microbiology chapter 1

biology

study of living things

bios = life

microbiology

the study of living things that are too small to be seen with our naked eyes (microscopic organisms)

• we need microscope to see them!

microbes

AKA germs, bugs, viruses, infectious agents,

• not all cause disease

• not all of them are harmful

• many/some of them are useful or essential for human life

are most of the microorgs that exist in nature considered to be pathogenic + harmful to mankind?

microorganisms - where are they found

• they are found EVERYWHERE on earth - THEY ARE "Ubiquitous"

• AKA germ, microbes

microbe categories

bacteria

fungi

viruses

protozoa

algae

archae

prions

helminths

fields of microbiology (SKIP)

microbe-centered:

bacteriology

phycology

mycology

protozoology

parasitology

virology

process-centered:

microbial metabolism

microbial genetics

environmental microbiology

use of microorganisms

microorganisms (e.g. bacteria) does what for the environment **

• decompose organic material of dead organisms + recycle organic material back into the life cycle

• manage waste

• —> there is northwest ohio dairy that produce electricity with manure!

• bioremediation (a decontamination process)

• —→ the remediation of contamination with the use of biological agents

• produce oxygen + ethanol

• —→ e.g. bacteria in manure produces ethanol

WHAT DO WE USE BIOREMEDIATION FOR? (mainly)

• when we have oil spill in water, we use net to get rid of big chunks (of trash, floating debris, or think oil sludges) to prevent mechanical equipment from clogging and protect wild life.

• but inside of the water, there is still contamination so we will put oil-eating microbes in the water to decontaminate

• —> the crude oil that was spilled contains hydrocarbon - this is mixed with water (which contains oxygen)

• the oil-eating microbes will break apart the hydrocarbon and combine it with oxygen to create water and CO2

• when we are using biological agent to bioremediate smth that we did wrong we have to have control of it cuz we dont want to release smth bad into nature

• if we have another problem in nature, we need to use other living things to put right what we did wrong but we have to keep the biological things that we are using under control!

• we have to master how we pour the bacteria into the water

which of the following is an example of bioremediation?

a. application of bacteria to a crop to prevent frost damage

b. fixation of gaseous nitrogen into usable nitrogen

c. bacteria using light energy to convert CO2 into organic compounds

d. application of oil-degrading bacteria to an oil spill

e. all of the above

d.

IT IS NOT C BECAUSE THAT IS A NORMAL ECOLOGICAL PROCESS THAT DOES NOT INVOLVE CLEANING UP ENVIRON CONTAM/ WASTE. - it does not say that we put the CO2 there!

how does making electricity from manure work? - THIS IS EG OF BACTERIA USE IN DAILY LIFE

we collect the manure

it is pumped + goes into a chamber

hot water pipes heat manure so the bacteria in the manure release methane gas

the methane gas is sucked out + we use it to produce electricity!

we use the manure as a fertilizer!

microorganisms do what for energy production (she didnt go over it)

• produce chemical products such as ethanol, acetone

• —→ e.g. bacteria in manure produces ethanol

microorganisms do what for food industry

produce fermented foods such as vinegar, cheese, yogurt, alcoholic beverages, and bread

e.g, yeast needed to make bread

microorganisms do what for manufacturing

• they Produce products used in manufacturing (e.g., cellulose)

microorganisms do what for pharmaceutical industry

• we can genetically engineer (manipulate their genes) them to produce what we need e.g. vitamins + disease treatment like insulin

probiotics

• help us get healthy

• we eat them in yoghurt

antibiotics

• against life

• they kill ONLY BACTERIA

• THEY ARE ONLY EFFECTIVE/EFFICIENT AGAINST BACTERIA

• antibiotics kill bad bacteria (infection causing bact) and also the good bacteria that our bodies need!

• we must restore the good bacteria afterwards!

prebiotics

• nutrients that will help our probiotics to get well

• elements that we eat for our gut to be well - it feeds the beneficial microorganisms in our gut

why do physicians give antibiotics when you have flu (a virus)

• when you are attacked by virus you dont go to physician yet cuz u try to get rid of it yourself

• when you cant get rid of the virus yourself, you go to the physician

• the virus you cant get rid of already diminished your immune sys

• and then the bacteria (whether bad or not bad) are opportunistic

• —> when we healthy, those opportunistic bacteria wont do anything cuz we have strong immune sys

• —> but when we weakened by virus, the opportunistic bacteria that were not harmful to u when we healthy will take over

• thats why we develop fever etc. cuz we cant get rid of THE OPPORTUNISTIC BACTERIA??

• so the physician will prescribe antibiotics in order to fight against the opportunistic bacteria so our immune sys can recover better + fight the virus

WHAT CAUSES VIRAL infection

virus

WHAT IS EFFICIENT AGAINST VIRUS **

ANTIVIRAL ONLY

WE HAVE TO REMEMBER SOME OF HOW MICROORGANISMS ARE USED IN DAILY LIFE!

MICROBIOME DEFINITION

• a community of diverse microorganisms (e.g. fungi, bacteria, viruses) that exist in a particular environment (+ interact with each other + their specific environment)

• this interaction is not static; its dynamic, they will fight, love each other etc.

• —> DYNAMIC NATURE HIGHLIGHTS THE IMPORTANCE OF UNDERSTANDING HOW THESE ECOSYSTEM FUNC + RESPOND TO CHANGES

MICROBIAL ECOSYSTEM DEFINITION **

• a microbial ecosystem consists of microbiomes

• as microbial ecosystems are all microbial communities interacting together along with the environment they interact with!

microbiomes constitutes what

a microbial ecosystem

e.g. we have different types of microorgs depending on the environment e.g. you would not find some microorgs from the forest in the ocean

little friend =

beneficial microorganisms

bad guy =

harmful microorgs

microbiome in humans

• HUMAN MICROBIOME = MICROBIOTA - made up of normal microflora

• not all bacteria we have in our microbiomes is harmful; some benefit us

  • normal microflora: normal microorganism inhabitants of the body they are beneficial + help us to have good health

• —> some are transient: come + go whereas some colonize body indefinitely

• the microorgs species we have in our mouth are not necessarily the same as the microorgs species we have in the dig sys, skin, or urogentals

• —→ this is because all microorgs need a special enviro to grow; they all have different needs

• —→ so the microbial ecosys we have in our mouth is probs different from the microbial ecosys we have in other places, but we can find some microbe species that exist in 2 diff places

• 
  

• the normal microflora in human microbiome/microbiota can:

• prevent the growth of pathogenic microbes

• can help train the immune system to discriminate threats

• —> the immune sys is so used to the normal microflora that they will consider the normal microflora as beneficial, so when we have pathogens that do not belong thr, the immune sys will indicate that there is an intruder

• normal microflora begins to be acquired before birth, but most of them are acquired after birth when we are delivered

WHAT DOES E. COLI PRODUCE IN THE BODY

VITAMIN K2,

4 different places we could find microbiomes in the body **

• mouth

• skin

• digestive tract

• urogenital tract

biofilms

• DEF: microbes that attach to solid surfaces + grow into complex masses

• __> they are attached to a solid surface cuz they dont want to be gotten rid of!

• they grow on rocks, pipes, teeth, medical implants, catheter!

• some biofilms are beneficial

• —> e.g. a biofilm protect mucous membranes from harmful organisms

• —> a biofilm provides food in aquatic ecosystems

• some biofilms are harmful

• —> clog water pipes

• —> cause infections on medical implants

• —→ often bacteria in biofilms are resistant to antibiotics!

what biofilm do we have on the teeth? + what is the most common example of biofilm?

dental plaque

normal microflora

normal microorg inhabitants

quorum sensing

cell— cell communication for group collaboration behavior between microorganisms!

father of classification/taxonomy is ***

Karl Linnaeus

taxonomy is

study of classifying living things

classification is

classifying living things

nomenclature is

naming microorganisms

• 
  

identification is

discovering and recording traits of organisms so they can be named and classified

Order of Classification/taxonomy - need to know from bottom to top and top to bottom

Dear - Domain - biggest (highest?)

King - Kingdom

Philip -Phylum

Come - Class

Over - Order

For - Family

Good - Genus

Spaghetti - Species - smallest

Spaghetti - Species - smallest

Good - genus

For - family

Over - order

come - class

philip - phylum

king- kingdom

Dear - Domain - biggest, highest, includes greatest diversity!

scientific nomenclature is **

universal system for naming and classifying living organisms

binomial nomenclature

Each organism (species) has a two part scientific name. scientific Names are either italicized or underlined.

 Genus name: Always capitalized, always a noun. May use initial.

 species name: Always lower case, usually an adjective.

 Ex:

Panthera pardus

 Panthera pardus

binomial nomenclature explained **

Last Name first Name

Genus. species

Panthera. pardus

Streptococcus salivarus

Streptococcus pneumoniae

S. pneumoniae (abbreviated)

either italicise the name or underline

Genus always starts with capital letter

species always starts with lowercase

classification of Panthera pardus

species: Panthera pardus

genus: Panthera

family: Felidaea

order: carnivora (e.g. dog)

class: mammalia

phylum: chordata

kingdom: animalia

domain: eukarya

WHAT ARE THE 3 DOMAINS IN CLASSIFICATION/ TAXONOMY **

ARCHEA

BACTERIA

EUKARYA

6 kingdoms in classification/taxonomy (she didnt go over it)

• eubacteria

• archaea

• protista

• fungi

• plantae

• animalia

difference between prokaryote + eukaryote

their structure!

prokaryotic cell

• no nucleus

• no membrane bound organelles

• unicellular - in order to form organism, only need 1 cell

• —> on its own it is alr organism

• really simple

• smaller

• e.g. bacteria + archaea ONLY

PRO RHYMES WITH NO

eukaryotic cell

• main difference: has nucleus

• has membrane bound organelles (structures inside eukaryotic cell that accomplish different functions)

is uni or multicellular

—>multicellular: for humans + plants to exist, we need multiple cells

—→ unicellular: protozoa (e.g. amoeba + paramecium) is a unicellular eukaryotic cell

• more complex (has lots of things inside of em)

• larger

e.g. human cell

EU IS FOR TRUE!

prokaryotic cell + eukaryotic cell both have

• hereditary material: DNA

• enclosed by a membrane

• cytoplasm

bacteria is a what? does it have nucleus?

prokaryotic cell

• it has no nucleus

• we need lots of bacteria to contaminate 1 eukaryotic cell

kary/o- means

nucleus

bacteria

• reproduce through asexual reproduction called binary fission

• they have flagella that helps them to move/swim to invade your cells or get to proper environment or escape our immunity cell or move to food

• has cell wall w/ peptidoglycan

• Prokaryotes (Unicellular and lack

  nuclei

peptidoglycan is what

protein + carbohydrate

archaea

• has cell wall with no peptidoglycan, is composed of polymers other than peptidoglycan

• is a microorganism survives/found in extreme/harsh environment

• e.g. volcano, bottom of ocean, permafrost, hot spring, desert,

• is a type of bacteria but has differences that separate from bacteria

• Prokaryotes (Unicellular and lack

  nuclei)

• Reproduce asexually (binary fission

• Flagella : Motility. They can “swim”

bacteria vs archaea - diffs + similarities

• bacteria has cell wall w/ peptidoglycan

• archaea has cell wall w/ no peptidoglycan - composed of other polymers

• archaea mostly found in extreme environments (are extremophiles)

• however, both are prokaryotes - unicellular + lack nuclei

• both reproduce asexually thru binary fission

• they both have flagella for moving/swimming

microbiome vs microbial ecosystem

• microbiome is a community of diverse microorganisms interacting with each other + interacting with their specific environment!

• microbial ecosystem is all microbial communities interacting with each other and the environment they interact with

• microbiomes constitute microbial ecosystem

2 examples of protozoa + characteristics of protozoa

e.g. amoeba

e.g. paramecium

they are eukaryote but they are also unicellular

• have asexual reproduction or sexual reproduction

• live freely in the water (some live in animal hosts)

• similar to animals in nutrient needs + cellulat structure

• most are capable of movement by having:

• — pseudopodia/pseudopods - extensions of cytoplasmic membrane that allow protozoa to engulf other organisms ; celll extensions that flow in direction of travel

—> flagella: extensions of a cell that are fewer, longer, and more

whiplike than cilia ; allow them to swim

—→ cilia: numerous, short, hairlike protrusions that propel organisms

through environment ; shorter than flagella

pfc

one human cell that has flagella

sperm cell

fungi

• eukaryotic cell - has nucleus + membrane bound organelles

• can be multicellular or unicellular dependinding on the type

• may have spores (lil dust-like fluffy things we see in air when open fridge w/ moldy smth in it!)

• obtain food from other organisms

• spores: help fungi to reproduce

• has cell walls!

• 2 different types of fungi:

—> molds: multicellular eukaryote; have

hyphae; reproduce by sexual and asexual spores

• —→ yeasts: unicellular eukaryote; reproduce

  asexually by budding; some

  produce sexual spores

algae **

• multi or unicellular

• ARE EUKARYOTIC

• able to do photosynthesis cuz they have chloroplasts

• ALSO HAVE CELL WALL, are rigid

• Simple reproductive

structures

◦ Categorized on the basis of

pigmentation, storage

products, and composition

of cell wall

helminths

• are worm-like parasites

• e.g. parasitic flatworm + roundworm

• —> Some microscopic stages in

  their life cycles

• are eukaryotes

• ARE MULTICELLULAR ANIMALS

• Not strictly microorganisms

viruses

they do not have any classification cuz they are Not independently living cellular

organisms ; they are not cells

• similarity w/ eukaryotic + prokaryotic cell- they have genetic material: DNA or RNA

• they are obligate parasite: they cannot survive without the host

• Much simpler than cells- basically a small amount of DNA or RNA

wrapped in protein and sometimes by a lipid membrane

• Depend on the infected cell’s

machinery to multiply and disperse

• Individuals are called a virus

particle or virion

CLASSIFICATION MINDMAP - DRAW IT

• FUNGI CAN BE SINGLE OR MULTICELLULAR

• - PROTIST IS PROTOZOA - is single celled eukaryote

6 KINGDOMS

HISTORY OF MICROBIO - title

Robert Hooke

• - built first microscope

• came up with the cell theory: all living things are composed of cells

Anton van Leeuwenhoek **

• first who observed microbes ( with another type of microscope) + documented them with detailed drawings

• he did not identify bacteria at this point cuz it was too small

• he discovered protozoa (like the amoeba + the paramecium) and called them “animalcules”

• IS THE FATHER OF MICROBIOLOGY

spontaneous generation theory **

• nonliving matter gives rise to living organisms!

• by Aristotle

francisco redi’s experiments

• with the use of microscope, we discovered that there are lil things we can’t see with out naked eye!

• 2 scientists proved that microorganisms didn’t spawn from nowhere; they alr existed.

• —→ one of them is francisco redi: he disproved the theory of spontaneous generation - that microorganisms spawn from nowhere - through his experiement

• REDI’s experiment:

• - in 1 flask, he took meat, put it in the flask, and then the flies were attracted by the meat and then they laid their maggots on the meat inside the flask

• in the 2nd flask, he put meat inside the flask and he sealed it so flies did not come in, and he did not see any maggots forming on top of the meat

• in the 3rd flask, he put meat inside the flask and sealed it with gauze (a plastic with holes not big enough for the flies to come in)

• —> the flies were attracted to the meat by the smell, but there was still no maggots on top of the 3rd flask

CONCLUSION: maggots come from flies laying them; they do not spontaneously generate; so the spontaneous generation theory is disproved

2 scientists that disproved spontaneous generation theory SCIENTIFICALLY

Louis Pasteur + Francisco Redi

pasteur’s experiments

• his experiment also disproved the spontaneous generation theory

• broth is TSB

• - he took the swan-necked flask + put broth in it, heated it up to sterilize it (destroy any living things in the broth)

• the swan-necked flask has a tube with opening connected to the flask that allows air to move in and out of the flask, but his broth was still not contaminated

• however, some particles coming from the air (dust, which has microbes) settles in the bend of the swan-necked flask’s tube

• as long as the dust stays separated from the sterile broth, the broth stayed sterile

• pasteur tilted the swan-necked flask so that the sterile broth came into contact with the dust in the tube of the swan-necked flask

• the broth becomes contaminated because it came into contact with the dust

• THE CONTAMINATION CAME FROM THE DUST, AND THE DUST CAME FROM THE AIR

• the microbes that he observed at the end did not come from nowhere; they existed already.

• through this experiment, he disproved spontaneous generation theory

• —> this experiment supports the biogenesis theory

• —> BIOGENESIS THEORY: LIVING THINGS COME FROM PRE-EXISTING LIVING THINGS

biogenesis theory **

• Louis Pasteur’s swan-necked flask experiment supports it

• LIVING THINGS COME FROM PRE-EXISTING LIVING THINGS

• (Rudolf Virchow)

more things pasteur did

• he developed pasteurization: high pressure + high temperature to kill microbes

• he is the father of zymology (fermentation); he used microorganisms to develop wine/beer

• he discovered vaccinations against anthrax + rabies

• provided foundational evidence for germ theory of disease: the theory that stated disease is mainly due to germs

• is father of bacteriology

germ theory of disease

• Pasteur provided foundational evidence for the germ theory of disease

• the theory that stated disease is mainly due to germs

different foods made by microbes

robert koch

• FATHER OF MODERN MEDICINE

• he STUDIED) causative agents of deadly disease:

• anthrax (bacillus anthracis), tuberculosis (mycobacterium tuberculosis), cholera (vibrio cholerae)

• expanded upon germ theory of disease + demonstrate it

• Koch’s postulates:

—>4 generalized medical principles to ascertain the relationship of pathogens

with specific diseases

- (is designed to confirm 1 infectious agent is responsible for 1 type of disease)

e.g. these criteria must be met to prove mycobacterium tuberculosis causes tuberculosis disease.

koch’s postulates

Koch’s Postulates

 1-The suspected causative agent must

be found in every case of the disease

and be absent from healthy hosts.

 2. The agent must be isolated and

grown outside the host.

 3. When the agent is introduced to a

healthy, susceptible host, the host must

get the disease.

 4. The same agent must be found in the

diseased experimental host

if all these met, then you can conclude the infectious agent is responsible for the specific disease!

alexander fleming **

DISCOVERED THE FIRST ANTIBIOTICS

the antibiotics is penicillin

Semmelweis

importance of handwashing

Joseph Lister

• used phenol to control wound infections

• antiseptic technique (Listering)

John Snow

infection control and

epidemiology

Edward Jenner

• introduced technique of vaccination for smallpox

• field of

  immunology

Paul Ehrlich

“magic bullets” – field of

chemotherapy/ Gram staining

we are in modern age of microbiology!

molecular biology

the study of how genetic information is carried in molecules of D N A

microbial genetics

the study of how microbes inherit traits

JAMES WATSON + FRANCIS CRICK

• discovered double helix structure of DNA!

biotechnology

the use of microbes for practical applications, such

as producing foods and chemicals (e.g. produce insulin)

Recombinant D N A technology

• enables bacteria and fungi to

produce a variety of proteins, vaccines, and enzymes

• Missing or defective genes in human cells can be replaced in

gene therapy

◦ Ex: Production of human blood-clotting factor by

E. coli to aid hemophiliacs

◦ Agricultural applications: Genetically modified bacteria are used

to protect crops from insects and from freezing

gene therapy

• if have missing/ defective genes in human, we can use microbes to produce the missing/defective genes!

infectious disease

disease that results when a pathogen invades a

host and overcomes the host's resistance.

pathogen

microbes that can make you sick!

emerging infectious diseases (EIDs) **

new diseases and diseases increasing in incidence

e.g. COVID-19, ebola virus disease, marburg virus!

Factors contributing to emergence of diseases include:

◦ Evolutionary changes such as antibiotic resistance

—> e.g. if you dont finish the full course of antibiotics, some bacteria will still be left + they will develop resistance cuz of adaptation + not be killed by the same antibiotic anymore

◦ Modern transportation enabling rapid dispersal of diseases

◦ Increased human exposure to infectious agents due to

deforestation and construction

epidemic

An outbreak of a disease that affects a specific

population or region in a relatively short period

pandemic

A global outbreak of a disease that spreads widely

across multiple continents or countries

e.g. COVID-19

epidemiology

is the study and analysis of the distribution,

patterns and determinants of health and disease conditions in

a defined population, and application of this knowledge to

prevent diseases.

epidemic vs pandemic - write!

• Epidemic: An outbreak of a disease that affects a specific

population or region in a relatively short period.

• Pandemic: A global outbreak of a disease that spreads widely

across multiple continents or countries

multidrug resistant bacteria + C. diff

• MRSA Methicillin Resistant

Staphylococcus aureus

 VRE Vancomycin Resistant

Enterococcus

 VRSA Vancomycin Resistant

Staphylococcus aureus

 MDR-TB Multidrug Resistant

Tuberculosis

TOP 4 are best!

• Clostridium difficile (2004) - is emerging infectious bacterium

—> Increasing number of drug resistant strains

including Nosocomial and Community Acquired

microorganisms