In the review entitled “Diet-microbiome-immune interplay: an emerging influence on the pathology of Multiple Sclerosis” Lehman and colleagues outline aspects of the state-of-knowledge regarding the role of the intestinal microbiota in multiple sclerosis. The authors roughly summarize findings linking the intestinal microbiome to MS, the association between HLA haplotypes, microbiota and MS, environmental factors (primarily diet) and very peripherally the role of bacterial products/metabolites. In more detail, the authors discuss the role of phytoestrogen metabolism of intestinal bacteria summarizing primarily their own work on this topic (Ref. 87, 88, 89).

The review gives a rather superficial view of the topic promised in the title and there is little connection between the first and the second half of the review. For example, the host genetic factors are not picked up again. In my opinion, a more focused discussion of the diet-microbiome-MS axis would better raise the interest of the readers and would perhaps add novel aspects to the discussion of how the intestinal microbiome could impact CNS inflammation. Perhaps a more detailed, even speculative, discussion of the mechanisms how isoflavone diet or dietary intervention in general results in an anti-inflammatory environment would make the review more attractive.

Another major point of criticism is that about half of the citations are reviews themselves. It would be good to give credit to the primary literature and cite the works which actually showed the aspects which are pointed to in the review. Citation of reviews in a review itself should be kept to a minimum.

I find Fig. 1 unnecessary, as it portrays merely the general view of microbiota in health and disease. In particular in view of the more detailed aspects of this review, I would have liked a figure summarizing, for example, the phytoestrogen pathways.

The abstract is very generic. It would be helpful if it were more focused, in particular regarding the detailed discussion of phytoestrogen metabolism.

Minor points:

p.3 lines 5-10: Here, studies are cited which on the one hand show a decreased abundance of Clostridium and a Danish study which showed an enrichment of Clostridium in PwMS. It is not further discussed why there is this discrepancy. Clostridium is a big group, thus at least this should be mentioned.

p.3 line 31: It is stated that “Thus, this study provides data that the gut microbiota can directly contribute to MS disease severity.” The data are still just correlative (“positively associated”).

p.4 lines 22-26: The authors refer to the ability of SFB to induce IL17A-secreting CD4+ T cells. First, why not name the segmented filamentous bacteria? Second, why not cite the work, e.g. PMID: 20660719, where people have looked at SFB in EAE? I also did not understand the evidence that a DQ8-associated microbiota has anything to do with IL-17 T cell response.

p.6 lines 55- : The statement “Such a significant change in the microbial community was not detected when the diet was changed from phytoestrogen-free to isoflavone-diet, suggesting that the presence or absence of phytoestrogen strongly impacts gut microbiota diversity” seems a contradiction.

p.7 lines 42-45: “mice switched from an isoflavone to a phytoestrogen-free diet showed reduced EAE severity compared to the mouse which was switched from a phytoestrogen-free to an isoflavone-diet”. I do not understand, why EAE severity decreases when switched to a phytoestrogen-free diet. In the context of the argumentation before, it does not make sense.

There are several grammatical mistakes in the manuscript which should be corrected.

The authors have improved the manuscript, making it more concise and focussed. I still wonder through how specific the phytoestrogen metabolism is for MS/EAE. The impact on inflammatory cytokine production seem quite generic. Would the points raised in the review also apply to other immune-mediated diseases, e.g. rheumatoid arthritis, colitis, etc.?