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The Use and Types of Alpha-Diversity Metrics in Microbial NGS

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Alpha diversity (α-diversity) is defined as the mean diversity of species in different sites or habitats within a local scale. This term was coined by Robert Harding Whittaker along with other connected terminologies such as beta diversity (β-diversity) and gamma diversity (γ-diversity). Summarizing and comparing alpha diversity is considered as a ubiquitous approach in analyzing community surveys because there are many perturbations that can affect the alpha diversity. In terms of microbial ecology, analyzing the alpha diversity of amplicon sequencing data is known to be the common first step in assessing differences between microbial environments.

Species richness, which the count of the number of species or operational taxonomic units (OTUs) present in an area, is the simplest measure of alpha diversity. But there are many other metrics or indices which consider the abundance or frequencies of the OTUs. Most of the time, the abundance of distribution is noticeable when using an octave plot. Alpha diversity has been given different definitions by several ecologists. And these various definitions might be influenced by different assumptions of species diversity. This is the reason why most researchers have been utilizing more than one index of diversity. Some of the common alpha diversity indices are the following: (1) Chao Index, (2) Simpson Index, (3) Shannon Index, (4) ACE Index, and (5) Good's Coverage Index.

Chao Index

Chao index has two types: Chao 1 and Chao 2. Chao 1 is an estimator based on abundance; thus, it requires data that refers to the abundance of individual samples belonging to a certain class. On the other hand, Chao 2 is an estimator based on the incidence; thus, it requires data that specifies the absence or presence of a species in a sample. Chao's index for estimation of species richness is given by the equation: The Use and Types of Alpha-Diversity Metrics in Microbial NGS.

Simpson Index

Simpson index is the measure of the degree of concentration when individuals are classified into types. This was introduced by Edward H. Simpson in the year 1949. Simpson index is equal to the probability of the two entities taken at random from the dataset of interest represent the same type, or The Use and Types of Alpha-Diversity Metrics in Microbial NGS.

Shannon Index

The Shannon index, also known as Shannon's diversity index or Shannon entropy, is one of the popular diversity indices in the ecological literature. The idea of this metric is that the more different letters present, and the more equal their proportional abundances in the string of interest, the more difficult it is to predict which letter will be the next one in the string. It is calculated by the following equation: The Use and Types of Alpha-Diversity Metrics in Microbial NGS. Shannon's diversity index quantifies the uncertainty in predicting the species identity of an individual that is taken at random from the dataset.

ACE Index

Abundance-based coverage estimators (ACE) index is a diversity metric that involves an arbitrary abundance threshold to label Sabun as the number of abundant taxa, Srare as the number of rare taxa. It is calculated by the following equation: The Use and Types of Alpha-Diversity Metrics in Microbial NGS. Basically, this equation inflates the number of rare taxa and inflates again the number of taxa with abundance 1.

Good's Coverage Index

The Good's Coverage Index is another alpha diversity estimator which is calculated by the following equation: The Use and Types of Alpha-Diversity Metrics in Microbial NGS, where F1 is the number of singleton OTUs, and N is the total number of individuals or the sum of abundances for all OTUs.

References

  1. Chao, A., & Chiu, C. Species Richness: Estimation and Comparison. Wiley StatsRef: Statistics Reference Online, 2016, 1-26.
  2. Thukral, A. K. A review on measurement of Alpha diversity in biology (2017). Agricultural Research Journal, 2017, 54(1), 1.
* For research use only. Not for use in diagnostic procedures or clinical purposes.

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