Microbiome basics

• Eukaryotes include Animalia, Plantae, Protista, and Fungi.
• Prokaryotes include Bacteria and Archaea.
• Eukaryotes possess a distinct nucleus and membrane-bound organelles, unlike prokaryotes.
• A habitat is a specific site where an organism grows.
• A microbial community refers to the collection of microorganisms in a particular habitat.
• Microbiota is the complete collection of microorganisms within a microbial community.
• A microbiome consists of the microbiota and all its associated genes.
• Metagenome refers to the total genomic DNA of all organisms in a community.
• Biofilm is a cluster of microorganisms adhering to each other, like plaque biofilm.

Importance of the Human Microbiome

• The human microbiome is crucial for health, with specific microorganisms protecting against disease and pathogenic bacteria.
• Microbial genes within the microbiome modulate fundamental human physiological processes, such as metabolism.
• Changes in the composition of the microbiome are linked to diseases like obesity.

Approaches to Studying the Microbiome

• Two primary approaches exist for studying the microbiome: the Traditional Culture (TC) Approach and the New Molecular (NM) Approach.

Traditional Culture Approach

• This involves directly growing microbes from a sample.
• TC approach is cheap.
• TC approach is labor-intensive.
• TC approach only allows for basic species discrimination.
• TC approach requires prior knowledge of expected species to establish suitable growth conditions.

New Molecular Approach

• This reveals what microorganisms are present, not just those that can be cultured.
• NM approach identifies which genes are present.
• NM approach offers higher discriminatory power for species identification.
• NM approach may have sequence bias due to primer specificity.
• NM approach is expensive, time-consuming, and computationally demanding.

Discriminating Bacteria Genera

• The Bacterial 16S rRNA gene, a 1542 bp gene, is targeted to discriminate bacteria genera.
• Variable regions within the 16S rRNA gene enable discrimination of bacterial genera.
• The process involves DNA extraction, library preparation using PCR, sequencing, and interpretation.

Shotgun Metagenomics

• A process where entire genes are sequenced, covering all kingdoms.
• Shotgun metagenomics can identify variants and polymorphisms.
• Shotgun metagenomics provides functional insights into the genes.

Interesting Genes in Microbiomes

• Virulence Genes: Contribute to the pathogenicity of an organism.
• Resistance Genes: Induce antibiotic resistance.
• Diagnostic Markers: Assist in the rapid diagnosis of disease.
• Genes for biotechnology applications: Involved in novel production processes.

Dynamics and Determinants of the Microbiome

• The human microbiome undergoes significant changes in the first three years of life.
• The primary determinant of a microbiome's composition is the individual.

Microbiome of Specific Body Sites

• Stomach: Contains Helicobacter pylori, associated with gastritis, ulcers, and stomach cancer.
• Small Intestine: Contains Streptococcus and Lactobacillus.
• Colon/Large Intestine: Predominantly contains anaerobic bacteria.

Skin Microbiome

• Microbes are sparse on exposed skin areas and highly populated in protected areas, such as the groin, between toes, and around orifices.
• Two main principle species are Propionibacterium acnes (related to acne) and Malassezi furfur (related to dandruff).

Oral Microbiome

• Saliva is the main representative for oral microbiome studies.
• Salivary bacteria associated with a healthy oral microbiota include Streptococcus, Peptostreptococcus, Actinomyces, and Lactobacillus.
• Fusobacterium is associated with gingivitis.
• Prevotella and Porphyromonas are associated with periodontitis.
• Gram-negative anaerobic species appear and dominate, which leads to periodontitis.

Dysbiosis

• An imbalance in microbiota caused by malnutrition, antibiotic consumption, or infection.
• Dysbiosis leads to infectious and non-infectious diseases.

Importance of Post-Genomic Microbiology Research in Dentistry

• It can lead to a greater understanding of dental diseases.
• It can lead to improved diagnosis.
• It can lead to novel antimicrobial drugs.