Fall 2020: Investigating Microbial Communities
9
Different metrics.
BIT 477/577 Fall 2020 Students
Module Learning Objectives (MOs)
- MO 3.1. Define alpha and beta diversity.
- MO 3.2. Explain three different diversity metrics.
- MO 3.3. Identify and describe the limitations and assumptions of certain diversity metrics.
Alpha Diversity: Species richness (how many different species are present in one sample) and species evenness (whether any species dominate). This measure ignores how closely related species are. Consider Rarefaction- Did the sequencing go deep enough?
Beta Diversity: The comparison of species between environments. To measure the overall change between samples from different systems or environmental conditions.
I know we’re not calculating diversity by hand, but I found this video helpful to visualize what the 0-1 diversity score actually means! https://www.youtube.com/watch?v=wELXzETjRM0
Here is a graph from my thesis project that shows the Shannon Index in response to the application of two nitrification inhibitors using soils of low pH (LpH) and optimum pH (OpH). V and I refer to soil with the two inhibitors, the control is soil without anything added, nitrogen is soil with N fertilizer, and N-V and N-I refer to soil with an inhibitor and N fertilizer. It is interesting to learn about the Shannon Index and other diversity indexes as they are definitely important in soil microbiology and I was not too familiar with what the indexes actually mean. For my project specifically, I thought that it was interesting that my control samples had the highest Shannon Index. This suggests that under high nitrogen conditions, certain nitrifying species are able to outcompete others while a nitrification inhibitor suppresses these species, leading to a low Shannon Index value.
This is a little off-topic, but as a wet-lab biologist trying to understand bioinformatics, I can get lost in the jargon. I don’t think I am alone in that! I know it scares many of my colleagues away from working to understand it (so many acronyms. Help!). Here is a link to a quick compilation of some common metagenomics terminology. https://campylobacter.fbns.ncsu.edu/2016/11/18/know-your-lingo-microbiome-and-metagenomic-article-terminology/
I found a cool poster discussing MetaBat1 that has some overview figures: http://jgi.doe.gov/wp-content/uploads/2013/11/Kang_JGIUM-14-Poster-w-Title-Page.pdf
You may find a really nice paper published in Frontiers about rarefaction and alpha diversity. In this paper, it is proposed that we should use estimates of diversity that account for unobserved species and to also use measurement error models to compare diversity across ecosystems. https://www.frontiersin.org/articles/10.3389/fmicb.2019.02407/full
I found this video very helpful in providing an explanation on how normalized abundance is used when an algorithm is binning contigs. https://www.youtube.com/watch?v=zmZvlNglAU0&feature=emb_title
When I was doing my project I found this link really helpful to understand the metrics of alpha and beta diversity!
How many different species are present in one sample
whether any species dominate