The gut holds most of the body's serotonin, and in 2015 Yano and colleagues showed in Cell that gut bacteria help regulate its production. Specific indigenous spore-forming bacteria promoted serotonin synthesis in the colon's enterochromaffin cells; germ-free mice had substantially reduced gut serotonin, restored by these microbes.[1]
Bacteria that make GABA
Bacteria can also produce GABA, the brain's main inhibitory neurotransmitter. In 2018, Strandwitz and colleagues reported in Nature Microbiology that they found a gut bacterium (KLE1738) that would only grow when supplied with GABA, and used it as a living sensor to hunt for GABA producers — finding that Bacteroides species make large quantities. Pairing sequencing with brain fMRI in patients with major depression, fecal Bacteroides abundance correlated with depression-associated brain signatures.[2]
Making a neurotransmitter in the gut is not the same as it reaching the brain. Serotonin and GABA don't freely cross the blood-brain barrier — the pathways to mood are indirect, via neural, immune and metabolic signalling.