



Genus

Escherichia

:

E. coli

is common inhabitant of human

intestinal tract. Most strains are not pathogenic, but others can

cause

UTIs

(urinary tract infections), traveler’s diarrhea, and

food-borne disease.

(15)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

d.

Facultative Anaerobic Gram-Negative Rods

1) Family Enterobacteriaceae (Enterics)

1) Family Enterobacteriaceae (Enterics) Lanjutan

Lanjutan

 Genus SalmonellaGenus Salmonella: Almost all members are potential pathogens. : Almost all members are potential pathogens.

Common inhabitants of animal GI tract. Can contaminate food (eggs,

meat).

 Salmonella typhiSalmonella typhi: Typhoid fever, severe illness.: Typhoid fever, severe illness.

 S. enteritidisS. enteritidis: Causes salmonellosis, the second most common bacterial : Causes salmonellosis, the second most common bacterial food-borne disease. Over 1.3 million cases/year in the U.S.

food-borne disease. Over 1.3 million cases/year in the U.S.

 Genus ShigellaGenus Shigella: Only found in humans. Second most common cause of : Only found in humans. Second most common cause of

traveler’s diarrhea.

 Genus KlebsiellaGenus Klebsiella: Cause respiratory and UTIs.: Cause respiratory and UTIs.

 Klebsiella pneumoniaeKlebsiella pneumoniae: Antibiotic resistant strains cause pneumonia and : Antibiotic resistant strains cause pneumonia and nosocomial infections.

nosocomial infections.

 Genus SerratiaGenus Serratia: Opportunistic respiratory and urinary tract infections.: Opportunistic respiratory and urinary tract infections.

 Serratia marcescens: Produces a red pigment. Important cause of Serratia marcescens: Produces a red pigment. Important cause of nosocomial infections.

(16)

d.

Facultative Anaerobic Gram-Negative Rods

1) Family Enterobacteriaceae (Enterics)

1) Family Enterobacteriaceae (Enterics) Lanjutan

Lanjutan



Genus Proteus

: Actively motile. Cause UTIs, wound infections,

and infant diarrhea (nosocomial).



Genus Yersinia

:

 Yersinia pestisYersinia pestis: Causes bubonic plague (black death). Transmitted : Causes bubonic plague (black death). Transmitted by fleas, respiratory droplet, and contact with animals.

by fleas, respiratory droplet, and contact with animals.



Genus Erwinia

: Important plant pathogens.

(17)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

d.

Facultative Anaerobic Gram-Negative Rods

2)

Family Vibrionaceae

Found in aquatic habitats.

Straight or slightly curved rods



Genus Vibrio

_{Genus Vibrio}

: Slightly curved rods.

(18)

d.

Facultative Anaerobic Gram-Negative Rods

3)

Family Pasterellaceae

Found in aquatic habitats; Straight or slightly curved rods



Genus Pasteurella

: Pathogens of domestic

animals.



Genus Hemophilus

:

_{Important pathogens that inhabit}

mucous membranes of upper respiratory tract, mouth,

vagina, and intestinal tract. Require blood in culture.

 Hemophilus influenzaeHemophilus influenzae: Causes meningitis, ear : Causes meningitis, ear

infections, bronchitis, arthritis, and pneumonia in

children.

 H. ducreyiH. ducreyi: Cause of sexually transmitted chancroid.: Cause of sexually transmitted chancroid.



Genus Gardnerella

:

_{Not assigned to any family.}

(19)

May be straight, helical, or curved.

–

Genus

Bacteroides

:

Nonmotile

.

Live in human

intestinal tract (1 billion/gram of feces) and gum

crevices. Cause peritonitis, abscesses, and deep

tissue infections.

–

Genus

Fusobacterium

: Long slender rods with

:

Long slender rods with

pointed tips. Found in gingival crevices, cause

dental abscesses.

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

e.

(20)



Obligate anaerobes that release H

₂2S into the atmosphere.

S into the atmosphere.



Found in soil and intestinal tract of animals.



Ecologically important.

f.

(21)

B. BAKTERIA

1. Gram-Negative Bacteria (Divisi I)

g.

Anaerobic Gram-Negative Cocci

(22)

h.

Rickettsias and Chlamydias

Gram negative bacteria; Obligate intracellular parasites.

Rickettsias: Rod shaped bacteria or coccobacilli, highly pleomorphic. Transmitted to

humans by insects and ticks (except for Coxiella burnetti which causes Q fever).

Genus Ehrlichiae: Live in white blood cells.

Genus Rickettsia: Cause spotted group fevers (Rocky mountain spotted fever, endemic typhus).

Chlamydias

Chlamydias: : Cocci shaped bacteria. Transmitted to humans by interpersonal contact or by Cocci shaped bacteria. Transmitted to humans by interpersonal contact or by airborne respiratory routes.

airborne respiratory routes.

Unique life cycle: Form a reticulate and elementary bodies in infected cells.

Three species:

– Chlamydia trachomatisChlamydia trachomatis: Causes blindness in humans and nongonococcal : Causes blindness in humans and nongonococcal urethritis (most common STD in U.S.).

urethritis (most common STD in U.S.). – C. psittaci_{C. psittaci}: Parrot fever.: Parrot fever.

(23)

(24)

1. Gram-Negative Bacteria (Divisi I)

2. Gram-Positive Bacteria (Divisi II)

3. Wall-Less Bacteria (Divisi III)

(25)

B. BAKTERIA

2. Gram-Positive Bacteria (Divisi II)

a. Gram-Positive Cocci



Non-spore forming cocci.



Aerobic to strictly anaerobic.



Pyogenic (pus-forming)

– Genus Genus StaphylococcusStaphylococcus: Tend to form grape-like clusters. Grow well under high : Tend to form grape-like clusters. Grow well under high osmotic pressure and low moisture.

osmotic pressure and low moisture.

Very common infections, because almost always found on skin and in nasal mucous Very common infections, because almost always found on skin and in nasal mucous membranes.

membranes.

 Staphylococcus aureusStaphylococcus aureus:: (aureus = golden) Yellow pigmented colonies. (aureus = golden) Yellow pigmented colonies. Produce several toxins. Cause pimples, sties, skin abscesses, toxic shock Produce several toxins. Cause pimples, sties, skin abscesses, toxic shock syndrome, food poisoning, and nosocomial infections.

syndrome, food poisoning, and nosocomial infections. Antibiotic resistance is big problem.

Antibiotic resistance is big problem. Vancomycin

(26)

a. Gram-Positive Cocci (lanjutan)



Genus Streptococcus

:

Most are pathogens. Tend to appear in chains or pairs. Do not use

oxygen, but most are aerotolerant. Classified based on their effect on red

blood cells (hemolysis).



Cause a wide range of diseases: Strep throat, respiratory infections,

abscesses, puerperal fever, and opportunistic infections.



A flesh eating Streptococcus strain emerged in 1994 and 1998. After

initial infection, bacteria live on dead flesh, produce toxins, and are not

treatable by antibiotics.

– Streptococcus pneumoniaeStreptococcus pneumoniae: : Bacterial pneumonia, ear infections, meningitis, Bacterial pneumonia, ear infections, meningitis, and sinus infections.

and sinus infections.

– Streptococcus pyogenes_{Streptococcus pyogenes}: Strep throat, scarlet fever, rheumatic fever, : Strep throat, scarlet fever, rheumatic fever, impetigo, skin infections, erysipelas, puerperal fever, glomerulonephritis.

(27)

B. BAKTERIA

2. Gram-Positive Bacteria (Divisi II)

b. Endospore-Forming Gram-Positive Rods and Cocci

Aerobic to strictly anaerobic; Motile and nonmotile; Survive harsh

environmental conditions

environmental conditions.

.

 Genus BacillusGenus Bacillus: : Rod shaped bacteriaRod shaped bacteria..

 Bacillus anthracis_{Bacillus anthracis}: : Causes anthrax a disease of cattle. Large (4-8 um) Causes anthrax a disease of cattle. Large (4-8 um) nonmotile facultative anaerobe

nonmotile facultative anaerobe..

 Bacillus thuringiensis_{Bacillus thuringiensis}: : Kills insects, used by gardenersKills insects, used by gardeners..

 Genus ClostridiumGenus Clostridium: : Rod shaped bacteria, obligate anaerobesRod shaped bacteria, obligate anaerobes. .

 Clostridium tetaniClostridium tetani: : Causes tetanus (T in DPT vaccine).Causes tetanus (T in DPT vaccine).  Clostridium botulinumClostridium botulinum: : Causes botulism.Causes botulism.

(28)

b. Endospore-Forming Gram-Positive Rods and Cocci

Aerobic to strictly anaerobic; Motile and nonmotile; Survive harsh

environmental conditions

environmental conditions.

.

 Genus BacillusGenus Bacillus: : Rod shaped bacteriaRod shaped bacteria..

 Bacillus anthracis_{Bacillus anthracis}: : Causes anthrax a disease of cattle. Large (4-8 um) Causes anthrax a disease of cattle. Large (4-8 um) nonmotile facultative anaerobe

nonmotile facultative anaerobe..

 Bacillus thuringiensis_{Bacillus thuringiensis}: : Kills insects, used by gardenersKills insects, used by gardeners..

 Genus ClostridiumGenus Clostridium: : Rod shaped bacteria, obligate anaerobesRod shaped bacteria, obligate anaerobes. .

 Clostridium tetaniClostridium tetani: : Causes tetanus (T in DPT vaccine).Causes tetanus (T in DPT vaccine).  Clostridium botulinumClostridium botulinum: : Causes botulism.Causes botulism.

(29)

B. BAKTERIA

2. Gram-Positive Bacteria (Divisi II)

d. Irregular Nonsporing Gram-Positive Rods

Club shaped (Corynebacteria); Pleomorphic; May be anaerobic or aerobic.

Corynebacterium diphtheriae

Important pathogens; Cause diphtheria (D in DPT vaccine);

Propionibacterium acnes

(30)

e. Mycobacteria

 Aerobic, non-spore-forming rods._{Aerobic, non-spore-forming rods.}

 Stain Gram-positive, but cell wall structure is more similar to Gram-negative Stain Gram-positive, but cell wall structure is more similar to Gram-negative bacteria.

bacteria.

 Waxy cell wall with mycolic acids (instead of peptidoglycan)._{Waxy cell wall with mycolic acids (instead of peptidoglycan).}

 Acid-fast, drug resistant, resistant to drying, and pathogenic due to waxy cell wall._{Acid-fast, drug resistant, resistant to drying, and pathogenic due to waxy cell wall.}

 Grow very slowly.Grow very slowly.

 Tend to cause chronic infections.Tend to cause chronic infections.

 Important pathogens: Important pathogens:

 Mycobacterium tuberculosis: Causes tuberculosis._{Mycobacterium tuberculosis}: Causes tuberculosis.

(31)

B. BAKTERIA

2. Gram-Positive Bacteria (Divisi II)

f. Nocardioforms



Gram-positive, filamentous, aerobic.



Many are acid fast.

_{Many are acid fast.}



Common in soil.



Genus Nocardia

: Form filaments which fragment into short rods to

reproduce.

(32)

g. Actinomycetes



Gram-positive, filamentous, resemble molds.



Common in soil.

_{Common in soil.}



Genus Streptomyces:

Genus Streptomyces

:

 Live in soil. _{Live in soil.}

 Give soil its musty odor. _{Give soil its musty odor.}

(33)

(34)

1. Gram-Negative Bacteria (Divisi I)

2. Gram-Positive Bacteria (Divisi II)

3. Wall-Less Bacteria (Divisi III)

(35)

B. BAKTERIA

3. Wall-Less Bacteria (Divisi III)



Mycoplasmas



Do not form cell walls

.



Most are aerobes or facultative anaerobes.



Highly pleomorphic.



Can produce filaments that resemble fungi.



Produce very small colonies (1 nm in diameter).



Very small cells: 0.1 to 0.25 mm in diameter.



Can pass through bacterial filters.



Most important human pathogen:

Mycoplasma pneumoniae

(36)

The Tree of Life

(http://phylogeny.arizona.edu/tree/phylogeny.html)

The Tree of Life is a multi-authored, Internet project containing information about the diversity of organisms on Earth, their history, and characteristics. The information is linked together in the form of the evolutionary tree that connects all organisms to each other.

Bergey's Manual of Determinative Bacteriology

(37)

(38)