Microbiology Lecture: Microbiome, Viruses, Pathogenicity, and Innate Immunity

Vocabulary flashcards summarizing crucial microbiology terms on the human microbiome, virology, mechanisms of pathogenicity, and innate immune defenses.

Microbiome

The collection of all microorganisms and their genetic material living in and on the human body.

Necrobiome

Microbial community that participates in decomposition after death, used to estimate post-mortem intervals.

Cesarean (C-section) Colonization

Initial infant microbiota dominated by skin and hospital microbes such as Staphylococcus after surgical delivery.

Vaginal Birth Colonization

Newborn microbiota obtained primarily from the mother's vaginal and intestinal flora, rich in Lactobacillus species.

Breastfed Infant Microbiota

Gut community enriched with beneficial Bifidobacteria transferred through breast milk.

Bottle-fed Infant Microbiota

More diverse gut flora that may include potentially pathogenic species compared with breast-fed infants.

Clostridioides difficile (C. diff)

Opportunistic bacterium that overgrows after antibiotic use, causing severe colitis.

Fecal Microbiota Transplant (FMT)

Therapeutic transfer of stool from a healthy donor to restore normal gut flora, often for recurrent C. diff infections.

Sterile Body Sites

Anatomical locations normally free of microbes, e.g., blood, cerebrospinal fluid, internal organs, lower respiratory tract, bladder.

Non-Sterile Body Sites

Areas routinely hosting normal microbiota, such as skin, mouth, gastrointestinal tract, upper respiratory tract, vagina, and urethra.

Virus

Genetic material (DNA or RNA) enclosed in a protein coat that requires a host cell to replicate.

Virion

A complete, infectious viral particle outside a host cell.

Viroid

Small, circular RNA molecule lacking a protein coat that infects plants.

Prion

Misfolded protein capable of inducing abnormal folding of normal proteins, causing neurodegenerative diseases.

Enveloped Virus

Virus possessing a lipid membrane with embedded glycoprotein spikes surrounding the capsid.

Non-enveloped Virus

Virus consisting only of nucleic acid and a protein capsid, without a lipid envelope.

Bacteriophage

Virus that infects bacteria, featuring a head, tail sheath, and tail fibers for attachment.

Capsid

Protein coat surrounding the viral genome, composed of capsomeres.

Glycoprotein Spikes

Surface proteins on enveloped viruses that mediate attachment to host cell receptors.

Plaque Assay

Method to quantify bacteriophages by counting clear zones of lysis on a bacterial lawn.

Lytic Cycle

Viral replication pathway that results in host cell lysis and release of progeny virions.

Lysogenic Cycle

Viral life cycle in which phage DNA integrates into the host genome as a prophage and remains dormant.

Prophage

Phage genome integrated into bacterial DNA during the lysogenic cycle.

Uncoating

Process in which an animal virus removes its capsid to release nucleic acid inside the host cell.

Attachment (Adsorption)

Initial viral step where virion binds specific receptors on the host cell surface.

Penetration

Entry of virus or its genome into the host cell.

Biosynthesis

Stage in which viral components are produced using host machinery.

Maturation

Assembly of viral components into complete virions.

Release

Exit of new virions from the host cell by lysis or budding.

Endocytosis (Viral Entry)

Host cell engulfment of an animal virus within a vesicle.

Fusion (Viral Entry)

Merging of an enveloped viral membrane with the host cell membrane to deliver the nucleocapsid.

Budding

Process by which enveloped viruses acquire their membrane and exit the host cell without immediate lysis.

Influenza Virus

Enveloped RNA virus with segmented genome; undergoes antigenic drift and shift.

HIV

Retrovirus targeting CD4 T cells, causing persistent infection and AIDS.

Herpesviruses

Family of DNA viruses capable of establishing latent infections (e.g., HSV, VZV).

Human Papillomavirus (HPV)

Non-enveloped DNA virus associated with oncogenic transformation and cervical cancer.

Antigenic Drift

Gradual accumulation of point mutations in viral genes, leading to seasonal variation.

Antigenic Shift

Abrupt reassortment of segmented viral genomes, potentially producing pandemic strains.

Retrovirus

RNA virus that uses reverse transcriptase to synthesize DNA from its RNA genome.

Pathogen

Microorganism capable of causing disease.

Pathogenicity

Ability of a microorganism to cause disease.

Virulence

Degree or severity of pathogenicity of a microbe.

Vector

Living organism that transmits pathogens from one host to another, e.g., mosquitoes.

Reservoir

Natural habitat where a pathogen normally lives and multiplies.

Fomite

Inanimate object that indirectly transmits pathogens between hosts.

Incubation Period

Time between pathogen entry and appearance of first symptoms.

Prodromal Period

Short stage of mild, nonspecific symptoms following incubation.

Illness Stage

Phase where disease signs and symptoms peak.

Decline Stage

Period of diminishing symptoms as the immune system overcomes the pathogen.

Convalescence

Recovery phase when the body returns to normal after infection.

Direct Contact Transmission

Spread of pathogens through physical person-to-person contact.

Indirect Contact Transmission

Pathogen spread via contaminated fomites.

Droplet Transmission

Spread of infectious agents in respiratory droplets traveling short distances.

Vehicle Transmission

Spread through contaminated water, food, or air.

Vector Transmission

Disease spread by insects or arthropods.

Mechanical Vector

Arthropod carries pathogen on body surfaces without infection (e.g., fly feet).

Biological Vector

Arthropod in which the pathogen multiplies before transmission (e.g., mosquito).

Common-Source Epidemic

Outbreak in which all cases arise from exposure to a single contaminated source.

Host-to-Host Epidemic

Disease spread from person to person over time.

Adhesin

Microbial surface molecule that binds specific host receptors to facilitate adherence.

Fimbriae

Hair-like bacterial appendages used for attachment to surfaces.

Capsule

Polysaccharide layer surrounding bacteria that inhibits phagocytosis.

Coagulase

Bacterial enzyme that forms fibrin clots to shield microbes from immune attack.

Streptokinase

Bacterial enzyme that dissolves fibrin clots, aiding spread through tissues.

Hyaluronidase

Enzyme that degrades connective-tissue hyaluronic acid, promoting invasion.

Exotoxin

Potent, secreted bacterial protein toxin with specific cellular targets.

Endotoxin

Lipopolysaccharide (LPS) component of Gram-negative outer membrane that triggers inflammation.

A-B Toxin

Two-part exotoxin: B subunit binds host cell; A subunit exerts enzymatic damage.

Cytolytic Toxin

Exotoxin that disrupts host cell membranes, causing lysis.

Superantigen

Exotoxin that overstimulates T cells, leading to massive cytokine release.

Enterotoxin

Exotoxin acting on intestinal mucosa, causing diarrhea and vomiting.

Antigenic Variation

Strategy whereby pathogens alter surface antigens to evade immune detection.

M Protein

Streptococcal cell wall protein that resists phagocytosis and aids adherence.

Mycolic Acid

Wax-like lipid in Mycobacterium cell walls that impedes immune recognition.

Innate Immunity

Non-specific, immediate defense mechanisms present from birth.

Adaptive Immunity

Specific immune response involving lymphocytes and immunological memory.

First Line of Defense

Physical and chemical barriers preventing pathogen entry, e.g., skin, mucous membranes.

Second Line of Defense

Internal innate mechanisms such as phagocytes, inflammation, fever, complement, and interferons.

Physical Barrier

Structural blockade like intact skin that prevents microbial invasion.

Chemical Barrier

Antimicrobial substances (lysozyme, stomach acid, defensins) that inhibit pathogens.

Phagocyte

White blood cell (e.g., neutrophil, macrophage) that engulfs and destroys microbes.

Natural Killer (NK) Cell

Innate lymphocyte that kills virus-infected and tumor cells without prior sensitization.

Inflammation

Localized tissue response to injury or infection characterized by redness, heat, swelling, and pain.

Fever

Systemic rise in body temperature that enhances immune function and inhibits pathogens.

Interferon

Cytokine produced by virus-infected cells that inhibits viral replication in neighboring cells.

Complement System

Plasma protein cascade that opsonizes microbes, promotes inflammation, and forms membrane attack complexes.

Defensin

Small antimicrobial peptide that disrupts microbial membranes.

Lysozyme

Enzyme in tears, saliva, and mucus that breaks down bacterial cell walls.