Microbiome Summary

Introduction to the Microbiome

Key Definitions

• Microbiome: A community of microorganisms, their genetic content, and interactions within a defined environment.

• Microbiota: A community of microorganisms within a defined environment.

• Human Microbiome: All microorganisms found on and in the human body.

  • Comprises 30-40 trillion cells and 2-20 million genes.

• Human Microbiota: Microorganisms naturally found within a defined environment (normal microbiota).

  • Also known as endogenous microorganisms.

Microbiota Composition and Location

• Endogenous Communities:

  • Oral cavity: $1 \times 10^9$ cells/cm in the mouth, $1 \times 10^8$ cells/ml in saliva.

  • Skin: $1 \times 10^6$ cells/cm (general), $10^7$ cells/cm (armpit/groin).

  • GI Tract: $10^{1-3}$ cells/g (stomach), $10^{3-4}$ cells/g (jejunum), $10^8$ cells/g (ileum), $10^{11-13}$ cells/g (colon).

• "Sterile" Sites (0 cells/cm):

  • Eyes, brain, circulatory system, liver, kidneys, lower respiratory tract.

Microorganism Types

• Endogenous Microorganisms: Normally found within a defined environment.

  • Can cause disease with bad hygiene, acquired virulence, different host, if immunocompromised, or broken barrier.

• Exogenous Microorganisms: Introduced from the external world.

Microorganism Classifications

• Commensal Microorganisms: Live on or within a host, deriving benefits without causing harm.

• Pathogenic Microorganisms: Infect a host, causing disease and/or damage, regardless of immune status.

• Opportunistic Microorganisms: May infect a host when specific conditions are met.

Dominant Phyla in Human Microbiota

• Firmicutes

• Bacteroidetes

• Actinobacteria

• Beta-Proteobacteria

• Gamma-Proteobacteria

• Epsilon-proteobacteria

Factors Influencing Microbiota Composition

• Microorganisms vary significantly between body sites due to differing environmental conditions.

• Oral microbiota differs based on microenvironment and saliva composition.

• Gastrointestinal microbiota varies along its length, influenced by pH, oxygen levels, and nutrient availability.

• Urogenital microbiota varies by anatomical site and is influenced by pH and hormonal fluctuations.

• Skin microbiota differs depending on skin type (sebaceous, dry, moist).

Dynamics of Human Microbiota

• The human microbiota is not static and is influenced by:

  • Innate Factors: Birth, genetics, immune system

  • Environmental Factors: Feeding type, vaccines, antibiotics, infections, siblings, daycare, hygiene, smoking, season

Microbiota Diversity

• A stable balance with a diverse group of microorganisms contributes to homeostasis.

• Less diversity with an imbalance can disrupt homeostasis.

Microbiota and Host Metabolism

• Gut microbiota is key to the metabolism and absorption of nutrients.

• Gut microbiota composition is altered during obesity, with an increase in Firmicutes and Actinobacteria, and a decrease in Bacteroidetes.

Virome

• A community of viruses, their genetic content, and interactions within a defined environment.