microbiomes_micro5

Microbiomes Overview

• Definition: Microbiomes refer to all the microorganisms in a particular environment, including bacteria, viruses, fungi, and archaea.

  • Example Locations: Soil, water, plants, and the human gut.

• Sources: Nayfach et al., 2020.

Learning Goals

• Define microbiomes.

• Describe techniques for studying microbiomes and their benefits.

• Understand the normal microbiome and common locations on the body.

• Identify how the human microbiome benefits its host.

• Discuss the role of the human microbiome in disease.

Identifying Microbiomes

Traditional Methods

• Culture Bacteria: The classic approach for identifying bacteria.

  • Limitations: Not all bacteria can be cultured in a lab setting, leading to incomplete microbiome profiling.

Modern Approaches

• Sequencing Technologies: Essential for identifying microbes present in environments where traditional culturing fails.

  • Considerations:

    • Cost and Time: Sequencing the entire genome is expensive and slow, often requiring only a portion of the genome (for example, a specific gene).

Sample Preparation

• Example Technique: Collecting human saliva to gather DNA from both human and bacterial cells.

• PCR Amplification:

  • Amplify human DNA to study genetics (e.g., PV92 locus).

  • Amplify bacterial DNA to study the oral microbiome (e.g., 16S rRNA gene).

• Outcome: Sufficient DNA obtained for sequencing both human and bacterial DNA.

Highly Conserved Sequences

• Definition: Highly conserved sequences are those that remain unchanged over evolutionary timescales.

• Importance: Useful for tracing evolutionary relationships among organisms.

• Related Questions: What biological processes are considered highly conserved in different organisms?

Phylogenetic Trees

• Understanding Evolution Trees: How to read and interpret the evolutionary relationships between species.

  • Example Species: Fish, birds, humans, rats, and mice.

  • Common Ancestors: Each branch represents a speciation event in evolutionary history.

16S rRNA Gene Sequencing

• Role of the 16S rRNA Gene: Critical for identifying and classifying microorganisms.

  • More similar sequences between organisms indicate closer evolutionary relationships.

• Sequence Examples: Differences and similarities in the 16S rRNA gene sequences for various organisms.

Microbial Distribution in the Human Microbiome

• Common Locations:

  • Mouth: Various bacteria (e.g., Streptococcus, Neisseria).

  • Skin: Diverse microbial populations (e.g., Staphylococcus, Corynebacterium).

  • Stomach & Intestines: Major contributors to digestion (e.g., Helicobacter, Lactobacillus).

  • Urogenital Tract: Notable species (e.g., Corynebacterium).

Understanding Normal Microbiota

Current Research Questions

• Definition and consistency of the 'normal microbiota' across individuals.

  • Variability exists even among healthy individuals (Wang et al., 2019).

Maintaining Normal Microbiome

• Fecal Transplants: Investigated as methods to restore disrupted microbiome communities (Kelly et al., 2015).

Microbial Interactions

Microbial Antagonism

• Concept: Normal microbiota can prevent pathogenic microbes' overgrowth.

  • Important for maintaining health by minimizing space for harmful microorganisms.

Microbial Functions

• Key Roles:

  • Digestion: Breaking down plant polysaccharides that humans cannot digest.

Factors Affecting the Human Microbiome

Environmental Influences

• Factors include temperature, pH, oxygen, salinity, sunlight, and nutrient availability.

Dietary Impact

• Host diet has a significant effect on microbiome composition.

  • Studies show differences in microbial compositions between individuals with varying diets (e.g., low-fat vs. high-sugar).

Genetics and Microbiome Similarity

• Twin Studies: Show microbiome similarities based on genetic relatedness.

  • Monozygotic Twins: Share 100% of their genome, leading to more similar microbiomes compared to dizygotic twins.

Probiotics and Their Effects

• Definition: Beneficial bacteria naturally occurring or supplementation to help maintain health.

  • Current research is ongoing regarding their efficacy in preventing conditions like eczema and dermatitis.

• Factors to Consider: Timing of administration, strain of bacteria used, and study size.

Coevolution with Human Hosts

• Definition: The impact of closely associated species on each other's evolution.

  • Example: Human proteins on tooth surfaces that bacteria recognize and attach to.