Temporal analysis tools, what is available?

Dear All,
I have a dataset from an experiment done to evaluate the temporal succession of the microbial community over time from different sites. I know that both qiime 1 and 2 does not have such an option. I wondering if there is any tool you could suggest to analyze these data, especially the community dynamics.
Anything would be useful and appreciated,

Thank you
Ahmed

Hi @Ahmed_Abdelfattah,

Have you had a chance to check out q2-longitudinal? That plugin contains several methods for longitudinal analyses, such as yours. Comparing community dynamics over time at different sites may be a good application for NMIT (see the tutorial).

Other than that there are lots of longitudinal analysis tools in R. You will need to be more specific about what your samples and hypothesis are to make any specific suggestions.

I hope that helps!

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Hi Nicholas,
Thanks for your suggestion. I actually haven’t. Now that I looked, I think they will be useful tools.
About your question, in addition to what you already suggested, I was looking for a test that that measure the changes of taxa or OTUs over time to find common trends or features.

Thanks again for your suggestion,

Ahmed

NMIT will effectively tell you whether different samples/groups share the same longitudinal profiles, i.e., the same OTUs are shifting in the same ways over time. Usefully, it reports this similarity as a distance measure so you can determine the similarity between individual groups and input this distance matrix to other methods (e.g., for permanova testing and PCoA). It will not, however, tell you exactly which species are shifting.

There will be a method added to q2-longitudinal in the next release or two, which might be of interest here — stay tuned for when that comes out in a month or so.

You can use linear-mixed-effects in q2-longitudinal to look at individual OTUs in relation to different groups, if you have a handful of important taxa that you wish to examine.

Beyond that, let’s see if anyone else has suggestions for methods that specifically address that question. We are always open to feature requests in QIIME2 plugins :smile:

I hope that helps!

Though not available via Qime2, might be of interest: the new SplinectomeR package

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Thanks to all of you. Your answers were very helpful..

@Mehrbod_Estaki, From the quick look I gave it looks like a combination between ELSA and TiCONE.

http://psbweb05.psb.ugent.be/conet/microbialnetworks/conet_new.php
https://ticone.compbio.sdu.dk/
I will give a try afterwards.
Thanks again :slight_smile:

Ahmed

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