Microbial Genetics, Fungi, and Body Odor: Key Concepts for Biology Students

What is the core genome?

Genes shared by all members of a species

What is the accessory genome?

Extra genes only some strains carry

Why are some E. coli harmful and others not?

Pathogenic strains have extra virulence genes in their accessory genome

What is quorum sensing?

Chemical signaling between bacteria that triggers group behavior

What did the Human Microbiome Project do?

First large-scale project to map the microbiome at all body sites

What determines which microbes dominate a body site?

The environmental conditions at that site

What is dental plaque?

A biofilm formed when Streptococcus produces a polysaccharide matrix on teeth

What is the critical pH for enamel dissolution?

5.3

What happens below pH 5.3 in the mouth?

Acid produced by bacteria dissolves tooth enamel

What systemic diseases are linked to poor oral health?

Cardiovascular disease, Alzheimer's, diabetes, colon cancer, respiratory infections

Who discovered H. pylori?

Two Australian researchers in 1984

Where does H. pylori live?

In the stomach lining

Why was the stomach thought to be sterile?

Its low pH was believed to kill all bacteria

What is citizen science?

Data collection by the general public, often in collaboration with scientists

What did Joy Milne demonstrate?

She could smell Parkinson's disease before clinical diagnosis

How many fungal species are estimated to exist?

Up to 5.1 million

How many fungal species have been described?

~100,000

What is a hypha?

A long branching filament produced when a fungal spore germinates

What is a mycelium?

A network of many branching hyphae

What is a fungal fruiting body?

A reproductive structure (like a mushroom) that produces and disperses spores

What part of a fungus is responsible for spreading infections?

Spores

What is the fungal life cycle order?

Spore, germination, hyphae, mycelium, fruiting body, new spores

What antibiotic is produced by a fungus?

Penicillin, from Penicillium chrysogenum

How does penicillin kill bacteria?

Blocks cell wall synthesis

What drugs besides antibiotics come from fungi?

Immunosuppressants and statins

What are mycorrhizae?

Symbiotic fungal networks on plant roots that help absorb nutrients

What is the Wood Wide Web?

The fungal network through which trees exchange nutrients and signals underground

What is absorptive nutrition?

Secreting digestive enzymes externally into a substrate, then absorbing the broken-down molecules

What is catabolism?

Breaking down macromolecules for energy and nutrition

How do fungi make fruit soften?

They secrete digestive enzymes that break down cell wall components of fruit

What is ergosterol?

The main sterol in fungal cell membranes; the target of antifungal drugs

What is the target of most OTC antifungal compounds?

The cell membrane via ergosterol

Why are antibiotics ineffective against fungi?

Fungi are eukaryotes; antibiotics target prokaryotic structures

What are the three main antifungal drug classes?

Azoles (Monistat), Allylamines (Lamisil), Amphotericin B

What are mycoses?

Fungal diseases

What causes athlete's foot?

A fungal infection known as ringworm

What is mucormycosis?

A severe fungal infection that occurs mostly in immunocompromised patients

What is a mycotoxin?

A toxin produced by a fungus; can cause neurological disorders or grow on crops

Which mycelium facts are true?

Found in soil, passes nutrients to tree roots, helps keep forests healthy

What causes body odor?

Commensal microbes metabolize sweat into stinky compounds

What makes us stink when we workout?

Bacteria on skin feed on sweat nutrients and produce stinky byproducts

Is sweat itself odorous?

No; sweat is nearly odorless

What are volatile organic compounds (VOCs)?

Airborne compounds including volatile fatty acids and thioalcohols, produced by microbes like Corynebacterium

What are the three types of sweat glands?

Apocrine, eccrine, sebaceous

Where does body odor arise from?

Anywhere with apocrine sweat glands

What are apocrine glands?

Sweat glands in hairy regions, active at puberty, the main source of body odor

What bacterium produces the main armpit VOC 3M3SH?

Staphylococcus hominis

What does 3M3SH smell like?

Rotten onions or meat

What VOCs does Corynebacterium produce?

3MSH (sweat/onions), 3M2H (goat-like), HMHA (cumin-like)

What causes smelly feet?

Staphylococcus epidermidis breaks down leucine into isovaleric acid (cheesy smell)

How do deodorants work?

They kill microbes on the skin

How do antiperspirants work?

They block sweat glands using aluminum chloride

Which BoZone has the most unique VOC profile?

Bowels

Do mosquitoes prefer certain body odors?

Yes; some people's smells are more attractive to mosquitoes than others

How can body odor diagnose disease?

Specific volatiles are released from the skin of people with certain diseases

What type of organism has a greatly reduced genome?

Obligate parasite

What are extrinsic skin microbiome factors?

Hygiene, diet, climate, sunlight, chemical exposure, physical activity

What are intrinsic skin microbiome factors?

Age, genetics, hormones, immunity, sleep, stress

What are the 8 most common STIs?

Syphilis, gonorrhea, chlamydia, trichomoniasis, hepatitis B, HSV, HIV, HPV

What causes syphilis?

Treponema pallidum

What causes chlamydia?

Chlamydia trachomatis

What type of bacterium is T. pallidum?

A spirochaete

What is a unique feature of spirochetes?

They have endoflagella

What is the shape of T. pallidum?

Spiral (corkscrew) shaped

What is T. pallidum's genome size?

1.1 million base pairs

Why does T. pallidum have a reduced genome?

It is an obligate pathogen fully dependent on the host

How does T. pallidum enter the body?

Through small breaks in the outer epidermis

What is the primary sign of syphilis?

A painless chancre (ulcer) at the site of infection

What is a secondary sign of syphilis?

Rash on palms of hands and soles of feet

What happens in tertiary syphilis?

Severe systemic damage; occurs in ~1/3 of untreated patients

How does syphilis evade the immune system?

Its outer sheath contains compounds that look like human compounds

Which STI pathogen produces elementary bodies that survive outside a host?

Chlamydia

What is true about Chlamydia?

More prevalent in college-age women; it enters and reprograms the host cell

Is there a vaccine for Chlamydia?

No

Why does Chlamydia spread so easily?

Most infections are asymptomatic

How does Chlamydia evade the immune system?

It hides inside host cells as an intracellular pathogen

What is a virus?

Genetic material (DNA or RNA) inside a protein capsid; obligate intracellular parasite

What do all viruses contain?

Protein and nucleic acid

What size are viruses?

20 to 500 nm

Why can't viruses replicate alone?

They have no enzymes or replication machinery; must hijack a host cell

What is a capsid?

The protein shell surrounding viral genetic material

What is a viral envelope?

A lipid membrane acquired from the host cell

Which is more resistant to disinfectants: enveloped or non-enveloped?

Non-enveloped

What is the Baltimore classification system based on?

The type of genetic material (how the viral genome is replicated)

What is viral tropism?

The specificity of a virus for certain cells, tissues, or hosts

What cells does HIV infect?

T immune cells (CD4+ T helper cells)

What cells does HPV infect?

Skin and mucosal epithelial cells

What cells does HSV infect?

Skin cells and nerve cells

What cells does SARS-CoV-2 infect?

Lung and gut epithelial cells

What is HPV?

Human Papillomavirus; most common STI; dsDNA virus; infects 75% of sexually active people

Is HPV preventable?

Yes; with vaccination (Gardasil)

What are high-risk HPV types?

Types 16 and 18; cause cancer

What are low-risk HPV types?

Types 6 and 11; cause genital warts

What cancers does HPV cause?

Cervical, oropharyngeal, anal, vulvar, vaginal, penile

What is oncogenesis?

The process by which a virus causes cancer

What is Gardasil?

HPV vaccine available since 2006; targets capsid proteins L1 and L2

When is Gardasil effective?

Only before exposure to HPV

How are HPV and HIV similar?

Both integrate into the host genome

What is HSV?

Herpes Simplex Virus; dsDNA; glycolipid envelope; HSV-1 causes cold sores, HSV-2 causes genital herpes

How is HSV distinct from HPV?

HSV travels through nerve cells, has a lipid envelope, and has a linear genome; only HPV has an effective vaccine