The headline version writes itself: coffee changes your gut bacteria, and your mood follows. The study, summarised by ScienceDaily this week, reports that coffee may influence mood and brain function by changing the activity of microbes in the gut. Both caffeinated and decaf coffee were linked to lower stress, depression and impulsivity.

Start with the mechanism, because it is the reason anyone takes this seriously. Gut microbes ferment what reaches the colon and release chemical byproducts into the bloodstream. Some of those compounds reach the brain, and the gut also talks to the brain through the vagus nerve, a long cable of nerve fibre running between the two. Coffee is full of plant polyphenols that the small intestine mostly cannot absorb. They travel on to the colon, where the microbes get first access. A change in what the bacteria eat plausibly changes what they excrete.

Now the decaf detail. If caffeine drove the mood effect, decaf should have done little. It did not. That points away from the stimulant and toward something else in the cup, which fits the microbe explanation. It also fits a duller reading: people who drink coffee of any kind differ from people who do not, in diet, routine and income. The summary describes the results as links. A link is an observation, and it says nothing yet about which way the arrow points.

Depressed or stressed people also change what they eat and drink, so mood could be shaping the coffee habit rather than the reverse. Only a trial that assigns people to coffee or no coffee, and tracks their microbes and mood together, can separate those. The summary I have does not report that design, so I will not credit it with one.

Microbiome research keeps producing findings of this shape. A separate piece of research, being presented at the annual meeting of the European Association for the Study of Diabetes, suggests shifts in gut bacterial composition could give early warning of type 2 diabetes. Same organ, same caution: a signal that something is happening is not a lever anyone can pull.

What the science establishes: coffee drinkers, caffeinated or not, scored better on these mood measures, and gut microbes are a credible route. What it does not: that a cup of coffee treats anything.