Humans are colonised by a vast array of microbes living in and on our bodies including bacteria, archaea, fungi and viruses. The collective genomes of these resident microorganisms is known as the human microbiome. The interactions between these microbes and their human host plays a crucial role in the health of the individual.

What is the function of the human microbiome? Humans have microbiomes in a variety of different locations that are in contact with the outside world e.g. skin, mouth, vagina, lung and the gastrointestinal tract, which is the most diverse and best studied human microbiome. This gut microbiome carries out many essential functions for the host such as; helping digestion by breaking down foods; immune system development; preventing infections by competing with pathogens (disease causing microorganisms); the synthesis of essential nutrients such as vitamins (K and B12) and short chain fatty acids.

How does the human microbiota change with age? Our human microbiota evolves with the different stages of life, and is very influenced by our habitual diet. For example, infants fed breast milk have a different microbiota to infants that are formula fed. Other factors that influence the microbiota composition in infants is their mode of birth (vaginal delivery versus c-section), early weaning foods and exposure to antibiotics. Usually by 2-3 years of age the gut microbiota has reached a steady state, and remains relatively stable until old age. When people become older their microbiota becomes less diverse, possibly due to a less diverse diet. The more diverse the gut microbiota during adulthood the better, and you can help your gut microbes flourish by feeding them a healthy and varied diet with lots of fibre.

Various diseases, such as obesity, inflammatory bowel disease and asthma, are associated with a reduction in the diversity of the gut microbiome while healthy ageing may also be compromised by gut bacteria deficits. Other factors which help shape the composition and function of the gut microbiome, in addition to diet, include exercise, the use of antibiotics or other medications, exposure to animals/pets, geography (e.g. city versus countryside) and access to environmental green space. The Gut Microbiota for Health website is a great resource for learning more about the human microbiome.

Brain-gut-microbiome interactions: Have you heard the phrases “sick with fear”, butterflies in my tummy”? The gut is sensitive to emotion – anger, anxiety, sadness, elation – many feelings can trigger symptoms in the gut. Scientists now realise that the gut microbes can influence brain function and behaviour. This is possible due to the brain-gut-microbiome axis, a three-way communication system between the brain, the gut and its resident microorganisms. Controlling this dialogue is important in many stress-related disorders such as depression and it has even been shown in animal studies that the prominent features of depression can be transferred via a gut microbiota transplant. This suggests that it might be possible to therapeutically target the gut microbiome to improve mental health. Youtube Video

Taken together all these studies point to one simple message – mind your microbes and they in turn will look after you!

A great video on the “Guardians of the Gut” from Lindsay Hall’s lab in The Quadram Institute, can be watched here. This describes the species of bacteria present in the gut and their functions.


For more fun information about microbes and the human body, check out APC Microbiome Ireland’s website Microbe Magic










Please take a look at following graphic, produced by The International Scientific Association for Probiotics and Prebiotics (ISAPP) on Human Gut Microbiota