Coffee appears to rewire the gut-brain connection

That sounds hilarious. So I had to look. It's the ISIC: Institute for Scientific Information on Coffee, "compris[ing] five of the major European coffee companies: illycaffè, JDE Peet's, Lavazza, Paulig, and Tchibo."

https://www.coffeeandhealth.org/about-isic

But it's okay, because

> ISIC is dedicated to contributing and consolidating balanced scientific information on coffee consumption – providing a reference for professionals and authorities who address health and wellbeing. [---]

Though

> ISIC works with the European Coffee Federation as well as with national coffee associations in the following countries [---]

suggests they don't work with any tea or soda federations to compare the scentific effects of coffee to other beverages.

Main authors study neuroscience (Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland,) so I bet the results are real, but as you point out, they knew that before even starting.

Also from what I can tell in my skimming the study mostly focused on small (decaf) amounts of caffeine in the gut biome. There are still more components of coffee such as bitter compounds that presumably have other effects.