Neurotransmitters in the gut cannot reach the brain due to the blood brain barrier (or very limited at best). Reuptake proteins and breakdown enzymes also prevent outside neurotransmitters from interfering. Your gut already produces large amounts of serotonin and it was first identified in the gut. 90% of the serotonin in the body is made in the lining of the stomach where it modulates smooth muscle contractions. About 50% of the dopamine is produced in the gut also.

However, microbes could affect gut behavior and that could effect mood simply by feeling poorly or well. There is also the matter of inflammatory responses and signaling (i.e. cytokines) that could affect one’s general sense of health. The small intestine is packed with immune cells that will also react to changes in the gut biome.

Finally there is the vagus nerve, a highway running from the gut, lungs and heart straight to the hindbrain, bypassing the spine. More here. We are still learning about how much this ancient nerve controls and influences. I’ve even wondered if it is related to dementia and Parkinson’s because of its physical proximity to locations such as the substantia nigra (Parkinson’s) and areas that show the first signs of dementia, possibly due to influences traveling up the nerve similar to the way rabies viruses travel. People who have had their vagus nerve cut, in an effort to stop severe stomach ulceration, showed a significant drop in Parkinson’s. More here, and here.