60 second summary
- Communication between out gut microbes and brain is via the brain gut axis
- Microbes can send messages to our brain via many pathways such as: hormones, immunity signalling molecules and their own metabolites
- A barrier of cells separating the microorganisms from the bloodstream means that signals are conveyed indirectly
What is the brain gut axis?
One of the most important communication pathways in the body is through the gut brain axis. It is a complex network allowing transport of chemical messages between out brain and digestive tract, mediated through 2 main routes : the autonomic system and circumventricular organs.
Autonomic nervous system (AN)- division of the nervous system controlling non voluntary functions essential for your survival such as heart rate and digestion- functions you don’t have to consciously think about.
Think “autonomous”/ “autonomy” all relating to the prefix auto- which means by itself. The AN is regulated by itself!
Circumventricular organs– structures in the brain with highly permeable vessels called capillaries. These provides an alternative route for hormones to move from neural tissues into the bloodstream.
(This is in contrast to most of the other capillaries in the brain which are hardly accessible to other molecules due to a border of cells called the blood brain barrier.)
What does communication via the autonomic system look like?
The main structure responsible for control of the autonomic nervous system in terms of gut-brain communication is the vagus nerve. This nerve is able to detect molecules released by microbes in the gut and transfer them to the central nervous system.
Central nervous system- brain and spinal cord
Appropriate responses from the vagal nerve are crucial in communication. Certain diseases such as Irritable bowel syndrome have shown to have decreased vagal tone.
Vagal tone- the continuous baseline impulses the nerve exerts. 
How do microbes communicate with us?
- The vagus nerve
- Through hormonal pathways eg HPA axis
HPA axis- also known as the hypothalamic pituitary adrenal axis, it is a set of hormone secreting glands: the hypothalamus, pituitary gland and adrenal gland
- Immune system via signaling molecules called cytokines
- And its own metabolites such as short chain fatty acids
Short chain fatty acid- fatty acids with less that 6 carbon atoms produced when gut bacteria ferment fiber in your large intestine. 
Are our microbes directly in touch with the vagus nerve?
No, fibers relaying information from the gut to the brain are not found in the lumen of the gut, in other words its inside, which is where the gut bacteria reside. The bacterial layer is separated from the vagus nerve by a single layer of lining cells which are covered in mucus. Molecules releases by microbes are therefore relayed indirectly. Amongst the single layer of cells lining the gut 1% of these are enteroendocrine cells which can detect signals from microbes and then interact with the vagus nerve affecting food intake and gut contractions.
Entero- related to the enteric nervous system. Overall there are 3 types of nervous systems central nervous system (brain and spinal cord); peripheral nervous system ( rest of nerves) and enteric nervous system (unique to the gut)
-Endocrine= means releasing hormones
The science– enteroendocrine cells can interact with aspects of the vagus nerve by releasing serotonin. The nerve has receptors for serotonin on its surface. Communication can be mediated through other hormones too such as CCK
 PMC. (2018). The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808284/ [Accessed 20 Jul. 2019].
 Wikipedia. (n.d.). Circumventricular organs. [online] Available at: https://en.wikipedia.org/wiki/Circumventricular_organs [Accessed 20 Jul. 2019].
 2 minute neuroscience: the HPA axis. (2019). Youtube: Neuroscientifically challenged.
 Healthline. (2016). How Short-Chain Fatty Acids Affect Health and Weight. Available at: https://www.healthline.com/nutrition/short-chain-fatty-acids-101#section1 [Accessed 20 Jul. 2019].
 Wikipedia. (n.d.). Enteroendocrine cell. [online] Available at: https://en.wikipedia.org/wiki/Enteroendocrine_cell [Accessed 20 Jul. 2019].