An animal study conducted by The Ohio State University showed that consuming a greater amount of tomatoes led to a more diverse gut microbiome.
I’m not sure how meaningful this study is when the “control” diet contains basically no vegetables at all, except for soybeans. I don’t think that any conclusions can be made specifically about tomatoes from this study, in comparison to other vegetables/fruits. For all we know, they could have gotten the exact same results with the addition of any fruit or vegetable to the pig’s diet.
To increase gut diversity you need food variety.
So sure if you never eat tomatoes or other vegetables, sure adding them can have that effect, but I doubt its just tomatoes that are special for this effect.
Tomatoes also contain lycopene which can help prevent some chronic diseases and prostate cancer. Lycopene I’d more absorbable when the tomato is cooked and processed such as in salsa and ketchup.