biomi!

What is the core genome?

Genes shared by all members of a species; defines who the organism is

What is the accessory genome?

Extra genes only some strains carry; determines what the organism can do (e.g., virulence factors)

How do pathogenic and non-pathogenic E. coli differ?

Pathogenic strains carry extra virulence factor genes in their accessory genome

What is quorum sensing?

Chemical signaling between bacteria; when signal reaches a threshold, the whole group acts together

What is the Human Microbiome Project (HMP)?

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

What determines which microbes dominate at a body site?

The environmental conditions at that site (pH, oxygen, moisture, nutrients)

What is dental plaque?

A biofilm on tooth surfaces formed when Streptococcus spp. produce a polysaccharide capsule matrix

What is the "hedgehog" structure in dental plaque?

A specific spatial arrangement of Streptococcus and Corynebacterium in dental plaque

What is the critical pH for enamel dissolution?

~5.3; below this, acid from lactic acid bacteria dissolves tooth enamel

What systemic diseases are linked to poor oral microbiome health?

Gingivitis, colon cancer, diabetes, respiratory infections, cardiovascular disease, Alzheimer's, Parkinson's

What is Helicobacter pylori?

A spiral-shaped bacterium living in the stomach lining; discovered in 1984; causes gastric ulcers

Why was the stomach thought to be sterile before H. pylori's discovery?

Its very low pH was believed to prevent any bacterial survival

What is citizen science?

Data collection and analysis by members of the general public, often alongside professional scientists

Who was Joy Milne and why is she significant?

A citizen scientist who could smell Parkinson's disease before clinical diagnosis; led to microbial VOC research

How many fungal species are estimated to exist?

Up to 5.1 million; only ~100,000 have been formally described

What is a hypha?

A long, branching filament produced when a fungal spore germinates

What is a mycelium?

A network of many branching hyphae; the main body of a fungus

What is a fungal fruiting body?

A reproductive structure (e.g., a mushroom) that produces and disperses spores

What is the fungal life cycle?

Spore, germination, hyphae, mycelium, fruiting body, new spores; involves asexual and sexual reproduction

What antibiotic comes from a fungus?

Penicillin, produced by Penicillium chrysogenum; kills Staphylococcus aureus

What drugs besides antibiotics are derived from fungi?

Immunosuppressants and statins (anti-cholesterol drugs)

What are mycorrhizae?

Symbiotic fungal networks on plant roots that help absorb nutrients; part of the Wood Wide Web

What is the Wood Wide Web?

The underground fungal network through which plants exchange nutrients and chemical signals

What is absorptive nutrition in fungi?

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

What is ergosterol?

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

Why can't antibiotics treat fungal infections?

Fungi are eukaryotes; antibiotics targeting prokaryotic structures do not affect them

What are the three main classes of antifungal drugs?

Azoles (Monistat), Allylamines (Lamisil), Amphotericin B (prescription only); all target ergosterol

What are mycoses?

Fungal diseases; examples include jock itch, athlete's foot, vaginal candidiasis, fungal nail infections

What is mucormycosis?

A severe fungal infection that occurs almost exclusively in immunocompromised patients

What are the main pathogens causing viral outbreaks in swimming pools?

Adenovirus, enterovirus, norovirus, hepatitis A; mostly enteric viruses

What percentage of viral waterborne outbreaks occur in swimming pools?

48% in pools; 40% in lakes/ponds; 12% in other water sources

What is the main cause of pool-related outbreaks?

Failure in disinfection; inadequate or inconsistent chlorine levels

What are refugia in pool microbiology?

Protected microenvironments (biofilms, filters) where microbes survive disinfection and re-emerge

What are indicator organisms in pool water?

Staphylococcus aureus and Enterococcus faecalis; their presence indicates human contamination

Why is cultivation not the best way to count microbes in water?

No universal growth medium exists; not all microbes grow on plates; gives a severe undercount

What is epifluorescence microscopy?

A direct-count method using fluorescent DNA stains and light from above; counts all microbes including unculturable ones

What is DAPI?

A fluorescent DNA stain used since ~1977 for direct microbial counts; non-specific, can stain debris

What is SYBR Green I / SYBR Gold?

Cleaner fluorescent DNA stains used since 1997; standard for counting bacteria and viruses in water

How do you calculate bacterial counts from epifluorescence microscopy?

Count particles per field, back-calculate to total filter area, divide by volume filtered

What is the bacterial density in Cayuga Lake?

10 to 100 million cells per milliliter

Why do inland lakes have more bacteria than the open ocean?

More organic matter (food) supports higher bacterial growth

Is sweat itself odorous?

No; sweat is nearly odorless; bacteria metabolize it into VOCs that cause body odor

What are the three types of sweat glands?

Apocrine (hairy regions, main BO source), Eccrine (cooling), Sebaceous (sebum oil)

Why do apocrine glands cause body odor?

They secrete oily fluid into hairy regions at puberty; bacteria metabolize it into smelly VOCs

What bacterium produces the main armpit odor compound 3M3SH?

Staphylococcus hominis; 3M3SH smells like rotten onions or meat

What VOCs does Corynebacterium produce?

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

What causes smelly feet?

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

What is the difference between a deodorant and an antiperspirant?

Deodorant kills bacteria or masks odor; antiperspirant blocks sweat glands using aluminum chloride

What are extrinsic skin microbiome factors?

Hygiene, diet, climate, sunlight, chemical exposure, physical activity, air/water pollution

What are intrinsic skin microbiome factors?

Age, genetics, pigmentation, gender, immunity, hormones, sleep, stress, metabolism

Why does more soap not always mean less body odor?

Over-washing removes beneficial bacteria and disrupts the healthy skin microbiome

Can microbial VOCs be used to detect disease?

Yes; certain diseases produce characteristic VOC profiles in breath and skin

What are the 8 most common STIs?

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

What bacterium causes syphilis?

Treponema pallidum

What bacterium causes chlamydia?

Chlamydia trachomatis

What type of bacterium is Treponema pallidum?

A spirochaete; spiral-shaped, gram-negative, with endoflagella; can be anaerobic or microaerophilic

What are the size characteristics of T. pallidum?

0.1 to 0.2 um diameter, 6 to 20 um long; invisible under light microscopy; requires electron microscopy

What is T. pallidum's genome size and what does it lack?

1.1 million base pairs; lacks genes for enzyme cofactors, fatty acids, and nucleosides; obligate pathogen

What are the three stages of syphilis?

Primary (painless chancre), Secondary (rash on palms/soles, systemic symptoms), Tertiary (severe systemic damage)

What are symptoms of secondary syphilis?

Rash on palms and soles, warts, bald spots, fever, swollen lymph nodes, weight loss, nerve/eye/kidney damage

Why is syphilis still prevalent despite being curable?

Stigma, lack of testing, and healthcare barriers keep it spreading

How does T. pallidum enter the body?

Through small skin breaks; reaches lymph nodes within hours causing systemic infection

Why is chlamydia so easily spread?

Most infections are asymptomatic; people spread it without knowing they have it

How does Chlamydia trachomatis evade the immune system?

It is an intracellular pathogen; hides inside host cells to establish chronic infection

What is the microbial ecology of the bedroom?

S. hominis, S. epidermidis (skin), HSV and HPV (viral), C. trachomatis (bacterial STI)

What is a virus?

DNA or RNA inside a protein capsid, sometimes with a lipid envelope; 20 to 500 nm; obligate intracellular parasite

Why can't viruses replicate on their own?

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

Why are viruses invisible under a standard light microscope?

At 20 to 500 nm they are smaller than the wavelength of visible light (400 to 700 nm)

What is a capsid?

The protein shell that surrounds a virus's genetic material

What is a viral envelope?

A lipid membrane acquired from the host cell during viral budding

What is the difference between enveloped and non-enveloped viruses?

Enveloped: lipid membrane, destroyed by soap. Non-enveloped: protein capsid only, more environmentally resistant

What is the Baltimore classification system?

A system categorizing viruses by genome type and how they produce mRNA; not based on common ancestry

What is viral tropism?

A virus's ability to infect only specific cell types based on receptor compatibility

What cells does HIV infect?

CD4+ T helper cells (T immune cells)

What cells does HPV infect?

Skin and mucosal keratinocytes

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; a dsDNA Group I virus with 150+ types; infects skin and mucosal cells; most common STI

What are high-risk HPV types and what do they cause?

Types 16 and 18; cause cervical, oropharyngeal, anal, vulvar, vaginal, and penile cancers

What are low-risk HPV types and what do they cause?

Types 6 and 11; cause genital warts

Why is HPV so stealthy?

No viremia, no cell death, no inflammation during initial infection; immune system barely triggered

How does HPV cause warts?

Infected basal cells extend out of the skin in massive growth, facilitating viral spread

What cancers does HPV cause?

Oropharyngeal, cervical, anal, vulvar, vaginal, and penile cancers

What is oncogenesis?

The process by which an oncovirus causes cancer by stimulating cell proliferation and suppressing immunity

What is Gardasil and how does it work?

HPV vaccine (2006); targets capsid proteins L1 and L2; only works before exposure

Who should get the HPV vaccine?

Women and men aged 9 to 26; MSMs under 26; must be given before exposure

What is HSV?

Herpes Simplex Virus; large dsDNA virus (120 to 250 kbp, 70 to 150 genes) with glycolipid envelope; HSV-1 (cold sores), HSV-2 (genital herpes)

What viruses are related to HSV?

Epstein-Barr virus, Cytomegalovirus, Varicella (chicken pox/shingles)

What is herpes gladiatorum?

HSV-1 transmitted between wrestlers via skin-to-skin contact; 34% infection rate at one high school wrestling camp

How does human skin act as a viral barrier?

Outer layer is dead non-dividing cells; viruses like HPV need abrasions to reach dividing basal cells underneath

What is antiretroviral therapy (ART)?

Drug treatment that suppresses HIV replication; does not cure it because the virus hides in a latent reservoir

What is influenza A's genome?

8 negative-sense single-stranded RNA segments; 10 genes; 13.5 kb total

What do H and N stand for in influenza classification?

H = Hemagglutinin (attachment); N = Neuraminidase (release of new virions)

How many types of H and N proteins exist?

18 H types and 11 N types

What is the function of hemagglutinin (H)?

Binds sugar molecules on lung cell surfaces; determines tissue tropism

What is the function of neuraminidase (N)?

Cleaves sugars on the host cell surface to release newly made virions

Why is influenza A a respiratory pathogen?

H binds sugars abundant on lung cells but scarce elsewhere

What is antigenic drift?

Small mutations of 2 to 3 amino acids in H or N; slight immune evasion; reason for annual flu vaccine updates

What is antigenic shift?

Genome reassortment between human and animal flu strains in a co-infected host; produces a completely new virus with pandemic potential

What is the difference between antigenic drift and shift?

Drift is slow gradual mutation (seasonal flu); shift is sudden genome reshuffling (pandemic risk)