Microbiology Taxonomy, Microbiota, and Infectious Diseases Concepts
Sterilization and infection control basics
Sterilizing instruments before use on patients and between patients; decontaminating surfaces. This helps to decrease transmission of infectious agents between the health care provider and the patient and between patients, reducing infection and disease incidence.
Taxonomy and binomial nomenclature
Taxonomy: groupings of organisms by shared features. Major idea: eight taxonomic rankings from domain to species; mnemonic example: domain, kingdom, phylum, class, order, family, genus, species (domain to species).
For microorganisms, there are eight rankings, but the key lower levels are domain, genus, and species. The broader levels above domain are less critical for lab naming but important for classification.
Binomial nomenclature uses only the bottom two parts of the pyramid: genus and species (two names).
Genus (first name): capitalized and italicized; species (second name): lowercase and italicized. In practice, after the first full mention, the genus is abbreviated (e.g., Escherichia coli becomes E coli in subsequent references).
Examples (as described):
Streptococcus kyogenes, also described as the base strep, causes flesh‑eating disease and strep throat. (Note: the transcript contains a likely misrendering of “Streptococcus pyogenes.” The point is to connect phenotype/disease to the name.)
Vibrio cholerae is a curved, vibrio‑shaped organism that causes cholera.
Staphylococcus epidermidis forms grape‑like clusters; “epidermidis” refers to its human skin location.
Neisseria gonorrhoeae is associated with gonorrhea; historically linked to its discoverer (Meisser in transcript).
Cellular microbes are organized into taxonomic groups based on shared characteristics, including whether they are prokaryotes or eukaryotes, morphology (size, shape, arrangement), distinguishing physiologic features, growth requirements, and staining characteristics; today, genetics also drives reclassification.
Prokaryotes vs. Eukaryotes and basic delineations
The first delineation is whether a cell is unicellular/multicellular and whether it has a nucleus (prokaryote vs. eukaryote).
If eukaryotic:
It is one of: animal, plant, fungus, or protist.
If prokaryotic:
It is either bacteria or archaea.
If bacteria, classification proceeds to genus and species; a classic example is Clostridium tetani, the organism that causes tetanus.
Extra point: looks can be deceiving; Gram‑stain appearance alone can be misleading about relatedness. Example from transcript: two organisms (Bacteroides and E. coli) can both be gram‑negative rods, yet have only ~40% genetic identity, illustrating that phenotypic similarity does not always reflect genomic relatedness.
Species, strains, and genetic/phenotypic definitions
Species (eukaryotes): groups of organisms that are genetically and phenotypically similar and that can naturally reproduce to yield fertile offspring.
Prokaryotic species: defined by multiple factors (phenotype, physiology, genomic markers); reproduction is largely clonal rather than sexual, so species delineation relies on a combination of characteristics.
Strain: genetic variant within the same species; mutations and horizontal gene transfer create subtypes.
Examples:
Escherichia coli K‑12 (lab strain).
Escherichia coli O157:H7 (pathogenic strain; serotype information indicates host interactions and virulence factors).
Host–microbe interactions are a key part of this topic: there is a host and a microbe (the microbe is the organism; the host is the human or other organism).
Host–microbe interactions: symbiosis and examples
Symbiotic relationships when two or more organisms are closely connected:
Mutualism: both microbe and host benefit (e.g., E. coli in the colon provides vitamin K and aids digestion; the host provides shelter and nutrients).
Commensalism: microbe benefits; host experiences no perceived benefit or cost.
Parasitism: microbe benefits; host is harmed (infection/disease).
Important terminology:
A pathogen is a microbe with the potential to cause disease.
An infection is the invasion and multiplication of pathogens within a host. It can occur after introduction of a microbe or when a microbe appears in a site where it should not normally reside (e.g., E. coli in the urinary tract).
An infection does not always resolve as disease, and an infectious host can transmit the pathogen without showing symptoms.
The term pathogen includes organisms capable of causing disease; parasites are often used for organisms that cause disease in a typical host (distinction between pathogen vs parasite is contextual).
Microbiota and microbiome
The microbiota is the collective community of microorganisms that reside in and on the human body.
It includes bacteria, archaea, viruses, and eukaryotic microbes.
There are roughly 5–10 times more microbial cells in and on the human body than human cells, making us largely microbial in number; estimates often cited around this ratio.
The human body mass contains several pounds of microbial mass (transcript mentions about 6–7 pounds).
The microbiome is the microbiota plus all their associated genetic material and gene products within the environment.
The human host and its microbiota function as a metaorganism; many physiological processes depend on this relationship.
Initial colonization begins at birth and is shaped by delivery mode (vaginal vs. cesarean) and feeding, with lifelong development and evolution of the microbiota.
The microbiota plays critical roles in health and disease: training the immune system, producing nutrients and vitamins, aiding digestion, and protecting against pathogens (crowding out pathogens; “no free campsites”).
Broadly, microbiota affect the gut–brain axis, influencing mood, brain function, and disease risk.
Normal microbiota are typically location‑specific and mostly harmless or beneficial; they are often commensals or mutualists.
Some normal microbiota can include potential pathogens (e.g., Staphylococcus aureus is carried asymptomatically by about a quarter of healthy adults on skin or nasal passages).
The skin barrier is a major defense; breaches (cuts, abrasions) can allow pathogens to enter and cause infections such as MRSA.
Microbiota research is rapidly expanding, linking microbiota to health, disease, and physiology; ongoing work aims at interventional microbiota modifications for therapy.
Dysbiosis, eubiosis, and health implications
Dysbiosis: disruptions to the normal microbiota that can increase disease risk.
Eubiosis: a healthy, balanced microbiota state.
Antibiotics can disrupt microbiota broadly, sometimes eliminating beneficial bacteria and allowing opportunistic pathogens to flourish (e.g., antibiotic treatment for sinusitis can cause gut perturbation and diarrhea; antibiotics for urinary tract infections can lead to yeast infections).
Dysbiosis is associated with various health issues: obesity, irritable bowel syndrome (IBS), liver disease, susceptibility to infections, diabetes, and other conditions; some studies report strong associations between dysbiosis profiles and health outcomes.
Antibiotic therapy is a major factor in microbiota disruption due to broad, non‑specific killing of bacteria throughout the body, not just the target pathogen.
The concept of dysbiosis emphasizes the ecological nature of human microbiota and its systemic effects on health.
Infectious disease terminology and pathogen taxonomy
Terminology:
Pathogen: a microbe with the potential to cause disease.
Infection: invasion and multiplication of pathogens in a host; can occur with or without disease symptoms.
Disease: impairment of body function due to infection.
Pathogen classifications:
True pathogens: cause disease in healthy individuals; do not require a weakened host (e.g., influenza virus, SARS‑CoV‑2).
Opportunistic pathogens: cause disease when host defenses are weakened or when they gain access to normally sterile sites (e.g., reactivation of varicella‑zoster virus; E. coli causing urinary tract infection when introduced into the urinary tract).
Emerging pathogens: newly appeared or identified in a population (e.g., SARS‑CoV‑2, West Nile virus, Zika virus).
Zoonotic pathogens: infectious diseases that spread from animals to humans (rabies, Salmonella, Lyme disease, SARS‑CoV‑2).
Reemerging pathogens: previously known pathogens that have resurged due to changes in humans, environments, or microbes (e.g., drug resistance, vaccine gaps, climate factors).
The broad classification mentioned in the transcript emphasizes true pathogens, opportunistic pathogens, emerging pathogens, and reemerging pathogens.
Examples from the transcript:
Influenza virus and SARS‑CoV‑2 as true pathogens.
SARS, MERS, Zika, West Nile as examples of emerging or related pathogens.
Measles as a reemerging disease in some contexts due to gaps in vaccination.
Cholera, Ebola as diseases with shifting epidemiology due to environmental and societal factors.
Transmission terminology and disease dynamics
Transmission and communicability: some pathogens are highly communicable and transmissible, especially respiratory pathogens that spread via the air.
Nontransmissible diseases: caused by organisms that do not typically spread from person to person (e.g., toxins, environmental exposures) or organisms that do not establish infection in humans.
Dead‑end or incidental hosts: infections that may infect an organism but do not transmit onward to other hosts.
Endemic infections: constantly detected within a population at a baseline level (e.g., common cold, some zoonoses).
Sporadic infections: infrequent or isolated cases.
Epidemic (outbreak): a sudden, local or regional increase in cases beyond what is expected.
Pandemic: a widespread epidemic affecting multiple countries or continents with a large number of people.
SARS‑CoV‑2 pandemic: historical progression (as described in the transcript)
2020 timeline (example in transcript):
Initial sporadic infections in Hunan, China.
Within one month, reported in 28 countries across continents.
Within two weeks after that, 66 countries affected.
By March, 165 countries affected; pandemic officially declared in March 2020.
The transcript presents a visual history of pandemics, illustrating relative impact by country count and time.
Influenza pandemics and other historical events are noted (e.g., Measles, Cholera, Ebola) to illustrate how infectious diseases wax and wane with changing conditions and interventions.
Active vs passive infections (infections terminology)
Infections can be categorized by how they present in hosts:
Active infection: ongoing replication and clinical signs/symptoms.
Passive infection: infection without active replication/signs in the host (contextual framing in the transcript; details not fully elaborated in the excerpt).
Miscellaneous notes and practical implications
“Looks can be deceiving”: phenotypic similarity (e.g., Gram staining) does not always reflect genetic relatedness; molecular/genomic analysis can reveal substantial differences.
Normal microbiota are location‑dependent and generally beneficial, yet they can include potential pathogens; disruption of barrier protections (e.g., skin) can permit infection.
The microbiome’s influence extends beyond digestion and immunity to neurodevelopment and mental health via the gut–brain axis; this is a rapidly expanding area of study.
When writing lab reports, observe binomial nomenclature conventions: Genus name is capitalized and italicized; species name is lowercase and italicized; abbreviate the genus after first mention (e.g., Escherichia coli → E coli in subsequent mentions).
The relationships between hosts and microbes are complex and dynamic, spanning mutualism, commensalism, and parasitism, and are influenced by genetics, environment, antibiotics, and lifestyle.
In health care, understanding taxonomy, microbiota, and infectious disease terminology informs infection control, diagnosis, treatment, and prevention strategies.
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