I don't work with antibiotics or directly with the microbiome, but I have some questions about how these rats were housed. As background, I work in autoimmune pharma discovery, and my role is primarily with rodent models of disease. I also sit on my institution's IACUC, so I see a lot of other departments' protocols.

One thing that has become common in some facilities is housing males and females in separate rooms. Female mice and rats get pretty stressed when you house them next to males, or when you handle males first and then females after. This is a damned-if-you-do-damned-if-you-don't situation, because either these rats were housed in different rooms, which could cause microbiome differences, or they were housed together, which could cause stress, which could cause microbiome differences.

I think overall, this study is reasonable, and the fact that it confirms previous studies bolsters the hypothesis, but I'm not sure how you actually tease these out without a mechanistic proposition.

Lastly, based on my experience, there's something a little odd about their weight data. We use weight as a loose proxy for wellness, so it's regularly measured. The body weight for both the males and females are about 30g higher than I'd expect for this age (8 woa). Most rats and mice are very consistent weight for a given age, and this is just a minor red flag, but it makes me wonder more about their husbandry.

Just my 2 cents.