Some good news this week for folks who have GERD, or chronic acid reflux, they discovered the cause: http://www.foxnews.com/health/2016/05/17/researchers-discove...
About 90% of the neurotransmitter serotonin in your body is produced by enterochromaffin cells in the stomach.
Though this does not directly affect the brain (the brain has it's own serotonine synthesis) it modulates a multitude of responses like blood pressure, body temperature, which, in turn, affect the mood.
Quote from Wikipedia:
Serotonin is a neurotransmitter and is found in all bilateral animals, where it mediates gut movements and the animal's perceptions of resource availability. 
In less complex animals, such as some invertebrates, resources simply mean food availability.
In more complex animals, such as arthropods and vertebrates, resources also can mean social dominance. In response to the perceived abundance or scarcity of resources, an animal's growth, reproduction or mood may be elevated or lowered. This may somewhat depend on how much serotonin the organism has at its disposal.
Cytokines are, generally, cell signalling molecules. In the case of GERD, if I understand the process correctly, these cytokines are instructing the tissue of the esophagus, and associated immune system cells, to initiate the inflammatory response.
Inflammatory responses in mucosal tissues typically include an increase in mucous production, which is the body's attempt to protect the tissue from the refluxed stomach acid.
So it follows that the first tissue changes you should expect to see are inflammation and increase mucous production as the body tries to protect itself from exposure to stomach acid.
This doesn't mean the cytokines cause the inflammation, nor that they cause acid reflux, they're just the cell signalling molecule that initiates the inflammatory response, released in response to increased acidity on the tissue surfaces, released long before gross changes occur as a result of acid damage.
If we give medicines to dampen the cytokine release, or dampen the inflammatory response to the cytokines, thereby reducing the inflammation, that doesn't mean the tissue won't be damaged by the acid reflux - if anything, down-regulating the normal inflammatory immune response will worsen the damage caused by the acid.
The question is: what is causing the acid reflux?
That is, both A and B can be said to cause C, in the standard counterfactual sense of the word "cause": if you hold everything but X constant, and add more X, and more Y occurs, then X causes Y.
That doesn't mean you shouldn't do B. If Q is worse than C, it's still a good choice. But it does cause C.
That is amazing news!.
From the end:
'“Too many large-scale, spurious claims are being made,” Dinan said, mostly by people with something to sell. Although we have “very good data” from animal studies, he said, there’s nothing that could be described as solid clinical data linking the gut microbiome to depression or anxiety in people.'
This research is super exciting. It's also super new. The technology for sequencing gut bacteria on a large scale has only been around in a real sense for about 10 years, and only been affordable for about 3-5. We'll get there, and almost certainly gut flora matters massively for all sorts of biology, but it's important to temper excitable headlines.
This is a pretty important thing to keep in mind. There are a lot of studies that I've seen, extending connections to humans from mice , even though understanding of the suitability of these mouse models has just recently (or hasn't) been studied .
So... "In humans, the data are more limited. Researchers have drawn links between gastrointestinal pathology and psychiatric neurological conditions such as anxiety, depression, autism, schizophrenia and neurodegenerative disorders — but they are just links." 
As for gut to brain transmission, the first thing that comes to mind is being hangry but that's probably a different thing :)
My reaction was only against the apparently underlying assumption that humans, biologically, are more complex than mice, a remain of the idea that they are more evolved or a biased perspective due to the fact we study them in more detail.
It's not necessarily neurological in nature, but one of my favorite papers in the field in the last couple years shows a potential causal relationship between obesity and gut biomes by using artificial sweetener and a fecal transplant in mice.
Paywalled version in nature:
Unpaywalled version after googling:
I get it here: http://www.customprobiotics.com/custom-probiotics-l-rhamnosu...
As I understand the anxiolytic effects, it is all about a proper balance between glutamate and GABA .
Some people get really stressed out when they eat too much glutamate-containing foods. So, perhaps probiotics can help address the glutamate too (?)
Note: some warnings here:  (some bacteria produce glutamate!)
One thing that stood out is that the highest concentration of this neural matter is in the stomach. Your stomach does have access to some information about the outside world: Bass sounds, orientation, and proprioceptive activities. But it is largely ignorant of the outside world because it doesn't have access to the main senses the way the brain does. This sits nicely with the "gut feel" lore, where your stomach is uneasy about something though your brain says things should be fine. Your stomach can't be fooled by your senses.
Long story short, the gut-brain axis is a compelling area of study, but based on the fact that nearly all studies have been in murine models coupled with the relative paucity of human trials, the jury in the medical community is still largely out.
[insert obligatory 'redesign-HN-to-be-responsive' thread here]