I am writing the result for my Master's thesis, but I am having a hard time understanding faith-pd concept. I am trying to find out whether there will be any difference on the soil microbial community structure
due to choice of different DNA extraction method and soil types. I have attached the figure here which is about the difference on faith-pd due to soil types. I want to know which soil has more community richness. For me it seems like Teller soil has. However, I do not know how to interpret the result for boxplot having long size and one with very short boxplot. Any help will be appreciated.
Thank you!
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Thank you for sharing these graphs. With quite a few soil types, and pretty good replicates for each, I think your Master's thesis is off to a good start!
Before we dive in to results, I have a few questions for you.
Did you run any other alpha diversity metrics? There are quite a few ways to measure this, so it might make sense to pick one that you understand well, or contrast the different results from different metrics. (If you need help choosing one, check out this guide.)
Do these 8 soil types come from large 'super-groups' like 'arid' vs 'tropical' or 'native' vs 'farmland'? While we can look at each soil individually, it would also be helpful to compare large groups of interest in this study.
Based on your literature review, what soil types would expect to have the highest alpha diversity values, and which ones would you expect to have the lowest?
(When you group your soils into 'super-group', which groups would expect to be the most and least diverse?)
All the graphs I can see mention soil type...
Can you edit your post to include the graphs comparing DNA extraction?
(While you are editing, you can remove the bottom section about "Is this post about a User Support Question ?")
Hello Colin,
Thank you for responding. For alpha diversity, I run both faith-pd and evenness group. However, I will focus on faith-pd only while writing my result. I mentioned faith pd only on both projects. This is one of my two projects of my master program. Do I need to inlcude evenness group result too, does that make a difference?
We collected these samples from eight different locations, but our prime concern is to include soil with diverse range which differ in pH, organic matter, etc.
We do not know which soil type will have high diversity, basically because we focus on soil characteristics rather than locations from where they were collected.
I compared efficiency of four different DNA extraction method. However, two of them were really poor enough for DNA sequencing so now we have only two methods available for comparison. I have attached the figure here.
I will be happy to provide you with any other essential documents if needed.
Thank you!
Urmila
You have some good high-level questions about how to interpret your data, @umanand.
Here are a couple videos on alpha diversity (brief concepts, tutorial/applied) that might help you build a framework for interpretation. For context, both are based on the Parkinson's Mouse tutorial.
Hi Chris,
Thank you so much for helping me out. I have watched these videos couple of times since I start using Qiime2. They are really awesome! But still I am not clear enough to tell my story. I really want to know what do these figures tell keeping p-value aside. I do not want to end up writing the result section focusing on what is statistically significant just looking at p-value. It would be really helpful if you could recommend me with some good papers so that I can interpret my results efficiently. One more question, what does that outlier really mean?
Thank you so much!
Urmila
Awesome! Interpretation of what your results mean may be your most valuable responsibility as a researcher, but if you have specific questions about the figures or data you're working with, you're welcome to post them. It's not entirely clear what you are looking for, so the more specific you can be about what you do, and what you do not know, the better.
The bacterial and eukaryotic composition of the biofilm community changed during the observed succession period. a Changes in alpha diversity as described by species richness (unique OTUs) and Simpson’s evenness. ...
I didn't want to do this either, so we started by looking at was was different in the graph and discussed it within the context of our study. We also did a stat test and added in p-values, because some people like them.
Here's what we wrote:
Species richness decreased strongly as the community developed. After a 79-day incubation, the mature microbiome had lost, on average, more than 59 and 15% of the total respective bacterial and eukaryotic OTUs observed from the initial 8-day (colonization) sample. These decreases were statistically significant as determined using post hoc general linear hypothesis testing with Tukey’s all-pair comparisons, which yielded p-values < 0.03. The colonizing community was very uneven, as measured by Simpson’s evenness. This metric ranges between zero and one, with zero representing a community dominated by a single member. The median evenness of 0.02 and 0.03 for 16S and 18S rRNA gene sequences, respectively, emphasizes that a relatively small number of abundant microbes dominated during the development of this community. Bacterial evenness did not mirror the reduction in species richness; evenness only decreased on day-56 (all p-values < 0.001) but rebounded by day-79. No statistically significant changes were observed in eukaryotic evenness during the development of this community.
Hi Colin,
Thank you so much for responding. So, looking at the box-plot for soil type, incase of faith_pd interpretation, the highest mean was from garden soil (120) followed by teller soil (116). However, garden soil has really narrow box-plot size whereas teller soil has wide box-plot size. I am wondering whether is it okay to focus on only mean value while writing the result? Does the wide range of box-plot mean samples have a lot of variation interms of phylogenetic diversity? I would be grateful for your suggestion.
Thank you!
Urmila
