clustering OTU time series

Hi Pat and Sarah, I was wondering whether it would be possible to include a program for clustering OTUs from a time series. In my particular case, I have sequenced 16S amplicons from fecal microbiota originating from a same subject over a period of several days and would like to see which OTUs cluster in terms of their change in abundance over time. As I’m sure you know, this approach is used extensively in microarray time series to identify co-varying genes. I assume the analysis with OTUs would in essence be the same if one uses OTUs instead of genes. I have used a program called ASTRO (, which is designed for microarrays, to analyze my OTU series but because I’m not using this program for the purpose it is intended, it is possible that I am violating some assumptions built into ASTRO. The program I am invisaging would generate time series clusters and, if feasible, use the output from classify.otu to find taxa which are enriched within clusters at a specific p value. If mothur already has a similar capability, I would appreciate you pointing me to the program.

as always, thanks for providing this valuable resource,

Tufts Cummings School of Veterinary Medicine
North Grafton, MA

I guess I don’t see what’s special about this design? This is essentially what we did in our recent Gut Microbes paper (the data in the SOP are part of that study). If you just throw all your sequences together with barcodes you’ll make one big shared file and can go from there.


Pat, is there any chance you can post the Gut Microbes manuscript? Can’t get it online and our library does not subscribe to this journal.

Can’t get it through interlibrary loan? Feel free to email me and I can get you a pdf.