How to compare OTUs/raw number of bacteria between samples using QIIME2?

What is the best way to compare raw number of bacteria between samples using QIIME2? I am looking at tissues which do not have enriched microbiomes (large bacterial numbers) so I was trying to compare raw numbers between samples. Is alpha diversity the way to go?

Hi @macrobiome,
More information about the goal of your study would be very helpful. What do you mean by enriched microbiomes? Alpha diversity will look at how many unique features you have and the diversity of the population you are looking at. Does that sound like the direction you are hoping to take?
-Hannah

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Hi @jphagen:

Thank you. I am trying to compare tumor microbiomes and I suspect certain types of tumor to have less microbial load compared to other types. What's the best way to compare the diversity and number of bacteria between these two types?

Hi @macrobiome,
I think the best way for you to do your comparison would be to follow the alpha diversity workflow in the 'Moving Pictures' tutorial. Run core metrics and then take the observed features vector and run alpha-group-significance.
I hope this is helpful to you!
-Hannah

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