If this non-scientist (me) is not mistaken, a fruit and veggie juice diet would have a lot of fructose. This contrasts with other diets that may be higher in other forms of sugar, like glucose. It seems quite possible that some intestinal flora would do a better job metabolizing one rather than the other. Also, juice does not have as much fiber as whole foods, so that sugar might be absorbed a lot more quickly. Might have a strong impact on blood sugar.
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You are correct. Sugar composition of what was consumed may indeed also play a role and that should be considered more highly in follow up studies. That said, sugars would be absorbed pretty well in the small intestine, especially ones like fructose which our bodies LOVE (for better or for worse... probably for worse), so much of it might not make it to the large intestinal microbiome at least. Still good points with regards to blood sugar as well. One thing to keep in mind was that this diet was still caloric restrictive (only ~1300 calories/day during the juice diet phase) so the participants would likely be in a state where blood glucose was fairly low.