Level of interest:

This paper is of interest to any microbial ecologist who wants to use a visualization tool to relate the distribution of microbes with the metadata, along gradients, time points or other categories, in a dynamic way and retrieving good quality images of lower sizes.

EMPeror is an already widely used tool integrated in QIIME (a pipeline that has become standard in the field) and has provided the community with endless possibilities of data interpretation due to the ability of changing each data point in the plots in a given metadata category.

Vazquez-Baeza et al, present a well-written manuscript on a strong, useful tool and clearly demonstrate how the tool compares to other packages that can be implemented through code or other manual approaches and evidences the usefulness of its QIIME integration.

EMPeror will definitely become a standard tool for beta diversity studies of large-scale projects allowing integrated, complex interpretations due to the ability to observe interactions among metadata categories in a easy a quick fashion.

Discretionary Revisions

As stated, the authors present a short, strong justification for the use of EMPeror, a versatile tool for visualizing 3D PCoA plots as a function of metadata. It is written for the advanced microbial ecologist that works with high amounts of data and is used to work with QIIME.

I have very few comments which I'd like the authors to consider:

1. I would suggest that a short paragraph could be added briefly discussing QIIME (in the background section) and justifying the importance of analyzing beta diversity (this contextualization would provide a nice start for those exploring high throughput datasets).

2. Page 3, last statement, about Fig A consider editing "EXPLAIND" to explained.

3. Page 4, please delete one of the two periods (before SpotFire).

Level of interest: An article of outstanding merit and interest in its field

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: I declare that I have no competing interests