micro 1

microbiology definition

the study of organisms that are too small to be seen by the naked eye

cell theory

All organisms are composed of cells 2. Cells are the smallest living things 3. Cells arise only from pre-existing cells • Last point was added later – The concept of ‘spontaneous generation’ was popular for a long time

spontaneous generation

The hypothesis that living organisms arise from nonliving matter

germ theory

1876: Robert Koch identified causative pathogens of specific diseases, → ”one microbe, one disease”

Koch’s postulates

1. The microorganism must be found in diseased but not healthy individuals

2. The microorganism must be cultured from the diseased individual

3. Inoculation of a healthy individual with the cultured microorganism must recapitulate the disease

4. The microorganism must be re-isolated from the inoculated, diseased individual, and matched to the original microorganism

spread of infection

• Source: Places where infectious organisms are found

• Susceptible person: With a way for germs to enter the body, eg: Immunocompromised, injured,

• Transmission: Mode by which infectious organism is moved to the susceptible person

koch’s postulate now

1. The microorganism must be found in diseased but not healthy individuals

2. The microorganism must be cultured from the diseased individual

3. Inoculation of a healthy individual with the cultured microorganism must recapitulate the disease

bacterial cell wall

Complex, semi-rigid structure

Prevents osmotic lysis

Made of peptidoglycan – Some antibiotics interfere with the its arrangement (e.g., Penicillin)

gram positive v gram negative

Peptidoglycan

• Repeating disaccharide connected by polypeptide cross-bridges

• Form a lattice

Gram-positive:

• thick peptidoglycan + granular layer + teichoic acids

Gram-negative:

• thin peptidoglycan + outer membrane (lipopolysaccharides, lipoproteins and phospholipids) - (NO teichoic acids)

internal to bacteria cell wall

Cytoplasm – 80% water, proteins, carbs, lipids, and more. – Very thin cytoskeleton

Nucleoid – Single long, continuous thread of double-stranded DNA

Ribosomes – Site of protein synthesis – Prokaryotes have 10s of 1000s → cytoplasm appears granular – Two subunits – ribosomes smaller + less dense than eukaryotes

Inclusion bodies – Stockpile of nutrients

possibly Polysaccharide, lipid, sulfur

glycocalyx

Dense, gel-like coat surrounding a cell

• Composed of polysaccharides • Secreted by prokaryotes onto surface

• Functions: – Protective barrier – Prevents dehydration/desiccation

Slime layer: – irregular, diffuse layer – Loose shield to prevent dehydration and nutrient loss

Capsule: – distinct, gelatinous coat firmly attached to cell wall – Protection – Adhesion to surfaces or development of biofilms – Protects against phagocytosis

flagella

Curved filament made from flagellin protein

– Flagella rotate → motility

– Different names depending on organization

endospores

In times of stress (e.g., nutrient depletion), some gram-positive bacteria will develop endospores

– Formed internal to the cell wall

– Very durable, dehydrated cells with thick walls and additional layers (hibernating cell)

– Process = sporulation

– Once spore forms, cell ruptures (dying)

• Method of protecting bacterial DNA for future – Very hardy

• dormant for 1000s of years

• Resistant to processes that typically kill cells

Fungi

crucial to the environment: decompose plants in ways that animals and insects cannot

helminths

• Parasitic animals that spend part or all their lives in humans

• Platyhelminthes (flatworms)

• Nematoda (roundworms)

• Multicellular eukaryotic animals

• Larvae are microscopic – studied by microbiologists

• absorb nutrienst from host

viruses

• Considered microorganisms

• Not cells - but informational parasite

• Consist of DNA or RNA core surrounded by a protein coat

• Inert when outside a host living cell

viral activation in host

• Once inside, viral nucleic acids become active → replication

• Use the host cell’s ribosomes

• Can only enter cells that are the right match

Pirons

Proteinaceous infectious particle – fragments of proteins – Seed the misfolding of endogenous proteins

viroids

Short pieces of naked nucleic acids (RNA) – Replicated continuously by host RNA polymerase – Cause plant diseases

gram staining steps

1. crystal violet

2. iodine

3. alcohol

4. safranin

gram positive garm staining

• During staining, crystal violet and iodine form a large, insoluble CV-I complex inside the cell.

• The alcohol decolorizer dehydrates the thick peptidoglycan, causing it to shrink and tighten. This process traps the large CV-I complexes inside.

• stains purple

gram negative gram staining

• Crystal violet stains the thin layer purple initially.

• The alcohol/acetone dissolves the lipid-rich outer membrane and increases permeability. Because the peptidoglycan layer is thin, it cannot retain the CV-I complex, which washes out

• doesn’t stain

bacterial biochemical properties

• Ability to ferment carbohydrates

• Carbon source used for growth

• Presence/absence of certain enzymes

serology

• Bacteria may have antigens that trigger an immune responses

• Grouping bacteria based on antigens = serotyping

• Work backwards using antibodies

genotypic analysis

eg: Whole genome sequencing, DNA fingerprinting (a small portion of genome), Nucleic acid hybridization.

Comparing the bacterial DNA sequence to that of another or a reference sequence – Gives us an idea of the origin of the bacteria.

DNA sequence changes can be used as a “molecular clock” to estimate time since two lineages diverged

ribosomal DNA genotyping

• Some bacteria have DNA plasmids which can replicate independently of bacterial DNA

• ribosomal genes are well conserved

• Can be tested by 16S rRNA sequencing

• Changes to 16s RNA are very slow = good reflection of an organism’s evolutionary history.

16s rRNA sequencing

SSU (small subunit) ribosomal RNA (rRNA) genes highly conserved and easily sequenced and analyzed in bacteria • Isolate bacterial RNA using PCR

microbial symbiosis

All sites on a human that contain microorganisms are part of a microbiome: – A functional collection of different microbes in a particular environmental system

types of microbiota

• Transient microbiota: may be present for days, weeks, or months (e.g., on skin)

• Normal microbiota: permanently colonize the host

• Resident microbiota are microorganisms that are always present on or in the host

• Some normal microbiota are opportunistic pathogens

• Some microbes are pathogens