There's been a common assumption that serotonin does not pass the blood brain barrier and that serotonin used by the CNS is produced there - but I've been seeing some studies that indicate that high serotonin in the blood can impair functioning of the BBB and others that indicate that it can pass even if the BBB is not in impaired state.

That said, there is a serotonin production system in the CNS (neurons originating in the raphe nuclei - at the midline of the brain, seems to also use tryptophan as a substrate and can also be blocked by glyphosate) so it's not clear how reliant the CNS is on serotonin originating in the gut.

All that said, I share your concern for the effects of glyphosate on the microbiome. At a minimum, slowed production there can affect the enteric nervous system (our 'second brain', located in the gut). It wouldn't surprise me at all to learn that it was involved with the ascendency of bacteria that produce bacterial lipopolysaccharide which can lead to loss of 'tight bonds' between enterocytes, which in turn can allow some of the microbiome to leak into the blood leading to an immune system reaction (hey, we are evolved to react to any bacterial markers internally).

As a side note, I'd mention that SSRIs don't just block the reuptake system in the CNS, but across the entire system, so if you're taking one of these and are experiencing gut issues, well, that's why.

Finally, I have yet to see a study that indicates that glyphosate bioaccumulates, so limited-time interference with the production system in the CNS, but WTH knows what long term supposedly nontoxic doses might do to the flora balance in the microbiome.

My usual disclaimer: I'm not a bio or medical pro.

A good friend was diagnosed with IBS a few months back and I decided to start digging into gastroenterology alongside my preexisting interest in CNS (AD/BBB/glial system), lipids, and insulin resistance. As it turns out, it's every bit as interesting. So, this is coming from a (probably over) enthusiastic amateur.