How to create an OTU table out of phyla abundance?

1

Dear community,

I have a very special problem. I've got data only about the abundance of specific phyla in a patient cohort. That means that I know how many of each Phyla a patient has, like:

Patient 1: 10 of phyla 1, 21 of phyla 2, 300 of phyla 3, ... etc.

Patient 2: 15 of pyhla 1, 26 of phyla 2, 365 of phyla 3, .... etc.

...

However I want to go on with microbiome analysis but therefore I need OTUs. However, OTUs are used to classify bacteria at the genus level, but now I have the data on phyla level and I have no 16S sequencing data. How can I create an OTU only by having the phyla abundance? Is is possible?

Do I really need OTUs? Can I analyse alpha-/beta-diversity without OTUs?

I would be really glad about any help!

Kind regards,
Hashirama


microbiome


OTU


diversity

• 67 views

Hi,

How can I create an OTU only by having the phyla abundance? Is is possible?

You can't get an OTU table from a taxonomic table with abundance at phylum level.

Do I really need OTUs? Can I analyze alpha-/beta-diversity without OTUs?

An OTU is just a taxonomic unit with the lowest taxonomic resolution as possible. The idea is to get an approximation for species. Doing alpha/beta-diversity without species level abundance data or its approximation, OTUs (or other taxonomic unit such as ASVs - Amplicon Sequence Variants) is not really meaningful or the point of the analysis. This is because you usually do alpha-/beta-diversity to study a microbial community. When you think well, a microbial community is comprised by several species with different number of individuals.

Although there are perhaps a few analyses that you might do that give you an idea of alpha and beta-diversity of the community. Regarding alpha-diversity, you can discuss how many different phyla were found in each sample. This gives you an idea of how much within alpha-diversity you have in one sample. Keep just in mind that if you look at a different taxonomic level or even at OTU level, the diversity can be different than at phylum level. Regarding beta-diversity, you can do an hierarchical heatmap, i.e., an heatmap with an hierarchical clustering, clustering the samples based on phyla distribution similarity across the different samples. This allow you to have an idea of between sample diversity. Although I would like to warn you for the same issue that I meantion previously: if you do the exact same analysis at a different taxonomic level or OTU level, you might get a different result and, that's why this kind of analyses are usually done at lower taxonomic resolution as possible - OTU level.

I hope this helps to answer your questions!

António


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