Human Microbiome

Collection of genomes of all the microorganisms found in a particular environment

Collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa, & viruses) that live inside/on the human body.

Metagenome

Collection of human & microbial cells & genes = blend of human & microbial traits

Commensal coexists without harming humans & Mutualistic means they both benefit

Founded in 2007 by the NIH, a research initiative to improve understanding of human microbiota for health & disease by characterizing the human microbiome & analyze its role in human health & disease

Sequencing the genome of the human microbiota specifically in the skin, mouth, nose, digestive tract, & vagina

Bacteria (>200)

Normal microflora, commensals, & indigenous microbiota

Genetics, age, sex, stress, diet, antibiotics/drugs, & environmental conditions

Resident - Fixed, established at a given age & area, & can reestablish if disturbed. Transient - Non-pathogenic/potentially pathogenic, inhibits skin or mucous membranes for hours-weeks, doesn't produce disease, & derived from the environment

Can be washed from external surfaces by bathing, not able to compete with resident microbes &can be killed by their substances, can't survive in acidic/alkaline conditions, & may be flushed away by bodily secretions

Skin, eyes (conjunctiva), nose (resp. tract), oral cavity, ears, genitourinary tract, & alimentary canal

Propionibacterium acne, staphylococcus epidermidis, staphylococcus aureus, diphtheroids, candida, mycobacterium smegmatis, etc.

Staphylococcus epidermidis, commensol neisseria, propoinibacterium acnes, etc.

Streptococcus viridans, lactobacilli, staphylococcus aureus, trichomonas, etc.

Staphylococcus epidermidis, corynebacteria spp, staphylococcus aureus, etc.

Non-hemolytic streptococci, alpha-hemolytic streptococci, streptococcus pneumoniae, neisseria meningitidis, etc.

Usually sterile, but can become infected from nasopharynx pathogens such as H. influenza or S. pneumoniae

Bifidobacteria

Enterobacteriaceae, enterococci, bacteroides, staphylococci, lactobacilli, & clostridia

Bacteroides, enterococci, lactobacilli, clostridia, & enterics

1. Synthesize & excrete vitamins. 2. Prevent colonization by pathogens by competing for attachment sites or essential nutrients. 3. Antagonize other bacteria through prod. of substances that kill/inhibit non-indigenous species. 4. Stim. prod. of cross-reactive antibodies. 5. Stim. development of immune system in newborns. 6. Stop/suppress entry of pathogens

The immunocompromised normal flora can overgrow = pathogenic. Dental caries, plaque, gingivitis, etc. Dental manipulation - oral streptococci can cause rheumatic fever. When substances that can be mistaken are ingested the Normal flora may cause confusion when diagnosing

Blood, brain, muscle, & CSF

Infectious pathogen that's normally commensal but can cause disease when the host's resistance is altered. Low resistance can be caused bc of HIV, genetic factors, leukopenia, or aging

Hospital settings

Administering immunosuppressants, advanced HIV, chemotherapy, damage of the skin (surgeries), or antibiotic intake disrupting the normal flora in the body

Impaired immunity, surgeries & instrumentation, broad spectrum antibiotic administration, or damage of an organ or system

Kaposi's sarcoma

AIDS & cancer patients

Candidiasis - mouth, throat, foot, & vagina. Cryptococcosis - brain & spinal cord. Pneumocystis pneumonia - lungs.

Cytomegalovirus - eyes, lungs, brains, & guts. PML - brain.

Cryptosporidiosis - gut. Toxoplasmosis - brain.

Mycobacterium avium complex - gut, lung, & skin

Mycobacterium tuberculosis - lung, heart, liver, & brain

True pathogens cause disease in healthy individuals & asso. with specific & reasonable diseases while opportunistic pathogens cause disease in immunocompromised & gain access/injury to sterile regions

Salmonella typhi, yersinia pestis, haemophilus influenzae, bordatella pertussis, shigella dysentriae, klebsiella pneumoniae, etc.

Pseudomonas aeruginosa - candida, acinetobacter baumanii, proteus vulgaris, enterobacter, etc.

Attach to host cells for colonization, evade host's innate & adaptive immune defenses to persist, obtain nutrients essential for growth to multiply, disseminate/spread within a host & other hosts (critical for species survival), & produce symptoms of disease in the host in order to be pathogenic

Components or structure of microorganism that helps in establishment of disease or infection

Virulence factors must overcome host's defense mechanisms

Attachment factors/adhesins, anti-phagocytic factors, spreading factors & enzymes, & toxins = exo/endotoxins

Capsules

Blood clotting

Pore forming cytotoxin that attacks WBCs by targeting phagocytes, NKCs, dendritic cells, & T lymphocytes

Bacteria from phagocytosis by releasing & rupturing lysosomes. Ex: S. aureus - LukED & leukocidin AB

A cytotoxic protein that causes lysis of RBCs by disturbing cell membrane & liberates hemoglobin

Secretes hemolysins that cause the incomplete lysis of RBCs

Secretes hemolysins that cause the complete lysis of RBCs

Protect the bacterium from phagocytosis & isolate it from other defenses of the host. Makes bacteria more virulent

Mixed with the drug to help spread the drug throughout a body tissue

Host collagenases destroy extracellular structures in the pathogenesis of bacteria. Bacterial collagenases allow bacteria to breakdown protein to invade the host.

Clostridium perfrinogens - gas gangrene

Bacteria invade the tissues, grow, & reproduce

Bacteria produce certain potent effective toxins which cause disease & symptoms of disease

State caused by toxins entering the bloodstream of the host

Lipopolysaccharides (LPS)

AB toxins, specific host site exotoxins, membrane disrupting exotoxins, & super antigen

Some gram pos & neg, protein location = secreted from cell & gene location = plasmid or bacteriophage, high toxicity, highly antigenic (antitoxins), vaccine from toxoids, & heat labile

Toxins prod. by S. aureus, bacillus cereus, streptococcus pyogenes, b. anthracis, & c. tetani

Most gram neg & listeria, protein location = part of cell/LPS that fragments off & gene location = bacterial chromosomes, low toxicity, poorly antigenic, no vaccine, & heat stable

Gram neg pathogens such as Escherichia coli, salmonella, shigella, pseudomonas, & neisseria

B portion binds to the receptors & A portion can cause toxicity

Type of AB toxin that affects the specific regions of the host such as neurotoxins affects CNS, enterotoxins affects intestines, & general cells or tissues are affected by cytotoxins

Type of AB toxin, but they act together by disrupting host cell membranes e.g., hemolysis, phospholipases

Unusual bacterial toxins that triggers T cells (T4 Lymphocytes) to release cytokines - bind to surface of target cell but don't enter

B subunit binds to the target cell & allows A subunit to enter the cell

They're degraded into epitopes, bind to peptide groove of MHC-II molecules, & are put on surface of the APC

Secretion of excessive amounts of IL-2 & activation of self-reactive T-Lymphocytes

Fever, nausea, vomitting, diarrhea, & malaise. Excess stim. leads to prod. of inflammatory cytokines like TNF-alpha, IL-1, inflammatory chemokines like IL-8, & platelet-activating factor (PAF) = shock & multiple organ system failure

Staphylococcal enterotoxins - food poisoning. Staphylococcal toxic shock toxin (TSST-1) - toxic shock syndrome. Staphylococcal exfoliating toxins - scalded skin syndrome. Staphylococcal pyrogenic exotoxins (exotoxin A & B) - shock.

Toxins produced by Staphylococcal aureus. Asso. with cuts or burns on skin, recent surgery, using contraceptive sponges, diaphragms, tampons/menstrual cups, or a viral infection like the flu or chickenpox

High fever, vomiting or diarrhea, redness around eyes & vagina, sunburn rash, low bp, headache, & muscle pain. Complications = shock, renal failure, or death

Reinfection is infection by the same organism in a host after recovery while superinfection is before recovery

Infection at localized site prod. general effects

Infections acquired within a hospital

State of health or adverse effect caused by medical treatment

Exo infections are pathogens enter the body from outside environment via contaminated device, healthcare worker, surface, or other vector. Endo infections are pathogens present on/in host itself without prior symptoms

Dysentery, cholera, influenza, & covid-19

Periodontal diseases, aspiration pneumonitis, & bacterial vaginosis