The Human Microbiota and Microbiome

Microbiota

Definition: Community of microorganisms living on and inside your body, including bacteria, fungi, viruses, and archaea. These organisms help digestion, immunity, and protection against harmful microbes.
Example: Gut bacteria help digest fiber.
Microbiology link: Normal flora maintains body balance.

Microbiome

Definition: All the genetic material inside the microbes living in your body. Your microbiome contains far more genes than your own human genome.
Example: Gut microbes code for enzymes humans do not have.
Microbiology link: Genetic potential controls metabolic power.

Genotype

Definition: The genetic code an organism carries. It determines what a microbe is capable of doing.
Example: Resistance genes in bacteria.
Microbiology link: Defines potential.

Phenotype

Definition: How genes actually show up in behavior and function. Influenced by environment.
Example: Same bacteria act differently inside the gut vs outside.
Microbiology link: Environment controls expression.

Gene Expression

Definition: Process where DNA is turned into RNA, proteins, and metabolites that perform work in the body.
Example: Microbes change enzyme output after antibiotics.
Microbiology link: DNA → RNA → protein → function.

Human Microbiome Project

Definition: Research project mapping microbes across body sites. Showed each site has its own community.
Example: Vaginal microbiota differs from skin and gut.
Microbiology link: Body sites host unique ecosystems.

Skin Microbiota

Definition: Microbes living on skin protect against pathogens and maintain acidity.
Example: Staphylococcus epidermidis blocks invaders.
Microbiology link: Competitive exclusion.

Oral Microbiota

Definition: Diverse community in mouth forming biofilms. Helps regulate pH and prevent disease.
Example: Tooth decay from imbalance.
Microbiology link: Biofilm dynamics.

Respiratory Microbiota

Definition: Microbes in nose and lungs that shape immune defense.
Example: Staph in nostrils without symptoms.
Microbiology link: Colonization resistance.

Vaginal Microbiota

Definition: Lactobacillus-dominated ecosystem producing acid to prevent infection.
Example: Yeast overgrowth when disrupted.
Microbiology link: pH control.

Urethral Microbiota

Definition: Low-density community that helps block pathogens.
Example: UTIs when E. coli overgrows.
Microbiology link: Entry defense.

Gut Microbiota

Definition: Largest and most diverse microbiota system involved in digestion, vitamin synthesis, and immunity.
Example: Fiber digestion to SCFAs.
Microbiology link: Metabolic engine.

SCFAs

Definition: Fatty acids made by gut microorganisms that reduce inflammation and strengthen intestinal lining.
Example: Butyrate supports colon cells.
Microbiology link: Host-microbe metabolism.

Bacteriocins

Definition: Antimicrobial proteins produced by good bacteria to kill competitors.
Example: Gut bacteria suppress pathogens.
Microbiology link: Microbial warfare.

Gut Vitamins

Definition: Vitamins produced by microbes including K and B family.
Example: Vitamin K for blood clotting.
Microbiology link: Nutrient synthesis.

Gut–Brain Axis

Definition: Communication between intestinal microbes and the brain using chemicals and nerves.
Example: Stress changes gut symptoms.
Microbiology link: Neuroactive metabolites.

Dysbiosis

Definition: Disrupted microbiota with harmful overgrowth and loss of diversity.
Example: Diarrhea after antibiotics.
Microbiology link: Ecosystem collapse.

Eubiosis

Definition: Balanced, healthy microbiota.
Example: Strong digestion and immunity.
Microbiology link: Homeostasis.

Pathobionts

Definition: Normally harmless microbes that become dangerous when balance is lost.
Example: Certain gut Proteobacteria.
Microbiology link: Conditional virulence.

Diet Effect

Definition: Food determines microbiota makeup. Fiber increases good bacteria.
Example: Western diet leads to dysbiosis.
Microbiology link: Substrate control.

Antibiotic Impact

Definition: Remove many normal gut microbes along with the target pathogen. Your gut loses balance, so harmful species grow without competition.

Example: C. difficile overgrows after broad antibiotics. Toxins irritate the colon and trigger diarrhea.

Microbiology link: Create strong selective pressure. Resistant microbes survive and multiply, which raises infection risk.

Probiotics

Definition: Live beneficial microbes taken as treatment.
Example: Lactobacillus supplements.
Microbiology link: Restoration tool.

Prebiotics

Definition: Non-digestible fibers that feed healthy bacteria.
Example: Inulin.
Microbiology link: Microbe nutrition.

Synbiotics

Definition: Combination of probiotics and prebiotics.
Example: Reinforcement of gut flora.
Microbiology link: Synergistic therapy.

FMT

Definition: Transfer of stool from a healthy donor to repopulate microbiota.
Example: Treating recurrent C. difficile.
Microbiology link: Whole-ecosystem repair.