Bioinformatics 101: Alpha Diversity

Bioinformatics 101: Alpha Diversity

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What is Alpha Diversity?

The notion of alpha diversity pertains to the quantity of species within a specific ecological domain. It is commonly associated with diversity within habitats, signifying the range of species present in a particular sample, irrespective of other samples.

Please refer to our article Bioinformatics 101: Microbiome Diversity Analysis for more information.

CD Genomics not only conducts comprehensive microbial amplicon sequencing but also offers advanced metagenome sequencing data analysis. Our services assist clients in meticulous species classification, precise determination of species abundance, and the unveiling of intricate interrelationships between environmental factors and microbial communities.

Our analytical approach goes beyond standard amplicon alpha diversity and beta diversity analysis. We provide valuable insights into environmental species composition and abundance.

Alpha Diversity Indices

In the realm of environmental microbiology research, various statistically analyzed indices are commonly employed to quantify alpha diversity. These indices fall into distinct categories:

Richness: Species Richness (S)

This metric, denoted as the number of observed species (OTU count), serves as a biased estimate of true species richness. The observed value increases non-linearly with sampling, requiring consistent sample sizes for species number comparisons. Regardless of species abundance, a higher Species Richness (S) value signifies a more diverse array of species in the sample.

  • Chao1: An index utilizing the Chao1 algorithm, initially proposed by Chao, estimates the number of OTUs in a sample. A larger Chao1 value corresponds to a greater number of species.
  • ACE: Another index by Chao, ACE estimates OTUs in a community. Differing from the Chao1 algorithm, ACE is commonly used in ecology to estimate the total species count.

Please refer to our article Operational Taxonomic Units (OTUs) Clustering Step by Step for more information.

Richness and Evenness

Various indices such as the Shannon index, Simpson index, Dominance, and PD whole tree in α-diversity synthesize species richness and evenness in the community. When species richness is equal, higher evenness among species results in greater community diversity.

  • Shannon-Wiener: Describing disorder and uncertainty in individual species occurrences, this index incorporates both richness and evenness. Increased species and even distribution boost diversity.
  • Simpson: Estimating microbial diversity, Simpson's index reflects the likelihood of randomly sampling a different species. A higher Simpson diversity index signifies increased community diversity.
  • PD_whole_tree: Based on phylogenetic trees, this diversity index constructs distances using representative sequences of OTUs. Summing up branch lengths yields a value where higher values indicate greater community diversity.

Assessment of Intergroup Disparities in Diversity Indices

Utilizing alpha diversity parameters derived from resampling each sample, the analysis of intergroup differences in alpha diversity indices is conducted. Box plots are employed to visually represent the median, dispersion, maximum, minimum, and outliers of species diversity within each group. Simultaneously, statistical tests, including the T-test, Wilcoxon rank-sum test, and Tukey's test (T-test and Wilcoxon rank-sum test for comparisons involving two groups, while Tukey's test and Wilcoxon rank-sum test for those involving more than two groups), are employed to ascertain the presence of significant differences in diversity indices among distinct groups.

Dilution Curve

In the construction of a dilution curve, a subset of sequences is randomly chosen from a sample, and the count of species (i.e., Operational Taxonomic Units or OTUs) or the diversity index of these sequences is tallied. The resulting curve is created by plotting the number of sequences on the horizontal axis against the number of species or diversity index on the vertical axis.

The position on the horizontal axis corresponding to the endpoint of the extended curve represents the number of sequences sequenced for that specific sample. In the case of the observed_species index, which characterizes the actual number of observed species, a plateau in the curve indicates sufficient sequencing data. This plateau suggests that additional data would yield only a marginal increase in new species (i.e., OTUs), while a declining curve suggests the potential for discovering more species with continued sequencing efforts. For other diversity indices, such as Shannon curves, a flat curve implies that the amount of sequencing data is substantial enough to capture the majority of microbial diversity present in the sample.

Rank-Abundance Curve

The construction of a Rank-Abundance Curve involves ranking Operational Taxonomic Units (OTUs) in a sample based on their relative abundance or the number of sequences they encompass. The corresponding rank number of OTUs is then assigned as the horizontal coordinate, while the vertical coordinate represents the relative abundance of OTUs or the relative percentage of sequences within each ranked OTU. Connecting these points with a broken line results in the visualization of the Rank-Abundance curve.

This curve serves to depict two key facets of sample diversity: abundance and homogeneity of species. Species richness is portrayed by the length of the curve along the horizontal axis—wider curves signify a richer species composition. Meanwhile, the uniformity of species composition is represented by the shape of the curve; flatter curves denote a more even distribution of species within the sample.

* For Research Use Only. Not for use in diagnostic procedures.
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