Alpha Diversity Metric

What is Alpha Diversity?

Alpha Diversity (alpha-diversity) is a measure of the diversity of species within a local ecological community or sample. In microbiome research, it quantifies how many different types of microorganisms are present in a single sample and how evenly they are distributed.

Key Components

Alpha diversity combines two aspects:

1. Richness: The number of different species (or taxa) present

   • Higher richness = more different types of organisms

2. Evenness: How equally abundant the different species are

   • Higher evenness = species have similar abundances
   • Lower evenness = one or a few species dominate

Common Alpha Diversity Metrics

Species Richness (Observed)

• Definition: Simple count of observed species/taxa
• Formula: Number of unique species detected
• Use: Basic measure of diversity
• Limitation: Doesn't account for evenness

Shannon Index (Shannon-Wiener)

• Definition: Measures both richness and evenness
• Range: 0 to infinity (higher = more diverse)
• Properties: More sensitive to rare species
• Formula: H' = -sum(pi * ln(pi))
  • p_i = proportion of species i

Simpson Index

• Definition: Probability that two randomly selected individuals belong to different species
• Range: 0 to 1 (higher = more diverse)
• Properties: More sensitive to common/dominant species
• Inverse Simpson: 1/D (higher = more diverse)

Chao1 Index

• Definition: Estimates total species richness including undetected species
• Use: Accounts for rare species that may have been missed
• Application: Good for comparing sampling completeness

ACE (Abundance Coverage Estimator)

• Definition: Species richness estimator based on abundance data
• Use: Similar to Chao1, useful for incomplete sampling

Faith's PD (Phylogenetic Diversity)

• Definition: Sum of branch lengths of phylogenetic tree connecting all species
• Use: Incorporates evolutionary relationships
• Value: Accounts for genetic relatedness between species

Interpreting Alpha Diversity Values

High Alpha Diversity

• Indicates: Healthy, resilient ecosystem
• Characteristics: Many species, relatively even distribution
• Examples: Healthy gut microbiome, diverse environmental samples

Low Alpha Diversity

• Indicates: Stressed, disturbed, or specialized ecosystem
• Characteristics: Few species, or one or a few dominant species
• Examples: Dysbiotic gut (disease), antibiotic treatment, polluted environments

Typical Values

Values vary by sample type and sequencing method:
- Human Gut: Shannon 2.5-4.0 (healthy), <2.5 (dysbiosis)
- Soil: Much higher diversity (Shannon 4-8)
- Aquatic: Variable depending on environment

Factors Affecting Alpha Diversity

Biological Factors

• Health Status: Disease often reduces diversity
• Age: Diversity changes with age
• Diet: Different diets promote different microbial communities
• Geography: Location influences microbial exposure

Technical Factors

• Sequencing Depth: Deeper sequencing detects more rare species
• Sampling Method: How sample collected affects results
• DNA Extraction: Efficiency varies by method
• Amplification Bias: PCR preferentially amplifies some taxa

Alpha Diversity in CMMI-DCC

In the CMMI Data Coordinating Center:

• Microbiome Studies: Alpha diversity is calculated for each sample
• Comparisons: Diversity compared across:
  • Cohorts (disease vs. healthy)
  • Sample types (stool vs. oral)
  • Time points (longitudinal studies)
  • Treatment groups
• Metrics Used: Shannon, Simpson, Chao1, Observed species
• Visualization: Box plots, violin plots to show distributions

Alpha vs. Beta Diversity

• Alpha Diversity: Within-sample diversity (how diverse is THIS sample?)
• Beta Diversity: Between-sample diversity (how different are samples FROM EACH OTHER?)

Both are important for understanding microbial ecology.

Related Terms

• Microbiome: Community of microorganisms being analyzed
• Sample Type: Biological material (stool, saliva, skin)
• Beta Diversity: Comparison of diversity between samples
• Taxonomic Profiling: Identification of microbial types

Common Applications

• Health Assessment: Low diversity often indicates disease
• Treatment Monitoring: How interventions affect microbial communities
• Ecosystem Health: Environmental quality assessment
• Probiotic Studies: Do probiotics increase diversity?

Limitations

1. Sequencing Depth: Rare species may be undetected
2. Taxonomic Resolution: Varies by gene region (16S vs. shotgun)
3. Database Dependence: Identification limited by reference databases
4. No Functional Info: Diversity metrics don't indicate what microbes are doing

References

• Microbial diversity measurement and interpretation
• Alpha diversity indices and their applications
• Microbiome diversity and human health