The link with mental health is a particularly interesting one. Known as gastroneuroenterology, this is an exciting emerging area of study. Scientists talk about the "gut-brain axis", suggesting these systems talk to each other via hormones, metabolic products or direct neural connections. We know gut bacteria play a crucial role in the production of serotonin, a neurotransmitter that helps stabilise mood and emotion.
It's possible in the future we could see mental disorders such as depression and schizophrenia treated with specifically developed probiotics that work on changing the gut bacteria.
It's fair to say, despite all this, that what science doesn't know about the microbiome is greater than what it does know. We have no definitive answer on what makes up an "ideal" population of gut bacteria and this is likely to be different for each of us.
But we do know keeping our gut microbes happily well-fed is good for general mood and health. And doing that is not too difficult.
Ditching the highly processed junk food and sugary drinks is a good start. Too much of these leads to less diverse gut bacteria and the overproduction of less beneficial ones. Load up on plant foods for a range of different types of fibre, including whole grains, beans and lentils. Prebiotic foods - specific carbohydrates that provide fuel for good bacteria - are worth including: try bananas, onions, legumes and cold, cooked potatoes.
And consider probiotic foods such as fermented foods and yoghurt that has live cultures. Sauerkraut, kimchi and kombucha are having a moment right now, possibly for good reason. They can potentially help boost the type and range of good bacteria in our guts.
We can expect to see even more research on the life in our bellies, including a closer look at allergies and cancer.
Niki Bezzant is editor in chief of Healthy Food Guide magazine.