Can diffrent sample-metadata-file can be used for the same data analysis

Dear all,
I have started analysing my 16S data using qiime2. However regarding the sample metadata file I have a question. It might have been answered somewhere in the forum but I could not find. Sorry for duplicates.
I will get some important environmental variables’ results related to my samples later. So if I keep SampleID, BarcodeSequence, LinkerPrimerSequence and Description part same can I use different metadata file (for instance after including temperature or POC data to the table) for my beta diversity analysis.

To be more clear, I use metadata file 1 for qiime feature-table summarize and then add some environmental variables to matadata file 1 and use the second one for qiime diversity core-metrics-phylogenetic analysis. Will that create problem or not?
Since data I am dealing is big, I do not wanna analyse it over and over again.

Thanks in advance,


Hi Selin,
As long as metadata file 1 and metadata file 2 contain the exact same sample IDs, that is absolutely fine.

You can even remove metadata columns from that file, so long as the sample IDs are not changed.

It would only cause an error if, for example, you change or remove some sample IDs in metadata file 2 but those samples are still present in your data.

Adding and changing metadata columns as one proceeds through an analysis is sort of expected and typical — so the QIIME2 developers made sure not to disturb that ability!

I hope that helps!


Hi Nicholas,

Thanks a lot for you quick reply. That was really helpful.



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