NDH - FM 1 Introduction

MIKROBIOLOGI DASAR (FUNDAMENTAL MICROBIOLOGY)

Darmawan Ari NugrohoDarmawan Ari Nugroho

Jadwal KuliahJadwal KuliahMikrobiologi DasarMikrobiologi Dasar

No Isi Kuliah

1 Pendahuluan : definisi dan aspek mikrobiologi; tujuan mempelajari mikrobiologi; sejarah mikrobiologi; mikrobiologi dan lingkungan; mikrobiologi sebagai ilmu dasar dan aplikasinya.

2 Evolusi, sistematik, dan taksonomi mikrobia, penggolongan organisme dan taksonomi mikrobia : sistim 2-, 3-, 5- kingdoms; prokariot dan eukariot; taksonomi modern (pilogeni)

3 Struktur sel : komponen-komponen sel dan fungsinya; perbedaan prokariot dan eukariot; membran sitoplasma, dinding sel, membran luar Gram negatif; Struktur internal (organel), flagella, pili, cilia, fimbriae, glycocalyx; bentuk dorman dari mikrobia (spora dan kista)

4 Pertumbuhan mikrobia : pertumbuhan sel dan reproduksi; populasi mikrobia; cara pengukuran pertumbuhan; siklus pertumbuhan; factor lingkungan yang berpengaruh pada pertumbuhan (oksigen, pH, air/ aktivitas air, suhu

5 Metabolisme : proses yang menghasilkan energi (energi kimiawi dan transfer energi, fosforilasi, jalur-jalur degradasi: nutrient komplek, glikolisa, regenerasi NAD, fermentasi dan respirasi); Proses yang membutuhkan energi (biosintesa komponen nitrogen, biosintesa karbohidrat, biosintesa lipida)

6 Genetika mikrobia : Informasi genetik, replikasi, transkripsi, dan translasi

Jadwal KuliahJadwal KuliahMikrobiologi DasarMikrobiologi Dasar

Lecture 1

Introduction to microbiology What is microbiology Why study microbiology The Historical Foundations of

Microbiology Abiogenesis – Biogenesis The golden age of microbiology Anthrax & Bioterrorism

The science of microorganisms (very small, unicellular organisms)

The discipline is just over a century old

Has given rise to molecular biology and biotechnology

What is Microbiology?

What are Microbes?

Prokaryotes

Nucleoid region (center) contains the DNA

Surrounded by cell membrane & cell wall (peptidoglycan)

Contain ribosomes (no membrane) in their cytoplasm to make proteins

Eukaryotes

Cells that HAVE a nucleus and membrane-bound organelles

Includes protists, fungi, plants, and animals

More complex type of cells

Organelles

Very small (Microscopic) Perform various functions for

a cell Found in the cytoplasm May or may not be

membrane-bound

Sel prokariot dan Sel prokariot dan eukarioteukariot

Why study Microbiology (1)?

Microorganisms were the first life on earth

Microorganisms created the biosphere that allowed multicellular organisms to evolve

Multicellular organisms evolved from microorganisms

>50% of the biomass on earth is comprised of microorganisms

Microorganisms will be on earth forever

4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0

BYA

Formation of O2 atmosphere

Cyanobacterial microfossils(oxygenic photosynthesis)

Earth formed

First microorganisms?

algae,marine invertebrates insects

mammals

No free O2

Reducing environment

All cells of the present time organisms share All cells of the present time organisms share a common ancestora common ancestor

An evolutionary phylogenetic treeAn evolutionary phylogenetic tree

Our understanding of life has arisen largely from studies of microorganisms (biochemistry and genetics)

Studies of microorganisms continue to contribute to fundamental knowledge of life processes


Figure 1.4

Health Agriculture Food Environment


Endang S. Rahayu Fak. Teknologi Pertanian UGM

The Historical Foundations of Microbiology

The Development of the Microscope The Debate over Spontaneous

Generation Redi Needham Spallanzani Virchow Pasteur

History of MicrobiologyHistory of Microbiology

Robert Hooke- First person to peer into the Robert Hooke- First person to peer into the microbial world, used compound lenses (1664)microbial world, used compound lenses (1664)

Anton van Leeuwenhoek- First true Anton van Leeuwenhoek- First true microbiologist, Dutch -Simple Microscopemicrobiologist, Dutch -Simple Microscope single lens microscopes capable of 300 to single lens microscopes capable of 300 to

500X (1632 - 1723)500X (1632 - 1723) drew and published (Proceeding of the Royal drew and published (Proceeding of the Royal

Society in London) accurate pictures Society in London) accurate pictures microscopic algae, protozoa, bacteria, microscopic algae, protozoa, bacteria, demonstrated “wee beasties” (“wee demonstrated “wee beasties” (“wee animalcules”)animalcules”)

Spontaneous Generation

Spontaneous Generation- the idea that life arose from non-living matter - Abiogenesis Aristotle (384-322 BC) believed some

simpler invertebrates could arise by spontaneous generation

Spontaneous Generation Spontaneous Generation DebateDebate

Francesco Redi (1626-1697)Francesco Redi (1626-1697)

belief at the time- maggots spontaneously belief at the time- maggots spontaneously arose from rotting meatarose from rotting meat

demonstrated that maggots were demonstrated that maggots were dependent on the presence of fly eggs and dependent on the presence of fly eggs and of rotting meatof rotting meat

Controversy Continues

Leeuwenhoek’s discovery added fuel to the controversy Some proposed microorganisms could arise from spontaneous generation even if higher organisms did not

They pointed out that boiled extracts of hay and meat could give rise to microorganisms

Spontaneous Generation (continued debate)

In 1748, English Priest John Needham reported the results of his experiments boiled mutton broth and then tightly sealed

the flask eventually many of the sealed flask became

cloudy with microorganisms he proposed that organic matter possessed a

‘vital force’ that could give rise to life

Spontaneous Generation disproved

Lazzaro Spallanzani - improved on Needham’s experimental design

first- sealed seeds and water in glass flask second- boiled them no growth took place as long as the flasks

remained sealed proposed that air carried microbes to the

culture

Controversy finally settled

1859, one of the fathers of modern microbiology, Louis Pasteur offered strong evidence against Spontaneous Generation

Pasteur was a chemist by training but became interested in biology during his early studies on fermentations.

At that time virtually nothing was known about microorganisms – except that they existed (this was discovered by Anton van Leeuwenhoek using home-made microscopes in 1684).

It was known that microorganisms could be found in decaying matter but it was not clear what role they were playing in the decomposition process.


Louis Pasteur (1822-1895)Louis Pasteur (1822-1895)

"Do not put forward "Do not put forward anything that you anything that you cannot prove by cannot prove by

experimentation"experimentation"

•

Drew out the necks of Drew out the necks of flasks so that they flasks so that they remained open to the airremained open to the airadded broth and boiled added broth and boiled it to destroy any it to destroy any microbes presentmicrobes presentflasks were incubated flasks were incubated for months and for months and remained sterileremained sterile

Pasteur’s Swan Neck Flask Experiment

•

The Golden Age of Microbiology

Fermentation and Pasteurization Pasteur

The Germ Theory of Disease Agostino Bassi and Pasteur Joseph Liter Robert Koch

Vaccination Edward Jenner Pasteur

Rapid Advances 1857 -Rapid Advances 1857 -19141914 Rudolf Virchow introduced the concept of Rudolf Virchow introduced the concept of

biogenesis: living cells can arise only from biogenesis: living cells can arise only from preexisting cells (1857).preexisting cells (1857).

Louis Pasteur demonstrated that Louis Pasteur demonstrated that microorganisms are in the air everywhere microorganisms are in the air everywhere and offered proof of biogenesis (1861).and offered proof of biogenesis (1861).

Agostino Bassi (1835) and Pasteur (1865) Agostino Bassi (1835) and Pasteur (1865) showed a causal relationship between showed a causal relationship between microorganisms and disease. microorganisms and disease.

Pasteur’s Contributions to Science

1800- French Government (Napoleon III) enlisted his help in their Wine Industry

showed the decline in quality was due to a contaminating microbe

process of pasteurization

Pasteur’s Contributions to Science

Recognized that chickens became immune to a bacterial pathogen if injected with a weaken avirulent strain.

Developed vaccines against rabies and anthrax


Pasteur’s perplexing problemPasteur’s perplexing problem while working on spontaneous generation he while working on spontaneous generation he

experienced an anomalyexperienced an anomaly no matter how long some flasks were boiled, no matter how long some flasks were boiled,

they always produced growththey always produced growth German botanist-German botanist-Ferdinand CohnFerdinand Cohn discovered discovered

the existence of heat resistant bacterial the existence of heat resistant bacterial sporesspores

Pasteur reasoned that the flask that Pasteur reasoned that the flask that produced growth contained heat resistant produced growth contained heat resistant bacterial sporesbacterial spores

English physicist English physicist John TyndallJohn Tyndall dealt the dealt the absolute final blow to Spontaneous Generation absolute final blow to Spontaneous Generation and resolved Pasteur’s problem, he and resolved Pasteur’s problem, he demonstrated the dust did indeed carry demonstrated the dust did indeed carry microbes and if the dust were absent, the microbes and if the dust were absent, the broth remained sterile.broth remained sterile.

He developed the process ofHe developed the process of tyndallization tyndallization which is fractional steam sterilizationwhich is fractional steam sterilization

similar to the process we use today in the lab.similar to the process we use today in the lab.

The Recognition of the Microbial Role in Disease

Agostino Bassi (1835)Agostino Bassi (1835) linked a microorganism to diseaselinked a microorganism to disease

Pasteur (1865)Pasteur (1865) disease of silkwormsdisease of silkworms

The Recognition of the Microbial Role in Disease

Joseph Lister English surgeon developed an antiseptic system of surgery

and heat sterilized his instruments as well as using phenol with surgical dressing

Robert Koch Robert Koch (1843 –1910)(1843 –1910)

Robert KochRobert Kochestablished a relationship between anthrax and the established a relationship between anthrax and the bacterium- bacterium- Bacillus anthracisBacillus anthracisKoch’s techniques are still used today Koch’s techniques are still used today Today we know these as Koch’s PostulatesToday we know these as Koch’s PostulatesReceived the Nobel prize 1905 for his work on Received the Nobel prize 1905 for his work on tuberculosistuberculosis

Direct evidence of the role of bacterial Direct evidence of the role of bacterial in disease transmissionin disease transmission

Koch’s Postulates

On the basis of these studies Koch proposed a series of criteria On the basis of these studies Koch proposed a series of criteria that should be used to establish the link between disease and that should be used to establish the link between disease and microorganisms. These are now known as Koch’s postulatesmicroorganisms. These are now known as Koch’s postulates ..

1: Microorganisms must 1: Microorganisms must alwaysalways be present in the infected be present in the infected animal and be absent in healthy individuals.animal and be absent in healthy individuals.

2: Pure cultures of the microorganism must be obtained from 2: Pure cultures of the microorganism must be obtained from the diseased animal.the diseased animal.

3: Such a culture must be capable, 3: Such a culture must be capable, in itselfin itself, of causing disease , of causing disease in healthy animals.in healthy animals.

4: The microorganism should be re-isolated from the diseased 4: The microorganism should be re-isolated from the diseased animal and should retain the same properties in pure culture animal and should retain the same properties in pure culture as the original pure culture.as the original pure culture.

Koch’s Tuberculosis studies• In 1881 Koch turned his attention to the study of a human disease In 1881 Koch turned his attention to the study of a human disease – – Tuberculosis (TBC).Tuberculosis (TBC).

• At that time TB killed 1 in 7 people and even today it accounts for At that time TB killed 1 in 7 people and even today it accounts for more than 1 in 20 human deaths worldwide. TBC was known to be more than 1 in 20 human deaths worldwide. TBC was known to be contagious but no “contagion” had been identified.contagious but no “contagion” had been identified.

• TBC is a disease of the lungs caused by the bacterium TBC is a disease of the lungs caused by the bacterium Mycobacterium tuberculosisMycobacterium tuberculosis. It is acquired by inhalation of . It is acquired by inhalation of infected droplets or dust particles in the air. infected droplets or dust particles in the air.

• The bacterium can persist in the lungs for long periods. It survives The bacterium can persist in the lungs for long periods. It survives and grows within macrophages.and grows within macrophages.

• In individuals with a low resistance acute pulmonary infection can In individuals with a low resistance acute pulmonary infection can occur with extensive damage to lung tissue. Spread of the occur with extensive damage to lung tissue. Spread of the bacterium to other parts of the body can then lead to death.bacterium to other parts of the body can then lead to death.

Robert Koch (1843 – 1910) Developing pure culture technique Use potato slices – first found individual

bacterial colonies growing with different appearance

Microscopic examination revealed cells within a single colony were similar

Pure Culture Key to Studying Pure Culture Key to Studying MicrobesMicrobes

Definition : Pure culture is a population of Definition : Pure culture is a population of organisms, all of which are the progeny organisms, all of which are the progeny of a single organismof a single organism

In nature, microbes almost never occur In nature, microbes almost never occur as pure culturesas pure cultures

Development of solidifying agents and complex media

Koch wanted to culture pathogens so he used something similar to the body tissue

Meat extracts Initially, gelatin (jell-o) was used to

solidify beef extract broth but : (1) many organisms can digest gelatin and (2) it melts at 37 oC, the favored incubation temperature for most pathogens

Development of solidifying agents

Agar was suggested by Fannie Hesse wife of Walther Hesse working in Koch Lab

Story : Walther was working with gelatin plates in summer and was having troubles

Asked wife : Why do your jellies and pudding stay solid in warm weather?

Fannie learned to use Agar-agar from a dutch neighbour in New York who spent time in Asia

Agar-agar had been used as a gelling agent in Asia for centuries

Agar

Agar is complex polysaccharides derived from seaweed

Its only melts at 100 oC, and solidifies at 45 oC

Non-toxic to most microorganism

Stable at sterilization temperature

Only a very few bacteria have enzymes that digest it

Petri dish was invented in 1877By an assistant of Koch –R.J. Petri

Shallow glass plates

Alexander Fleming

Observed that the mold Penicillium inhibited the growth of a bacterial culture.

Penicillin has been used clinically as an antibiotic since the 1940s

Anthrax & BioterrorismAnthrax & Bioterrorism

Bioterrorism 1Bioterrorism 1Use of biological material to inflict suffering Use of biological material to inflict suffering

and/or death on enemiesand/or death on enemies (board definition)(board definition)

• Biological warfare is not a new idea; In 184BC Hannibal Biological warfare is not a new idea; In 184BC Hannibal threw baskets of snakes onto enemy ships!threw baskets of snakes onto enemy ships!

• In 1346 Tartar soldiers catapulted plague victims into In 1346 Tartar soldiers catapulted plague victims into besieged Kaffka and successfully started an epidemic.besieged Kaffka and successfully started an epidemic.

• In 1763 the British army gave smallpox-contaminated In 1763 the British army gave smallpox-contaminated blankets to Indians who were loyal to the French.blankets to Indians who were loyal to the French.

• In 1925 the Geneva convention outlawed the use of In 1925 the Geneva convention outlawed the use of biological weapons.biological weapons.

• In 1969 the US “officially” ended its program of developing In 1969 the US “officially” ended its program of developing biological weapons.biological weapons.

• In 1972 the Biological and Toxin weapons convention In 1972 the Biological and Toxin weapons convention approved a treaty to outlaw biological weapons approved a treaty to outlaw biological weapons (140 countries signed this treaty)(140 countries signed this treaty)

• It is likely that many countries still have It is likely that many countries still have the capacity for biological.the capacity for biological.

Bioterrorism 2Bioterrorism 2

What is Anthrax?

Anthrax is a disease that is caused by the bacterium Bacillus anthracis (the link was first proved by Koch).

B. anthracis is a Gram-positive, spore-forming common soil microorganism.

Primarily a disease of livestock; catlle, sheep etc.

Pasteur devised the first vaccine against anthrax.

Today vacccination is still the primary means of control.

Anthrax in Humans

Contrary to reports in the popular press – B. anthracis is not a good human pathogen

Humans are fairly resistant to infection. Even textile workers exposed to infected animal products have a low infection rate.

Large numbers of spores (8,000-10,000) are required to infect humans. This exposure is very rare in the “normal” environment.

Breathing air around infected animal carcasses would lead to the inhalation of around 2-10 spores every 10 minutes!

Infection by Infection by B. anthracisB. anthracisThere are 3 routes of infection by this There are 3 routes of infection by this pathogen:pathogen:

1)1) Entry by ingestionEntry by ingestion

• Gastrointestinal anthrax can arise byGastrointestinal anthrax can arise by the ingestion of contaminated meat, usually from an the ingestion of contaminated meat, usually from an animal that died of anthrax.animal that died of anthrax.

• Infection reaches intestinal lymph nodes, then causes Infection reaches intestinal lymph nodes, then causes septacemia. Exact pathogenesis is not understood.septacemia. Exact pathogenesis is not understood.

• Very rare – but in cases that present clinically the Very rare – but in cases that present clinically the mortality rate is about 50%.mortality rate is about 50%.

2) ) Entry through skin lesionsEntry through skin lesions.

• Spores enter damaged areas of skin. Spores enter damaged areas of skin.

• Erythematous papule after 2-5 days (red bump).Erythematous papule after 2-5 days (red bump).

• Centre of lesion darkens after 7-10 days.Centre of lesion darkens after 7-10 days.

• Usually heals without Usually heals without intervention intervention (spread to blood occurs (spread to blood occurs in less than 5% of cases).in less than 5% of cases).

3) Entry by inhalationEntry by inhalation

• Inhalation of spores can lead to pulmonary anthrax – also Inhalation of spores can lead to pulmonary anthrax – also called “woolsorters disease”.called “woolsorters disease”.

• Malaise within 1-5 days, including cough, fever and chest Malaise within 1-5 days, including cough, fever and chest pain.pain.

• Difficulty with breathing, blueish skin colour, swelling of Difficulty with breathing, blueish skin colour, swelling of the chest.the chest.

• Once swelling is evident the Once swelling is evident the disease beyond treatment disease beyond treatment and death usually occurs.and death usually occurs.

Anthrax and bioterrorism

Advantages:

• Very easy to obtain and to grow.• Spores very stable.• Spores easily inhaled.• High fatality rate in cases of pulmonary anthrax.

Disadvantages:

• Dispersing spores over a wide area is difficult.• Not contagious – no person-to-person spread.• If diagnosed early it is easily treated with antibiotics.

Concept Check

Microorganisms can be both beneficial and harmful to humans. Although we tend to emphasize the harmful microorganisms (infectious and disease agents), many more microorganisms are beneficial than harmful.In what ways are microorganisms important in the food industries ?

NDH - FM 1 Introduction

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