Gut Feeling: The Microbiome & Mood

Gut health. It’s the issue of the day in the wellness bubble, with keywords like ferments, probiotics and microbiome peppered liberally throughout any self-help blog post worth reading. Why though? Why this incessant focus on the gut and all its bacterial flora rather than, say, the brain or the liver?  Short of phoning a friend, we can look to the relatively new (by serious scientific research standards) sphere of integrative medicine for the answer.

It was the father of medicine, Hippocrates, who so famously pronounced in the 5th Century BC,

"All disease begins in the gut."

As a holistic healing system, Hippocratic medicine treated the patient, not just the disease, and treatment often involved dietary measures. What Hippocrates stated so simplistically, we can now explain in greater detail, thanks to the growing body of research illustrating the links between gut dysbiosis and a number of degenerative conditions in the body. Somewhat newer to mainstream science is the link between the gut and mental and/or emotional health. While it may be common sense in some traditional cultures, the idea of treating depression with diet didn’t hold much water in the medical community until relatively recently. Similarly, viewing mood as flowing from gut-to-brain rather than only top-down, as was previously thought, puts a whole new spin on managing your own emotional state and general outlook on life.  

The second brain
Any talk about the gut must make mention of the ‘microbiome’, which refers to the unique combination of microbial cells in your body. Incredibly, your body contains more microbes than human cells, and most of these are found in the gut. The gut has its own neural system, the Enteric Nervous System (ENS), which is commonly termed the ‘second brain’ because it can function autonomously, controlling much of our gut reflexes and general goings on. It has been thought for some time that the Central Nervous System (CNS) communicates with the ENS in such a way that cognitive and emotional factors (eg: stress levels) influence gut behaviour causing, for example, the butterflies you get in your stomach when you’re nervous. What is of particular interest to researchers now, however, is the idea that the ENS also communicates gut activity to the CNS and that these messages can influence our perspective and cognitive performance. For example, your gut microbiota influences the amount of seratonin your body produces, which has a pivotal role in how happy you feel.

Prebiotics and probiotics
An interesting focus of studies into mood disorders and gut health is the potential benefits of prebiotics and probiotics in ameliorating depression, anxiety and stress. Put simply, probiotics are the ‘good’ bacteria that make your gut happy, and prebiotics are the food that these probiotics like to eat.  A 2014 study examining the effects of prebiotics on mood and stress levels compared healthy participants on a three week course of prebiotics against a like group on a placebo. The prebiotic group showed significantly reduced cortisol levels and a more positive outlook in comparison to the placebo group, leading the researchers to conclude that improved gut flora conditions can in turn improve general mood and reduce stress. Another recent study found a correlation between eating fermented foods (which contain probiotics) and reduced social anxiety amongst young adults. Supplement and vitamin companies capitalising on the trending status of prebiotics and probiotics have flooded the market with all sorts of pretty bottles guaranteed to make you glow, and they may well work a treat. It’s worth noting, though, that for thousands of years, humans have been ingesting these elements in the form of plain old food. Some natural sources of prebiotics and probiotics include (but are not limited to):

Probiotic:  pot set yoghurt, sauerkraut and kimchi, kefir, miso, kombucha and other ferments.

Prebiotic: garlic, onions, leeks, bananas, apples, oats and barley, flax seeds and cacao.

Healthy gut, healthy mind
Key to a healthy gut is bacterial diversity. Mono-diets of white carbs, simple sugars and highly processed foods all but wipe out gut flora diversity, leaving us open to inflammation, which sets the scene for bodily, mood and mental disorders. What’s exciting about the gut-brain link is the treatment implications - the idea that by caring for your gut, you may be able to regulate your mood and stress levels, and even manage symptoms of anxiety and depression to some degree.

Your microbiome is a unique snowflake and ultimately, finding what works for you is a personal journey. There are some good rules of thumb, though, which we can crudely group into dos and don'ts for good gut health:


  • Eat organic wholefoods from the ground, skin on. A little bit of dirt is good for your guts!
  • Include fermented foods in your diet, and cook as much as possible - there’s nothing wrong with buying pre-made food, but the more you eat out, the more likely that your food will be processed.
  • Listen to your body. Pay attention to your gut reaction to certain foods, and observe the effect of foods and eating behaviours on your emotions. If you’re new to this, keeping a food diary is a great way to orientate yourself.


  • Don’t eat lots of processed foods, simple carbohydrates or sugars, as they tend to cause inflammation.
  • Avoid taking antibiotics if you can help it - they disrupt your microbiome ecology, causing dysbiosis.
  • Be particularly wary of eating meat and dairy products from industrially farmed animals. Much of this production line ‘food’ contains antibiotics by way of those ingested by the animals in the feedlot, which means you are, in effect, eating second hand antibiotics. This is what Michael Pollan was talking about when he said, “you are what you eat eats.”

This article is in no way intended to claim that a healthy diet is a panacea to all ills. Mental, physical and emotional health is complex and any effective approach must be holistic. If you are suffering from depression, anxiety or any of the disorders mentioned in this article, please seek medical advice and support.