Microbiology Block 3

Where are the major microbial habitats in/on humans?

Ear, Nose, Hair, Skin, Gut and Mouth

How is the human microbiome originally inoculated?

Vaginal birth vs c section

Breast feed vs formula

What is the primary factor that drives community composition in the human microbiome?

Nutrients consumed, habitat and community.

Two locations of high microbial diversity in humans

Skin and nostrils are exposed to external environment

Two locations of low microbial diversity in humans

Mouth and gut because they are only exposed to what it given to them

Why might microbe diversity be different between different body parts?

Different areas of skin interact with different surfaces

Why is transplanting microbes between body parts mostly unsuccessful?

Habitats are the main driver of diversity so being moved to unfamiliar places doesn’t usually work

What bacteria is involved with tooth decay?

Gram-negative bacteria and spirochetes

What bacterium commonly is the source of ulcers?

Helicobacter pylori

How does H. pylori live in the stomach?

It burrows into the stomach lining and the ulcer is created by immune response

Why is microbial activity in small intestines minimal?

Rapid flow of contents washes bacteria away and human body takes many nutrients

Why is microbial activity in the colon greater than small intestine?

Flow is very slow and humans don’t absorb as many nutrients

What critical metabolic benefit to bacteria provide for the colon?

Polysaccharides are hard to be broken down so bacteria assist with this process

What is the relationship between C. diff and antibiotics?

Antibiotics disrupt normal microbiota, allowing hard to kill C. difficile to overgrow.

What benefits are provided by natural vaginal microbiota?

Some protect from fungal infection while some lower pH to protect from STIs

Probiotics

Contain living microbes such as Bifidobacterium and Lactobacillus

Prebiotics

Contain nutrients to feed beneficial bacteria

What is a fecal transplant and when is it used?

Transfer of healthy microbiota to restore gut balance, often for C. difficile infections.

What is an advantage of fecal transplants over antibiotics?

They restore microbial diversity instead of killing microbes broadly.

How can gut microbes affect other parts of the body?

They influence metabolism, immune function, and even brain activity.

What is the gut-brain axis?

The connection between gut microbiota and the brain/CNS.

How can microbiome knowledge shape future medicine?

Personalized medicine to boost beneficial microbial communities and prevent pathogen invasion

Main difference between beneficial and pathogenic bacteria

Pathogens have virulence factors that allow them to cause disease; most bacteria don’t have this

Why is adherence required but not sufficient for disease?

Bacteria must attach to a host but also need to colonize, invade, and produce damage for nutrients.

What are adhesins? Give 2 examples

Surface molecules that help bacteria attach to host cells;

Capsules and fimbriae

What is the difference between colonization and invasion?

Colonization is growth on surfaces where invasion is penetration and spread into tissue

Is septicemia due to colonization, invasion, or both?

Invasion since bacteria enters the bloodstream

What is a virulence factor?

A trait that enables a pathogen to cause disease

Why does virulence vary among pathogens?

Difference in virulence factors and genetic makeup

What is LD₅₀ and how does it relate to virulence?

The number of cells needed to kill 50% of hosts; lower value means higher virulence

How can virulence be attenuated/reduced?

By losing or mutating virulence genes

What is a pathogenicity island?

A cluster of virulence genes on a chromosome

What is the role of horizontal gene transfer in virulence?

It spreads virulence genes between bacteria

What is an example of an enzyme virulence factor?

Hyaluronidase breaks down host tissues to aid spread

What is the difference between exotoxins and endotoxins?

Exotoxins are secreted proteins where endotoxins are LPS components of gram-negative cell walls

What are three types of exotoxins and examples?

AB toxins: diphtheria toxin

Cytolytic toxins: hemolysins

Superantigens: toxic shock toxin

What is an example of an endotoxin and which bacteria use it?

Lipopolysaccharide (LPS) in gram-negative bacteria

In what context are antibiotics naturally produced?

Microbes produce antibiotics to compete with and inhibit other microorganisms

What is selective toxicity and why is it important?

It allows antibiotics to target bacteria without harming human cells, making them safe for treatment

Who discovered antibiotics and how?

Alexander Fleming discovered penicillin from mold inhibiting bacteria

What is the difference between bactericidal and bacteriostatic antibiotics?

Bactericidal kill bacteria where bacteriostatic stop growth so immune system can clear infection

Why use broad-spectrum antibiotics and what is a consequence?

Used when pathogen is unknown but can disrupt normal microbiota and cause infections

Why can’t antiseptics and disinfectants be ingested?

They lack selective toxicity and damage human tissues

How to β-lactam antibiotics work?

They inhibit peptidoglycan cross-linking in cell walls, causing cell lysis

Which bacteria are β-lactams most effective against and why?

Gram-positive bacteria because of their thick and exposed peptidoglycan layer

How do polypeptide antibiotics like vancomycin differ from β-lactams?

They bind directly to cell walls precursors instead of targeting enzymes

How do quinolones work and why are they selectively toxic?

They inhibit DNA gyrase in prokaryotes which differed from eukaryotic enzymes

How do tetracyclines work and why are they selectively toxic?

They bind to the 30S ribosomal subunit which difference from eukaryotic ribosomes

How do sulfa drugs work and why are they selectively toxic?

They inhibit folic acid synthesis which bacteria must produce but humans obtain from diet

How do bacteria resist penicillins?

By producing β-lactamase enzymes that degrade the antibiotic.

How do bacteria resist vancomycin?

By modifying the D-Ala-D-Ala target (3 enzymes) so the drug cannot bind

How do bacteria resist ciproflaxin?

By modifying DNA gyrase, reducing drug entry, or using EFFLUX PUMPS.

How do bacteria resist tetracycline?

By using efflux pumps to remove antibiotics

How do bacteria resist sulfonamides?

By modifying enzymes involved in folic acid synthesis

Why are efflux pumps a major concern?

They can remove multiple antibiotics which causes multidrug resistance

Where are antibiotic resistance genes found?

On chromosomes and plasmids

What is clavulanic acid?

A β-lactamase inhibitor that protects antibiotics like penicillin.

Why does resistance evolve at different rates for different antibiotics?

Some resistance mechanisms are more complex and harder to evolve

What is the concern with Neisseria gonorrhoeae?

It rapidly develops resistance to antibiotics

What factors spread antibiotic resistance?

Overuse of antibiotics, agriculture use, and horizontal gene transfer

Is there hope for antibiotics in the future?

Yes, through new drugs, better practices, and alternative therapies like phage therapy.

How are viruses different from bacteria in structure and metabolism?

Viruses lack cells, ribosomes, and metabolism structures and must replicate inside a host

What are viral capsids and envelopes?

Capsids are protein shells around the genome; envelopes are host-derived membranes some viruses acquire

What does the Baltimore classification system use?

Genome type and how viruses generate mRNA

Why can’t viruses be classified using rRNA?

They lack ribosomes and rRNA genes

What must all viruses ultimately produce?

mRNA (+ strand) for protein synthesis

What are the 5 stages of the viral replication cycle?

Attachment, penetration, synthesis, assembly, and release.

What happens during (virus) attachment?

Viral proteins bind specific receptor cells on host

What happens during (virus) penetration?

Viral genome enters the host (or entire virion in eukaryotes)

What happens during (virus) synthesis?

Viral genomes and proteins are made using host machinery

What happens during (virus) assembly?

New viral particles are constructed from genomes and capsid proteins

What happens during (virus) release?

Viruses exit via lysis (prokaryotes) or budding (eukaryotes)

How do bacteriophage T4 attach to E. coli?

Tail fibers bind to specific receptors on the bacterial surface

What role do endosomes and lysosomes play in viral infection?

They help engulf and uncoat viruses in eukaryotic cells

Where does viral genome replication and protein synthesis occur?

Replication occurs in cytoplasm in nucleus; translation occurs in cytoplasm

Why is ATP needed for phage genome packaging?

It powers the packaging motor that inserts DNA into capsids

What is the difference between lysis and budding?

Lysis destroys the host cell; budding releases the virus without killing the cell

What is the difference between lyric and lysogenic cells?

Lyric kills host immediately; lysogenic integrates into host genome and remains dormant

What viruses undergo lysogeny?

Temperature bacteriophages

How is a virus involved in diphtheria?

A phage carries the toxin gene that makes the bacterium pathogenic

How are retroviruses similar to temperate phages?

Both integrate their genome into the host DNA

What is a latent viral infection?

A virus remains dormant in the host and can reactive later (ex: herpes)

What is the main difference between influenza types A, B, C, and D?

They differ in severity and host range, with Influenza A causing pandemics and infecting multiple species.

What is the antigenic drift vs antigenic shift?

Drift is small mutations; shift is a major changes from recombination, leading to new strains

What is viral recombination and why is it important?

Exchange of genetic material between viruses during co-infection, creating new strains that can infect new host

Why was the 1918 influenza pandemic so deadly?

The virus had novel antigens the immune system couldn’t recognize, causing severe immune responses.

How did SARS-CoV-2 likely evolve to infect humans?

Through recombination of animal viruses (bats and pangolins), allowing binding to human receptors

Which part of SARS-CoV-2 mutates to increase infectivity and why?

Spike protein; it controls attachment to host cells

What stage of viral replication is affected by spike protein mutations?

Attachment

What are common targets for antiviral defenses?

Steps in viral replication like attachment, genome entry, replication, and assembly

How do microbes prevent viral adsorption?

By altering or masking receptors or producing decoys

How do viruses overcome adsorption prevention?

By mutating to recognize new receptors or degrading barriers

How does restriction-modification provide innate immunity?

Bacteria cut unmethylated viral DNA while protecting their own methylated DNA

How do viruses evade restriction-modification?

By methylating their DNA or altering recognition sites

How does CRISPR-Cas provide adaptive immunity?

stores viral DNA sequences and uses them to recognize and cut future infection

How is CRISPR used in gene editing?

It targets specific DNA sequences for precise cutting and modification

What is abortive infection?

Infected cells self-destruct to stop virus spread and protect the population

Why do microbes need multiple defense strategies?

Viruses evolve quickly, so multiple defenses increase survival chances

Why are defense genes often on mobile genetic elements?

They can spread quickly between microbes via horizontal gene transfer