IDT Terms -- Sikora

Microorganism

A microscopic organism, including bacteria, fungi, viruses, and parasites. In pharmacy, microorganisms serve as both tools (manufacturing antibiotics, vaccines, vitamins) and threats (contamination, infection, resistance).

Recombinant DNA technology

Laboratory techniques for combining DNA from different sources to produce therapeutic products such as insulin, growth hormones, and monoclonal antibodies

Dextran

A polysaccharide produced by lactic acid bacteria during growth on sucrose. Used clinically in the treatment of iron deficiency anemia and as an anticoagulant.

Siderophore

An iron-chelating agent produced by microorganisms to scavenge iron from the environment. Relevant to pharmaceutical development of iron-binding therapeutics.

Streptomyces

A genus of Gram-positive, filamentous soil bacteria responsible for producing approximately 80% of antibiotics used in medicine, as well as chemotherapeutics (actinomycin D, doxorubicin), antivirals, antihypertensives, and immunosuppressants (tacrolimus).

Secondary metabolite

A compound produced by a microorganism that is not essential for its primary growth but has pharmacological activity. Examples include antibiotics, chemotherapeutics, and immunosuppressants produced by Streptomyces species.

Good Manufacturing Practice (GMP)

A system of regulatory standards ensuring that pharmaceutical products are consistently produced and controlled to quality standards appropriate for their intended use, including prevention of microbial contamination.

Etiological agent

The causative organism responsible for an infectious disease.

Pyrogenic reaction

A fever response triggered when microbial products (especially endotoxins) are introduced into the body, even in the absence of active infection. This is why endotoxin testing (LAL test) is required for parenteral drug products.

Endotoxin (Lipopolysaccharide, LPS)

A component of the outer membrane of Gram-negative bacteria. The lipid A portion triggers pyrogenic and inflammatory responses when introduced into the bloodstream.

Limulus Amebocyte Lysate (LAL) test

A quality control assay that detects endotoxin contamination in parenteral drug products and sterile medical devices. Uses a reagent derived from horseshoe crab blood cells.

Antibiotic resistance gene

A genetic element that enables bacteria to survive exposure to an antibiotic. These genes can transfer horizontally between bacterial species, spreading resistance even to organisms never directly exposed to the drug.

Horizontal gene transfer

The transfer of genetic material (including resistance genes) between bacteria through mechanisms other than parent-to-offspring inheritance (e.g., conjugation, transformation, transduction).

Antimicrobial stewardship

Coordinated strategies to optimize antimicrobial prescribing and use, with the goals of improving patient outcomes, reducing adverse events, and slowing the development of antimicrobial resistance. Pharmacists play a central role.

Disinfectant

A chemical agent or physical procedure that kills microorganisms on inanimate surfaces (countertops, equipment, floors). Too toxic for use on living tissue. Mnemonic: D = Dead surfaces.

Antiseptic

An agent that inhibits bacterial growth with sufficiently low toxicity that it can be applied directly to skin, mucous membranes, or wounds. Mnemonic: A = Alive (skin/mucosa).

Sterilant

An agent that kills both vegetative cells and bacterial spores when applied at appropriate times and temperatures. Represents the highest level of microbial kill. Mnemonic: S = Surgical-level kill (spores included).

Vegetative cell

An actively growing and metabolizing bacterial cell, as distinguished from a dormant spore. Most disinfectants and antiseptics can kill vegetative cells; only sterilants reliably kill spores.

Spore (bacterial endospore)

A dormant, highly resistant structure formed by certain bacteria (e.g., Clostridium, Bacillus) that can survive extreme heat, desiccation, and chemical exposure. Elimination requires sterilization-level treatment.

Chlorhexidine

An antiseptic commonly used for pre-surgical skin preparation. Preferred over povidone-iodine in many surgical settings because it provides longer residual antimicrobial activity on the skin.

Povidone-iodine

A broad-spectrum antiseptic used for wound cleansing and pre-surgical skin preparation. Has broader antimicrobial coverage than hydrogen peroxide but shorter residual activity than chlorhexidine.

Sodium hypochlorite

A disinfectant (dilute household bleach, typically 1:10 dilution) recommended by the CDC for decontaminating surfaces after blood spills involving HIV or hepatitis B risk. For use on surfaces only, never on skin.

Autoclave

A sterilization device that uses pressurized steam at 120°C for 30 minutes to kill both vegetative cells and spores. The gold standard for instrument sterilization.

Ethylene oxide

A chemical sterilant used for heat-sensitive medical instruments and devices that cannot withstand autoclave temperatures.

Glutaraldehyde

A chemical sterilant used as an alternative to ethylene oxide for high-level disinfection and sterilization of heat-sensitive instruments.

Minimal Inhibitory Concentration (MIC)

The lowest concentration of an antimicrobial compound that inhibits visible growth of a microorganism after overnight incubation. The primary value reported on clinical culture and susceptibility reports.

Minimal Bactericidal Concentration (MBC)

The lowest concentration of an antimicrobial that kills the organism, confirmed by subculturing onto antibiotic-free media and observing no growth. Clinically important for serious infections (endocarditis, meningitis) where bactericidal activity is required.

Broth dilution method

The reference standard method for determining MIC. Serial two-fold dilutions of an antibiotic are prepared in liquid growth medium, inoculated with a standardized bacterial suspension, incubated overnight, and inspected for visible growth.

Etest

A plastic strip containing a predefined antibiotic concentration gradient. When placed on an inoculated agar plate, bacterial growth is inhibited in an elliptical zone; the MIC is read where the zone edge intersects the strip.

Disc diffusion test

A susceptibility testing method in which antibiotic- impregnated paper discs are placed on an inoculated agar plate. After incubation, the diameter of the zone of inhibition around each disc indicates susceptibility or resistance.

Zone of inhibition

The clear area surrounding an antibiotic disc or Etest strip on an agar plate is where bacterial growth has been prevented. Larger zones generally indicate greater susceptibility.

Bacteriostatic

Describing an antimicrobial agent that inhibits bacterial growth without killing the organisms. Removal of the agent allows growth to resume. Relies on the patient’s immune system to eliminate the remaining bacteria.

Bactericidal

Describing an antimicrobial agent that kills bacteria, reducing viable cell counts over time. Preferred over bacteriostatic agents in immunocompromised patients and in serious infections where immune clearance may be insufficient.

Breakpoint

The MIC threshold established by standards organizations (e.g., CLSI) that defines whether a clinical isolate is classified as susceptible, intermediate, or resistant to a given antibiotic at standard dosing.

Ames Test

A screening assay that uses Salmonella histidine auxotroph strains to detect the mutagenic or carcinogenic potential of chemical compounds. Required by the FDA as part of drug safety evaluation.

Histidine auxotroph

A bacterial strain that has lost the ability to synthesize the amino acid histidine and therefore cannot grow on histidine-free media unless a reversion mutation restores that ability.

Deep rough mutant

A bacterium with a defective lipopolysaccharide (LPS) layer, resulting in an incomplete outer membrane. This increases permeability to large hydrophobic molecules, allowing test compounds to enter the cell more easily in the Ames test.

Reversion mutation (revertant)

A mutation that restores a previously lost gene function. In the Ames test, a reversion mutation converts a histidine-negative strain back to histidine-positive, enabling growth on histidine-free media.

S9 fraction (rat liver extract)

A metabolic activation system prepared from rat liver homogenate, added to the Ames test to simulate mammalian liver metabolism. Detects pro-mutagens that become mutagenic only after enzymatic conversion.

Pro-mutagen

A compound that is not mutagenic in its original form but becomes mutagenic after metabolic activation (e.g., by liver CYP450 enzymes). Detected in the Ames test only when the S9 fraction is included.

Microbiome

The collective genomes (all genes) of the microbial species in a given environment. When we sequence microbial communities, we are studying the microbiome.

Microbiota

The collection of living microorganisms (bacteria, fungi, viruses, archaea) inhabiting a specific environment, such as the human gut. Distinct from the microbiome, which refers to their genes.

Human Microbiome Project (HMP)

In NIH initiative (2007–2016) that used genomic and metagenomic sequencing to build a comprehensive reference map of the human microbiome in healthy individuals. Sampled 15 body sites in men and 18 in women. Continued as the Integrative HMP (2014–2016), investigating microbiome changes in IBD, prediabetes, and preterm birth.

16S rRNA sequencing

A DNA-based method for identifying bacterial species by sequencing the 16S ribosomal RNA gene, which varies between species. Acts as a molecular barcode for bacteria. Replaced culture-based methods as the standard for cataloging microbial communities, including organisms that cannot be grown in the laboratory.

Metagenomic sequencing

A method that sequences all genetic material in a sample (not just 16S rRNA), providing information about the full gene content and functional potential of a microbial community.

Colonization (starting at neonatal)

The process by which microorganisms establish themselves

in a newborn. Influenced by mode of delivery: vaginal birth

exposes infants to maternal vaginal and fecal microbiota

(Lactobacillus, Prevotella), while cesarean delivery results in

colonization by skin and hospital environment bacteria

(Staphylococcus, Corynebacterium). Further shaped by

breastfeeding, which provides oligosaccharides that

selectively feed Bifidobacterium. The microbiome stabilizes to

an adult-like pattern by age 2–3.

Microbial diversity

The variety of different microbial species present in a given environment. In the human body, the gut has the highest diversity, the skin has moderate diversity, and the healthy vaginal microbiome has relatively low diversity (dominated by Lactobacillus). Loss of diversity is associated with disease.

Short-chain fatty acids (SCFAs)

Metabolic products (acetate, propionate, butyrate) generated by gut bacteria from dietary fiber fermentation. SCFAs fuel colonocytes, support drug absorption, maintain GI health, and regulate inflammation. Considered the metabolic currency of the gut microbiome.

Butyrate

A short-chain fatty acid that is the primary energy source for colonocytes (cells lining the colon). Produced by bacterial fermentation of dietary fiber. Supports gut barrier integrity and has anti-inflammatory properties.

Colonization resistance

The ability of the resident healthy microbiota to prevent colonization by pathogenic organisms. Mechanisms include competition for nutrients, secretion of antimicrobial compounds, and immune activation. Disrupted by broad-spectrum antibiotics, increasing susceptibility to infections such as Clostridioides difficile (C. diff).

Eubiosis

A state of healthy, balanced microbiota composition. Associated with intact intestinal mucous membrane protection, proper immune stimulation, efficient digestion, and vitamin synthesis.

Dysbiosis

An imbalance in the composition or function of the microbiota. Associated with damage to the intestinal epithelium, production of toxic metabolites (ammonia, biogenic amines), weakened immunity, and linked to conditions including IBD, obesity, diabetes, Alzheimer’s disease, RA, and cancer.

Tight junctions

Protein complexes between adjacent epithelial cells that seal the gut lining and regulate what passes between cells. A healthy microbiome strengthens tight junctions; disruption increases intestinal permeability.

Intestinal permeability

The degree to which substances can pass through the gut wall. Increased permeability can result from NSAID use, dysbiosis, or disease states (IBD), allowing bacteria and toxins to cross the epithelial barrier.

Small Intestinal Bacterial Overgrowth (SIBO)

A condition in which excessive bacteria accumulate in the small intestine, causing bloating, diarrhea, and malabsorption. Can be triggered by PPIs (which raise gastric pH) or motility disorders. Treated with non-absorbable antibiotics such as rifaximin.

Pharmacomicrobiomics

The study of how the human microbiome influences drug disposition, action, and toxicity. Examples: Eggerthella lenta inactivates digoxin; Enterococcus faecalis converts levodopa before absorption; colonic bacteria activate the prodrug sulfasalazine; Akkermansia abundance correlates with anti-PD-1 immunotherapy response.

Eggerthella lenta

A gut bacterium that inactivates digoxin in the GI tract, reducing its bioavailability. Clinically relevant: digoxin levels should be monitored in patients with GI changes or concurrent antibiotic use.

Azoreductase

A bacterial enzyme produced by colonic anaerobes that cleaves azo bonds. Required to convert the prodrug sulfasalazine into its active component, 5-aminosalicylic acid (5-ASA). Antibiotic use can reduce this activation.

Akkermansia muciniphila

A gut bacterium whose higher abundance is associated with improved response to anti-PD-1 checkpoint inhibitor immunotherapy (e.g., nivolumab) in cancer patients. Antibiotic use before immunotherapy may reduce this bacterium and thereby reduce treatment efficacy.

Inflammatory Bowel Disease (IBD)

A group of chronic inflammatory conditions of the GI tract, including Crohn’s disease and ulcerative colitis. Associated with significant loss of microbial diversity. Treatment increasingly includes microbiome restoration (probiotics, prebiotics, fecal transplants) in addition to immune suppression.

Crohn’s disease

A form of IBD characterized by transmural (full-thickness)

inflammation, most commonly affecting the ileum. Features include cobblestone mucosal appearance, fissures, muscle hypertrophy, fat wrapping, and profound loss of microbial diversity.

Ulcerative colitis

A form of IBD limited to the colon, characterized by disruption of colon-resident bacteria (e.g., Bacteroides), thinning of the mucus barrier, and mucosal ulceration. May benefit from butyrate supplementation and fecal microbiota transplantation.

Prebiotic

A non-digestible food ingredient (typically dietary fiber or oligosaccharides) that selectively promotes the growth or activity of beneficial gut bacteria. Examples include inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS).

Probiotic

A live microorganism that, when administered in adequate amounts. Characteristics include acid and bile stability, adherence to intestinal cells, persistence in the GI tract, production of antimicrobial substances, antagonism against pathogens, safety in clinical use, and clinically validated health effects.

Important: a probiotic does not have to be of human origin (e.g., Saccharomyces boulardii is a yeast), and the most critical requirement is safety Examples: Lactobacillus rhamnosus GG, Bifidobacterium infantis 35624, Saccharomyces boulardii.

Synbiotic

A product combining a prebiotic and a probiotic, designed to deliver live beneficial organisms together with a substrate that supports their growth in the gut.

Saccharomyces boulardii

A non-pathogenic yeast with the best-studied evidence for preventing antibiotic-associated diarrhea and as adjunct therapy for recurrent C. diff infection. Brand name: Florastor®. Demonstrates that effective probiotics do not have to be of human origin.

Lactobacillus rhamnosus GG

A probiotic bacterial strain with strong evidence for treating acute infectious diarrhea in children and moderate evidence for preventing antibiotic-associated diarrhea in adults. Brand name: Culturelle®.

Bifidobacterium infantis 35624

A probiotic strain with moderate evidence for improving global symptoms of irritable bowel syndrome (IBS).

USP Verified Mark

A certification from the United States Pharmacopeia indicating that a dietary supplement or probiotic product has been independently tested and verified for identity, potency, purity, and dissolution. Recommended as a quality indicator when counseling patients on probiotic selection.

Fecal Microbiota Transplantation (FMT)

The infusion of processed fecal material from a healthy donor into the GI tract of a recipient, with the goal of restoring a healthy microbial community. Primary indication: recurrent C. diff infection. Routes include colonoscopy, enema, nasogastric tube, and oral capsules.

Rebyota (fecal microbiota)

An FDA-approved live biotherapeutic product for recurrent C.diff infection. Administered rectally. One of the first regulated FMT-derived products.

Vowst / SER-109 (fecal microbiota spores )

An FDA-approved live biotherapeutic product for recurrent C. diff infection. Administered as oral capsules. Relevant to pharmacy dispensing practice as a prescription product.

Live biotherapeutic product

A biological product containing live organisms ( bacteria or bacterial spores) that is regulated by the FDA as a prescription therapeutic. Distinguished from dietary supplement probiotics by requiring clinical trial evidence and FDA approval. Examples: Rebyota, Vowst.

Extended-spectrum beta-lactamase (ESBL)

An enzyme produced by certain bacteria (e.g., E.coli) that confers resistance to most beta-lactam antibiotics. Relevant to FMT safety: that two immunocompromised patients received FMT containing ESBL-producing E. coli; one died. This led to mandatory donor screening for multidrug-resistant organisms.

Clostridioides difficile (C. difficile)

An anaerobic, spore-forming bacterium that colonizes the colon when normal microbiota is disrupted, most commonly by broad-spectrum antibiotics. Causes antibiotic-associated diarrhea and pseudomembranous colitis. Recurrent infection is the primary indication for FMT and FDA-approved live biotherapeutic products

Helicobacter pylori (H. Pylori)

A bacterium that colonizes the stomach and causes peptic ulcers and gastritis. Treated with triple therapy combining a PPI and two antibiotics.

Bacteroides

A genus of anaerobic bacteria that is a major component of the healthy colonic microbiota. Can cause abscesses and peritonitis if the gut barrier is breached. Requires anaerobic antibiotic coverage (e.g., metronidazole) in GI infections. Disrupted in ulcerative colitis.