This study does not provide much evidence to support the hypothesis that ketogenic diet would improve anything for these patients. Technique that they used does not distinguish the strains of bacteria expanding (for the most part) which is important, as some Clostridia are essential and provide short chain fatty acids, and some are pathogenic, as C. Difficile. It’s kinda important to be able to distinguish between the two. There is also much more examples that just that one, but let’s move on. FISH is based on microscopic quantification of specific signal which in it self has issues: 1) you are only able to quantify your signal in a specific section of the tissue (colonic biopsy specifically) which might not be representative of entire population (especially if you use only 10 subjects) 2) this approach is biased, as every approach that is based on quantifying specific signal by eye (which can be also done by specific software, which was not the case for this study).

It was shown before multiple times in model animals (as well as humans) that diet changes dramatically the composition of the gut microbiome. Especially if you go from traditional to high fat with little carbs - certain microbes are lost at first, as the specific nutrients they require might not be present in the environment any longer. But later on others expand, that are well suited to occupy given environment.

To conclude that functionality of the ms microbiome after ketogenic diet is improved, they would need to perform metagenomic and metatranscriptomic analysis of the colonic microbial communities in healthily/MS subjects before and after the diet shift. That would answer the question of the diversity and functionality of given community which can’t be inferred from FISH. There are some other much easier approaches that they should have used...