Show the results of compute_core_microbiome.py

[sdpapet]

I have ~ 20 sample from two groups, which are High temperature and Low temperature. I compute the core microbiome for each group.

I got the core microbiome of each group.

My question is about the best way to present/graphic the results in a paper or poster. I checked the  plot which generated from this script (See the attached file). I understand what it is, but I don't think this is good for a paper.

I did a literature search, but I haven't found a paper using compute_core_microbiome.py to compute the core microbiome. So, I have no idea how to show the results of  the core microbiome. I would like to show  the core microbiome from each group side by side in a bar chart (percentage distribution?). Maybe something like a summary_taxa command.

Can anyone provide some papers which compute core microbome? I would like to see how they interpret the results.

Thanks,
Ben

[Sophie]

Hi Ben,

You can try computing the core_microbiome for each sample type, then using Venn Diagrams.  You could also look at functional categories for the core microbiome as in Figure 4.

Thanks,

Sophie

[Pet Chiang]

Hi Sophie,

Thank you. Does Qiime have scripts to make Venn Diagrams? Do you know any software can make Venn?

Ben

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[Sophie]

Hi Ben,

No Qiime does not make Venn Diagrams.  You can try Venni, as suggested by Samik on 2/5.

Thanks,

Sophie

[Pet Chiang]

Hi Sophie,

How did you calculate the shared number of OTUs between two groups in qiime, when you built the Venn Diagrams. If I want to build the Venn Diagram, I need to know the shared otus between my two groups. Each of my groups have several samples. It seems that compute the core microbiome script won't give me the shared otus and non-shared otus in each group.

I found "shared_phylotypes.py" script, but this only supports the calculation between samples not between groups. It doesn't support mapping file.

Ben

[Sophie]

Hi Ben,

If you put the results of core microbiome (for each group) into Venny, one row per OTU, Venny will calculate it for you.

Thanks,

Sophie 

[Pet Chiang]

Hi Sophie,

I think I need a little more than just corebiome. I want to show all my otus using Venny. I have two groups (High Temperature and Low Temperature). Each group has 10 samples. For all of my otus, I want to use Venn Diagram to show how many OTUs only in HT group and how many OTUs only in LT. Also, how many shared OTUs between the two groups.

I tried the compute_core_microbiome.py with default settings. It gives me the a series of text files core_otus_50.txt. core_otus_55.txt, .... core_otus_100.txt. If I want to check the all OTUs, should I set the cutoff from 0%, which will give me all otus results? (Instead just core microbiome). Otherwise, I need to find a way to calculate share otus between groups.

Ben

[Sophie]

Hi Ben,

I would run core_microbiome on the HT/LT groups, then input the results into Venny.  Pick one of the files core_otus_50.txt, for example if you want to look only at OTUs present in 50% of the samples.  You can adjust using --min_fraction_for_core and --max_fraction.... options.  

However, I wouldn't set the fraction to 0% - as this increases your chances for spurious results due to contaminating sequences that only show up in some of the samples for example.  This is especially true given the smaller number of samples you have in each group.

Thanks,

Sophie

[Pet Chiang]

Thank you. Sophie. I will try it.

Ben