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Does the introduction explain the objective of the research presented in the preprint?

Partly

This is what they mention: "we aim to provide insights into the complex interplay between diet, gut microbiome, and human health" I like the aim framing in the sense that it is position in the write context given what has been said in the introduction. But I feel like the "SMART" Framework could help improve the phrasing of the aim to understand how this is going to be measured (which populations are going to be included, how many people, is it only at the taxonomy level or only at the gene/functional level).

Are the methods well-suited for this research?

Somewhat inappropriate

73 participants with different age groups ranging from 10-80 years: maybe a description of the demographics of the participants will establish a framework and also justify why comparing to HMP data is relevant. Were analyses were read-based or contig-based? This is not totally clear. There is no mention of how the cohort was separated into plant and meat consumers. Did you have the metadata for this ? were they food consumption surveys? How was the comparison at the species level between MD and PD calculated ? was this based on presence accounted by read-mapping ? what were the mapping quality and prevalence thresholds to decide those species were only present in one of the groups? BMI calculations and health status could also be included in the metadata description in methods. Maybe also including a table of the sample IDs, age, BMI of participants to also see the number of participants in each category (diet,BMI, health) Why did you use Bray-curtis dissimilarity metric if you had taxonomic information ? Why do IBS markers just show a few datapoints ?

Are the conclusions supported by the data?

Somewhat supported

I think that due to some things that weren't clear in the methods, the conclusions might be drawn with unclear evidence.

Are the data presentations, including visualizations, well-suited to represent the data?

Somewhat appropriate and clear

Yes but the way they generate some of them is unclear (see methods feedback)

How clearly do the authors discuss, explain, and interpret their findings and potential next steps for the research?

Neither clearly nor unclearly

I didn't notice a thorough discussion of the results and next steps are not clearly mentioned.

Is the preprint likely to advance academic knowledge?

Moderately likely

Would it benefit from language editing?

Yes

There are some typos and instructions from the journal that are included in the pre-print version.

Would you recommend this preprint to others?

Yes, but it needs to be improved

Is it ready for attention from an editor, publisher or broader audience?

No, it needs a major revision

Competing interests

The author declares that they have no competing interests.

Use of Artificial Intelligence (AI)

The author declares that they did not use generative AI to come up with new ideas for their review.