Microbiology LT 1

What is microbiology the study of

Microbiology is the study of different microorganisms.

What are microorganisms

Microorganisms are microbes are life forms too small to be seen by the unaided human eye (mostly because some fungi/algea/ bacteria are macroscopic)

What are the 8 types of microorganisms

1. Virus

2. Fungi

3. Viroids

4. Algea

5. Archaea

6. Protists

7. Bacteria

8. Prions

Are microorganisms commonly found?

Yes, Microorganism are ubiquitous ; They are the most diverse and most abundant form of life as it makes up 78% of the lifeforms in Earth

What are the general characteristics of Microorganisms

1. microscopic / macroscopic

2. cellular / acellular

3. unicellular / multicellular

4. complex structures

5. complex environments

What is microorganism’s significance in the creation of the aerobic environment?

cyanobacteria are the first and oldest oxygenic and photosynthetic organisms on earth

What are gnotobiotic organisms?

isolated and germ free animals are called gnotobiotic and are typically enoculate with a particular type of organisms to be used in laboratory experiments

What are biofilms

microorganisms form complex microbial communities known as biofilms (lake, human tongue and sewage sludge)

What do microorganisms do with regards to human health

Microbes encode enzymes that help digest food and help maintain our health. Some can synthesize certain vitamins [ E. coli > K2 & recombinant human insulin ]

What is the significance of microorganisms with regards to plant health

1. Microorganisms aid in cycling of key plant nutrients

   • nitrogen fixating bacteria convert [ nitrogen > ammonia ]

What is the role of microorganisms in the environment

Microbes can be used to clean up industrial pollution in a process called bioremediation. For biofuels they are used to convert [ biomass > ethanol ] & [ wastes > methane ]

What do microorganisms in the rumen do?

Microbes in the rumen help ruminants digest cellulose rich food. Gut-bacteria in our colon help digest food.

What does microbial fermentation do?

Microbial fermentation contributes to food production and improves food shelf life. Microbes can also be harnessed to produce commercially valuable products

Are microorganisms model organisms —> if so why?

They are model organisms that serve as tools in studying life processes (evolution) and medical advancement

Who invented the first compound microscope

Zacharias Jansen

What was Robert Hooke’s contribution to microbiology

• coined the term cell by looking at cork

• 1st one to discover / observe microorganisms (fungi)

What was Antoni Van Leeuwenhoek’s contribution to microbiology

Father of Microbiology

• 1st discovered bacteria and coined it as "wee animalcules"

What was Ferdinand Cohn’s contribution to microbiology

Founder of Bacteriology

• unicellular algaea & bacteria

• sulfur oxiding bacteria

• presence of endospores that makes bacteria resistant to extreme temp

• methods for preventing contamination of culture media - cotton plugs!

What was Edward Jenner’s contribution to microbiology

Father of Immunology

• discovered smallpox vaccination

• cow pustules as vaccinations

What is variolation, and what happened to it in the future

• variolation is when you use the virus itself to immunize the person ; it became prohibited once vaccination was created.

What was Joseph Lister’s contribution to microbiology

Used phenol or carbolic acid for surgical dressing / use of antiseptics to kill microorganisms for sterility during surgery (Aseptic Techniques

What did Francesco Redi and Lazzaro Spallanzani both do?

Proved that microorganisms were introduced from the environment via air | both researched to disprove spontaneous generation

What was Louis Pasteur’s contributions to microbiology

1. his development of vaccines for the diseases anthrax, fowl cholera, and rabies.

2. The defeat of spontaneous generation

3. Fermentation

4. Pasteurization

5. Sterilization

How did Louis Pasteur disprove spontaneous generation?

1. In the straight flasks, airborne microbes fell to the broth unobstructed.

2. In the swan neck flask airborne microbes got trapped around the curves.

3. Boiling point is at 100 C whereas sterilization is at 121 C (where dormant endospores that allow organisms to thrive in high temperatures— are killed)

Differentiate sterilization and pasteurization

Sterilization seeks to completely eliminate the microbes (—commonly used in the medical industry) whereas pasteurization seeks to merely reduce it's number (milk > curdles > dairy products)

What was Miasma Theory

is an abandoned medical theory that held that diseases—such as cholera, chlamydia, or plague—were caused by a miasma, a noxious form of "bad air", also known as night air.

What was John Snow’s contribution to microbiology

treated cholera patients under the hypothesis that it was waterborne more-so than airborne.

What was Robert Koch the father and creator of?

1. Medical Microbiology

2. Koch’s Postulates

What are the 4 postulates of Koch’s original postulate?

1. The pathogen must be absent in healthy organisms

2. The pathogen must be able to be grown in a separate culture

3. The pathogen must cause the same disease in a healthy organism

4. The pathogen must be isolated and then re-isolated into a different culture

What is the limitation of Koch’s first postulate

Opportunistic Pathogen —> Opportunistic pathogen will not cause disease in healthy but immune-compromised

What is the limitation of Koch’s second postulate

Natural and complex pathogens can't be cultured in the lab

What is the limitation of Koch’s third postulate

No model organisms for testing the microorganism / Asymptomatic cases

What is the limitation of Koch’s fourth postulate

Microorganisms have the tendency to mutate because of their haploid nature

What are the two modifications to Koch’s postulate

1. Molecular Koch’s Postulate

2. Ecological Koch’s Postulate

What is the modification in Koch’s Molecular Postulate

1. immunobased, detection of the gene coded by the pathogen

2. At the molecular level, you are investigating the genes

3. used to determine what genes contribute to a pathogen's ability to cause disease

What is the modification in Koch’s Ecological Postulate

1. dysbiosis is an imbalance in the composition of microorganisms within a microbiome, specifically referring to the gut microbiota

2. Health by the balanced normal microflora can help fight bad bacteria

What was Walther and Fannie Hesse’s contributions to microbiology

Fannie Hesse observed agar in the kitchen is better than gelatin as gelatin may sometimes be the source of nutrients or else it will liquefy.

What is agar derived from ?

Agar is from red algae

What are the benefits of agar vs gelatin?

1. Yields a transparent medium for clear visual of morphology

2. Remains solid at 37 C

   • optimal temp. ; most pathogenic microbes like this bc it's normal the body temp

3. Remains liquid to about 45 C

   • easier for manipulation so its not too hot.

4. It cannot be degraded by most bacteria

What was Martinus Beijerinck’s contribution to microbiology

1. Developed the Enrichment Culture Techniques used in the isolation of microorganisms in the natural environment

2. He was first to discover Lacticaseibacillus paracasei (lactic acid bacteria)

3. Described the 1st virus : Contagium vivum fluidum ( "Contagious liquid fluid" )

What was the Enrichment Culture Techniques of Beijerinck

1. [ nutrient + incubation (oxygen) requirement ]

2. A particular group of microorganisms would be able to grow under certain medium conditions

What technique was used before petri dishes

Flat Plate Technique : Robert Koch and his way of culturing media before Petri Dishes

What was Richard Petri’s contribution to Microbiology

developed the transparent double-sided "Petri dish" in 1887, this quickly became the standard tool for obtaining pure cultures.

What was the contribution of Sergei Winogradsky in microbiology

1. Soil microbiology ; 1st to demonstrate process of nitrogen fixation thru nitrifying bacteria: Clostridium pasteurianum

2. Focuses on the diversity of bacteria in the environment, generating lots of publication

3. defined chemolithotrophy

What is chemolithotrophy

1. any metabolic process in which energy for growth is produced using only inorganic chemical compounds.

What is Gene Amplifications

1. Generating copies of gene using PCR polymerase chain reaction.

2. During each round of amplification, the amount of DNA doubles,

3. an automated PCR machine called a thermal cycler

Where does the polymerase come from in the PCR machine

1. Taq polymerase, a DNA polymerase isolated from the thermophilic hot spring bacterium Thermus aquaticus

2. Pfu polymerase from Pyrococcus furiosus, a hyperthermophilic species of Archaea with a growth temperature optimum of 100°C

What is Reverse Transcriptase

1. generates DNA from an mRNA template

   • RT-PCR uses the retroviral enzyme reverse transcriptase ( like HIV virus ) to convert RNA into complementary DNA (cDNA)

What is reverse transcriptase used for and what does it produce?

1. Used if it is needed to detect gene activity like if an organism is expressing a gene! If an organism is producing mRNA then the gene is transcribed and expressed.

2. to produce an intron-free eukaryotic gene for expression in bacteria

What is an Intron and an Exon

1. Intron = noncoding sequences of DNA

2. Exons = coding sequences of DNA

What are Reporter Genes

1. These are tools for studying regulatory events They may be used to report the presence or absence of a genetic element (such as a plasmid) or DNA inserted within a vector.

2. it encodes a protein (gene-coding for fluorescent proteins) that is easy to detect and assay.

What are examples of Reporter Genes

1. lacZ from Escherichia coli — b-galactosidase (X-gal is the artificial substrate) for blue color

2. GFP / green fluorescent protein (GFP) — from the jellyfish Aequorea victoria,

What are gene fusions

genetic constructs that consist of segments from two different genes.

What is Gene Cloning

1. The movement of desired genes from their original source to a small and manipulable genetic element (the vector) to make a recombinant DNA

2. Major steps in gene cloning uses restriction enzymes. By cutting the foreign DNA and the vector DNA with the same restriction enzyme, complementary sticky ends are generated that allow foreign DNA to be inserted into the vector.

What is recombinant DNA

a recombinant DNA contains genes from different organisms

What is Transgenics

1. Genetically Modified Organisms

   • an example is BT Corn

What does CRISPR stand for

Clustered Regularly Interspaced Short Palindromic Repeat

What is CRISPR / Cas9 System

1. most powerful and precise tool yet for altering eukaryotic genomes in living cells (genome editing)

2. can be used to modify antibiotic resistance genes! ( person. hypothesis )

What is the function of CRISPR-Cas9 System

1. A major antiviral defense system present in both Bacteria and Archaea

2. functions to seek out and destroy nucleic acid) and works in tandem with Cas9 protein

   • IMMUNIZATION - destroys the virus upon the second encounter.

   • drawback: when the virus mutates and becomes unrecognizable

What is Taxonomy

the science in which organisms are characterized, named, and classified according to a defined criteria.

What approach does Microbial Taxonomy use?

It uses a Polyphasic Approach

What is Phenotypic Analysis

Morphological, metabolic, physiological, and chemical characteristics of the cell

What is Phylogenetic Analysis

1. Molecular sequence data

   • Phylogenetic looks at the nucleotide sequences & how similar they are

What is Genotypic Analysis

1. Characteristics of the genome

   • Looks at the present genes & their positioning

What is Classification

the organization of organisms into progressively more inclusive groups

• so that it's easier to study them and make generalizations

• Basis are Phenotype Similarity & Evolutionary Relationship

How does Taxonomic Hierarchy work

Lowest : species composed of 1-several strain | Highest : domain

What is a species composed of 1-several strain also known as

the fundamental unit of biological diversity

Is there a universally accepted definition of a microbial species

1. No, there is no universally accepted concept of a microbial species

   • Definition of species affect assessment of microbial diversity

How does the Phylogenetic Species Concept work in Bacteria

1. All members of a species should be genetically and phenotypically cohesive

2. Traits should be distinct from other species

3. Should be monophylectic sharing a recent common ancestor

What are the Ideal Phylogenetic Markers

1. Highly conserved

2. Variable regions that are species-specific

3. Length is sufficient to differentiate organisms statistically

4. Low length variability across species

5. Single copy gene

6. Primer availability

In the Ideal Phylogenetic Markers what does highly conserved mean?

1. Doesn't mutate alot

2. universal or present in all organisms

In the Ideal Phylogenetic Markers what does Single copy gene mean?

1. genes have multiple copies and it doesn't have anything to do with ploidy though

   • if u have multiple its hard to compare so it'll be simpler if its a single copy

In the Ideal Phylogenetic Markers what does Primer availability mean?

The ability to get the sequence and detect the presence of that gene

What are the Phylogenetic Markers of RNA in prokaryotes and eukaryotes

1. 16S rRNA gene (Prokaryote)

2. 18S or 28S rRNA gene (Eukaryote)

How does Phenotypic Characteristics work in identification?

1. Morphological, metabolic, physiological, and chemical characteristics of the cell

2. Dichotomous Key

What is Nomenclature

the actual naming ; Binomial System of Linnaeus ( genus & species epithet )

What is Systematics

1. is the study of diversity of organisms and their relationships.

   • Once you've identified the taxa u can do systematics studies

   • How is the organism related to another organism in their natural habitat

How does Microbial Classification work?

1. based on the Universal Tree of Life of Carl Woese

   • LUCA : last universal common ancestor

What is the universal tree of life?

• nucleotide sequence similarity in the ribosomal RNA genes

What are the Advantages of being Small in Bacteria?

1. Less metabolic energy • faster regeneration + reproduction rates

2. Difficult to detect

3. Greater volume-to-surface area ratio = faster nutrient exchange rate (smaller = fit)

4. Greater evolutionary possibilities, easily to immediately express characteristics wrought by mutations —evolve faster for speciation of the bacteria

Classifications of Prokaryotes

1. NOT primitive

2. More highly evolved than us

3. Domain Eubacteria (Bacteria) & Domain Archaebacteria (Archaea)

4. Bacterial & Archaeal Diversity

Classifications of Eukaryotes

to an extent, helminths

What are the 4 Universal Structures of a Bacterium

1. Ribosomes

2. DNA

3. Cell Membrane

4. Cytoplasm

The minimum requirement for a bacterium would be the smallest size being able to house all these requirements. We only know 1% of the total bacteria present in the world.

What are viruses compared to bacterial cells

Viruses are typically smaller than bacterial cells.

Bacteria Shapes

Bacteria Arrangement

What is the function of the Cell Surface Structure of Microorganisms?

1. sticky coat of polysaccharide / protein

2. NOT for rigidity nor strength

3. assist in the attachment to solid surfaces

4. Virulence factors - something that will trigger an immune response & contributes to pathogenicity

5. block detection against the host's immune system

6. Prevents dehydration

What is the Capsule in microorganisms?

1. organ. in a tight matrix

2. Exclude small particles

3. Seen by light microscopy

What is the Slime Layer in microorganisms?

1. easily deformed

2. Loosely attached

3. More susceptible

4. More susceptible to breakage

What is the cell walls functions ?

1. Function : Shape & Cell Rigidity / Strength

2. Protection from osmotic lysis & protects from cell membrane rupture

3. Antibiotic target : Once you rupture the cell wall, you remove rigidity

4. Is made up of Peptidoglycans

What are Peptidoglycans

1. Murein or Mucopeptide

2. Rigid Polysaccharide

3. Long chains of glycan tetra-peptide

What are Glycan Tetrapeptides

[ NAG + NAM + Amino Acids ] + B (1,4) glyosidic bond susceptible to lysozyme

What is the Periplasmic Space

1. gap between cell wall and cell membrane

2. Gel-like in consistency (↑ protein)

   • Hydrolytic enzymes (Initial food degradation)

   • Binding proteins (Substrate transport)

   • Chemoreceptors (Chemotaxis response)

     • motilic response to chemical sensitivity

What are the characteristics of Gram Positive bacteria?

1. 80-90% of peptidoglycan + several sheets of it stacked up another

2. Stacked sheets of peptidoglycan

What are the characteristics of Gram Negative Bacteria

1. 10% of peptidoglycan & more complex

2. Contains the Lipopolysaccharide (LPS) Layer

What is the Lipopolysaccharide (LPS) Layer

1. Outer membrane ; 2nd lipid bilayer (1st is the Cell Membrane)

2. Course Sieve — prevent entry/exit

   • porins in the outer membrane serve as channels

3. Presence of cell wall makes it less sensitive to penicillin

Between gram positive and gram negative bacteria where does antibiotics work best?

Gram positive → bc of the cell wall being much simpler

What is an acid fast cell wall?

1. mycolic acids + long chain fatty acids (lipid layer + peptidoglycan + cell membrane)

2. Looks like Gram + due to thickened peptidoglycan And Gram - because of the lipid layer

3. sequenced as Gram positive but not classified as 1

4. Acid fast staining uses a different stain to produce pink dye for acid-fast

What is the structure of the Lipopolysaccharide (LPS) Layer

1. O-specific polysaccharide

   • Outermost structure

   • means of differentiation & interactions with vaccines / bacteria

2. Core polysaccharide

   • middle layer

3. Lipid A

   • (inner) closest to peptidoglycan

What are the characteristics of a Cell wall-less microorganism?

1. Strengthened cell membrane: Sterol

2. simple staining to do, but will not respond to differential staining