How we know
The field has a name: the microbiota-gut-brain axis. The landmark review is Cryan and Dinan 2012 in Nature Reviews Neuroscience, "Mind-altering microorganisms," which laid out the three lines along which gut bacteria reach the brain: the vagus nerve, the immune system, and microbial metabolites that act on neural tissue. In germ-free animals, raised with no microbes at all, stress responses, anxiety-like behaviour and brain chemistry all change, and many of those changes reverse when a normal microbiome is restored.
Two anatomical facts make the connection concrete. First, the gut runs its own nervous system. Furness 2012 in Nature Reviews Gastroenterology and Hepatology describes the enteric nervous system, roughly 500 million neurons embedded in the gut wall that can control digestion without any input from the brain or spinal cord. That is the literal reason it is nicknamed a second brain. Second, the gut is where most of your serotonin is made. Yano and colleagues 2015 in Cell showed specific gut bacteria drive serotonin production in the intestinal lining, consistent with the long-standing estimate that 90 to 95 percent of the body's serotonin sits in the gut, not the head.
Scale matters too. Sender, Fuchs and Milo 2016 in PLOS Biology put the count at about 38 trillion bacterial cells against 30 trillion human cells. By cell count, you are slightly more than half microbe, and almost all of that colony lives in your gut.
What it means
The honest version is influence, not control. Gut microbes produce and modulate the same neurotransmitters your brain uses, signal up the vagus nerve, and are statistically linked to mood, appetite and stress. That is a real, measured channel. It is not a puppet string. When a craving hits, the urge is shaped by a system that includes the trillions of organisms feeding off what you eat, but you are still the one deciding.
Most of the strongest causal evidence is in animals, and human work is largely correlational so far, which is why careful scientists say the microbiome is associated with mood and behaviour rather than claiming it dictates them. The direction of the science is clear even where the mechanisms are still being mapped.
The takeaway
You are not a single organism issuing orders to a passive body. You are a partnership: roughly 30 trillion human cells and 38 trillion microbial ones, wired together through a nerve and a shared chemistry. The gut talks to the brain, the brain talks back, and your moods and cravings emerge somewhere in the conversation. You were never quite one person. You are closer to a colony.