Human Microbiota - Vocabulary Flashcards

A set of vocabulary flashcards covering key concepts about human microbiota and microbiome from the provided lecture notes.

Microbiota

The microbial populations living in and on a host; the collective community of microorganisms that inhabit a body.

Microbiome

All genetic material related to the microbiota; the combined genomes of all microbes in a given environment or host.

Metagenome

All genetic material found in a collected sample (e.g., tissue, water, soil), including microbial DNA.

Human Microbiome Project

A research initiative (2007–2014) that mapped the human-associated microbiota; thousands of samples were analyzed, identifying thousands of microbial species and viruses and shaping current understanding of bacterial populations.

Sterile body sites

Anatomical sites long considered free of microbes (e.g., blood, CSF, brain, heart, liver, spleen, kidneys, pancreas, lungs); modern methods show these sites can harbor very low levels of microbes.

Microbiota as an organ

The microbiota is regarded as an organ of the body, weighing about 1.5 kg and containing roughly 100 trillion cells, including bacteria, yeasts, viruses, and parasites.

Resident microbiota

Relatively fixed microorganisms regularly found at a given site; can reestablish after disturbance (e.g., E. coli in the gut).

Transient microbiota

Nonpathogenic or potential pathogens that inhabit body sites for hours to weeks; originate from the environment and may cause disease if resident microbiota is disturbed.

Dysbiosis

Imbalance between beneficial and harmful microbiota, linked to disease; associated with altered microbial metabolites and inflammatory mediators.

Probiotics

Live microorganisms that confer health benefits when given in adequate amounts; some species may be opportunistic pathogens.

Gut microbiota development

Fetus is usually sterile; newborns acquire microbes from mother and environment; colonization timing differs by birth mode; adults are dominated by Firmicutes, Bacteroidetes, and Actinobacteria; elderly show shifts in composition.

Dominant gut phyla

The six main bacterial phyla in the gut: Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, Fusobacteria.

Distribution of microbiota by body site

Estimated shares: GI tract 29%, Oral 26%, Skin 21%, Airways 14%, Blood 1%, Eye 0.3%, Urogenital 9%.

Stomach and small intestine counts

Stomach: about 10^1–10^3 CFU/mL; small intestine has lower counts overall, with counts increasing toward the colon.

Colon counts

Colon has the largest microbiota population: about 10^11–10^12 microbes per gram, predominantly anaerobes.

GI tract protective barriers

Stomach: low pH and digestive enzymes; Small intestine: low pH around 6 and bile; Large intestine: peristalsis, desquamation, and mucus.

Major gut bacteria groups

Anaerobes (e.g., Bacteroides, Fusobacterium, Eubacterium, Lactobacillus); coliforms (E. coli, Enterobacter, Klebsiella); Firmicutes; Archaea (methanogens); Fungi (Candida); Protozoa and numerous viruses.

Gut microbiota–host interaction

Microbiota contribute to defense, digestion, vitamin production, immune development, and can antagonize or compete with pathogens.

Healthy microbiota balance

A balanced microbiota features predominance of beneficial (probiotic) bacteria; pathogens comprise a smaller, controlled fraction.

Pathogens vs probiotics

Pathogens are disease-causing microbes; probiotics are beneficial microbes; some species can be opportunistic pathogens under certain conditions.

Skin microbiota

Skin is the largest organ; density ranges from 10^2–10^4 microbes/cm^2 on dry skin and ~10^6 on moist areas; major residents include Staphylococcus, Micrococcus, Corynebacterium; sebaceous glands harbor Propionibacterium; fungi like Pityrosporum and Candida.

Oral microbiota

Over 600 described species; major bacteria include Streptococcus, Neisseria, Staphylococcus, Fusobacterium, Lactobacillus, Bacteroides, Actinomyces, Eikenella; fungi such as Candida; dental plaque forms from oral microbes.

Dental plaque

An adherent dental deposit on teeth composed largely of bacteria from the oral microbiota; contributes to tooth decay when pathogenic species dominate.

Upper Respiratory Tract microbiota

Includes mouth, tonsils, nasopharynx, and throat; microbial population resembles the oral cavity; protected by mucus, lysozyme, and ciliated epithelium.

Lower Respiratory Tract microbiota

Trachea, bronchi, and lungs are not sterile in healthy people; microbial counts are low; cleared by ciliary action and alveolar macrophages; microaspiration can introduce microbes.

Gastrointestinal tract protective barriers

Stomach: acidic environment and enzymes; Small intestine: bile and modest pH; Colon: mucus, desquamation, and peristalsis help regulate microbes.

Female genital tract microbiota

Before puberty: neutral pH flora; reproductive-age: Lactobacilli predominate with acidic environment and cervical mucus protective factors; after menopause lactobacilli decline and diversity increases.

Eye microbiota (conjunctiva)

Conjunctiva hosts microbiota (e.g., Diphtheroids, S. epidermidis, nonhemolytic streptococci); tears deliver lysozyme for protection.

Blood and sterile sites reconsidered

Historically considered sterile; modern molecular methods detect microbial nucleic acids at very low levels, indicating these sites are not completely free of microbes.

Dysbiosis-associated metabolites

Dysbiosis can drive disease via microbial metabolites such as LPS, short-chain fatty acids, vitamin deficiencies, and inflammatory mediators.

Joining facts about body-microbe balance

Approximately 95% of body bacteria reside in the GI tract; microbes outnumber human cells by about 10:1; the GI tract surface is roughly 400 m^2 (about 2 tennis courts).