Main Themes in Microbiology

Chapter 1

Humans are outnumbered• We have ~ 10 trillion cells in our

body– We have 100 trillion foreign cells

in/on our body!!– Tiny life forms are called

microorganisms

What is a microorganism?• Could be…

– Bacteria– Viruses– Protists

• Protozoa and algae– Helminthes

• Worms

What is microbiology?• Microbiology is a special area of

biology that deals with tiny life forms not readily observed without magnification– Little guys are called:

• Microorganisms• Microbes• Germs• Bugs

Can I do this for a living?• Geomicrobiologist- roles of

microbes in the development of the earth’s crust

• Marine microbiologist- study the oceans and its smallest inhabitants

• Medical technologists- do tests to diagnose pathogenic microbes and their diseases

• Nurse epidemiologists- analyze the occurrence of infectious diseases in hospitals

• Astrobiologist- study the possibility of organisms in space

What do we focus on?• Genetics• Physiology

– Appearance and survival• + and – characteristics• Environmental interaction• Host interaction• Uses in industry/agriculture

How long have these guys been around?

• Practically forever!– Life on Earth started 3.5 billion years

ago!• Prokaryotes came first• Then eukaryotes

Good or bad?• Both!• We’ve been using microorganisms

for thousands of years!

Good Microbes• Yeast (microscopic fungi) = bread• Penicillin (moldy bread) = first aid

Biotechnology• Industry applications

– Bacteria that can mine metals!

Genetic Engineering• Manipulates genetics to make new

products and genetically modified organisms– Microbes can make drugs, hormones,

and enzymes

Bioremediation• Fixing environmental problems

with microorganisms

Bad Microbes• Pathogens- agents that cause

disease– Over 2000 types of microbes that

cause disease!– WHO says over 10 BILLION infections

caused by microbes worldwide

Bad microbes• Malaria

– Actually a microbe (protist)

Malaria Prevention• Malaria nets cost

$3-5• 1/3 world

population makes <$1/day

• Which kid will sleep under the net tonight?

The subtle side of microbes

• Gastric ulcers– Heliobacter

• Cancer– HPV– Hepatitis viruses

• Diabetes– coxsackievirus

• schizophrenia

• MS• OCD• Coronary artery

disease• Infertility

– Chlamydia

Associated with

General Microbe Characteristics

• TINY• Millimeters (mm), micrometers

(µm), and nanometers (nm)

• Prokaryotic or eukaryotic

• 1 or a few cells

• Free-living—live independently

• Parasitic—microbes harbored and nourished inside host

• Could be viruses– NOT ALIVE– NOT CELLS– Small amount of hereditary material

wrapped up in a protein coating– “Obligate intracellular parasites”

* Viroids are smaller viruses

Adenovirus

Rhinovirus

Rhinovirus

Where does life come from?

• Meat makes maggots

• Shrooms spring from spruce

• Rats from rotting refuse

Spontaneous Generation• The idea that life can arise from

non-living matter– Aka abiogenesis

• Competing theory—biogenesis– Life can only arise from living things

of a similar nature

How can we prove or disprove this hypothesis?

• Francesco Redi (1668)Hypothesis: Flies produce

maggots on meat. Lay small eggsSet up a controlled experiment to test his hypothesisFound that by keeping flies away from meat, no maggots appear

Variables1. Controlled variable:

Jar, meat, location, temperature, time

2. Independent or Manipulative variable: Gauze covering the meat jars

3. Dependant (responding) variable: Whether maggots appear

John Needham – 1745 Hypothesis: spontaneous generation

occurs under the right conditions– Boiled chicken broth and then sealed flask

(thought heat would kill)– “Animalcules” swarmed after a few days– Therefore, he felt his hypothesis was right.

What was wrong with Needham’s hypothesis? Was

it flawed?He assumed all the animalcules

would be killed by heat

Louis Jablot• Hypothesis: even microscopic

organisms must have parents• Boiled hay infusions very similar to

Needham’s work• However, his uncovered WAS

contaminated with growth

Lazzaro Spallanzani • 1776• Attempted to disprove Needham’s

work.• Took 4 flasks with broth in them

– Left open – went cloudy– Sealed but not boiled – went cloudy– Boiled but left open – went cloudy– Sealed then boiled – stayed clear

• Microbes were not found in this one but in all the other ones

What would have been Spallanzani’s hypothesis?

Microorganisms form not from air but from other microorganisms.

When broth was boiled and then sealed, no air could get in for organisms to reproduce.

What was wrong with what Spallanzani

assumed?

No air

Louis Pasteur - 1859

Tested Spallanzani’s work by using a curved neck flask to prevent microbes from

entering flask but would let air in

Boiled broth of control and experimental flasks.

Result: No growth in curved neck flask.

Microbes collecting in bend

Pasteur’s broth in the curved necked flask stayed sterile for years until he tilted it and the airflow carried the microbes into the broth

ConclusionContamination is due to microbes in the air.

Spontaneous generation theory died here!!

John Tyndall Heated hay infusions for various times. Found 2 kinds of bacteria – 1. Those readily killed by heating

2. Heat resistant forms (endospores)

**Between 1875 – 1918, most of the disease-causing bacteria were identified.

The MicroscopeAntonie von Leeuwenhoek

The MicroscopeLeeuwenhoek

looked at a drop of water and saw moving thingsCalled them

“animacules” Bacteria and

protozoa

The Pillar of Science: The scientific methodOrigin in the 1600s…enough of the

superstition!!

The Scientific Method

1. Ask a question Do some research

2. Propose a hypothesis3. Conduct a controlled experiment4. Collect data and make

observations5. Analyze data6. Make a conclusion7. Possibly, write a theory

Scientific method•NEEDS a testable hypothesis

•Use the deductive approach▫If…then (because)

•Test, test, and retest that hypothesis!

Do you know where bees come from?

Recipe for Bees

1. Kill a bull during the first thaw of winter

2. Build a shed3. Place the dead bull on branches and

herbs inside the shed4. Wait for summer. The decaying body of

the bull produces beesWords from a Roman poet about 2000 years ago

Know the jargonHypothesis- tentative explanation for what

has been observedTheory- very well supported idea

Many hypotheses and experimentsNOT A “FACT

Law- principle of scienceSuper accurate

Germ theory of diseaseGerm theory of diseaseLouis Pasteur

◦Human diseases could arise from infection

Robert Koch◦Koch’s Postulates

Verified germ theory Showed anthrax caused

by bacterium

Aseptic TechniqueAseptic TechniqueJoseph ListerGoal: reduce microbes in a

medical setting and preventing wound infections◦No handwashing prior to surgery

before Lister!!

TaxonomyWhat’s in a name?

Taxonomy- formal system for organizing, classifying, and naming organismsCarl von Linnie

Aka Carolus Linnaeus

StandardizedKeeps names short and consistentBinomial system of nomenclature

    •a two name system for writing scientific names.•The genus name is written first (always Capitalized).     •The species name is written second (never capitalized).     •Both words are

italicized if typed or underlined if hand written.

Example: Smith john (print)Smith john (written)

Felis concolor or F. concolor

Which is the genus? The species?    

Binomial Nomenclature

The major classification levels,from most general to most specific

(several of these have subdivisions)

A group at any level is a taxon.

Kingdoms are divided into groups called phyla Phyla are subdivided into classes

Classes are subdivided into orders

Orders are subdivided into families

Families are divided into genera Genera contain closely related species

Species is unique

Categories within Kingdoms

PhylogenyNatural relatedness of organisms

Related by evolution—theory that all life descended, with modification, from one common ancestor

EvidenceMorphology-

similar structures in organisms

Physiology- similar functions of organisms

Genetics- similar DNA in organisms

Dumpy Kings Play Cards On Fat Green Stools

•Domain•Kingdom

•Phylum•Class

•Order•Family

•Genus•Species

Kingdoms and DomainsOriginally, 2 kingdoms

Plantae and AnimaliaThen 3 (Protista)…and 4 (Add the Bacteria—kingdom Monera)

…finally 5 (Fungi!)

5 kingdom system

Associated with Robert WhittakerBased on the morphology and physiology-type of evidence

The domain systemNow we look at molecular biology

How do DNA, proteins, rRNA compare?

Bacteria Kingdom split into two:Domain BacteriaDomain Archaea

3 domain systemDomain eukarya—

the eukaryotesDomain archaea—

prokaryotes that live in extreme environments

Domain bacteria— “traditional” prokaryotes

What is classification?Why is classifying living things important?

What is taxonomy?Describe binomial nomenclature.

Who developed a system for naming living organisms?

What is a scientific name of an organism and how is it written?

KingdomPhylumClassOrder

FamilyGenusSpecies

What are the seven classification groups?

Kings Play Cards On Fat Green Stools