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The breakdown: What is your microbiome?

Gut Health 101

The microbiome (which you may have also heard referred to as gut bacteria, gut microbes, gut microbiota or gut flora) is having a moment. The topic of gut health is increasingly being discussed, but do you actually know what your microbiome is, and why it’s so important?

The microbiome is the home for what makes up the 10-100 trillion microbial cells in our body. While these microbes are primarily found in our gut, bacteria also colonise other areas in the human body such as the skin, mouth, nose and vagina.


The majority of our microbiome is established in the early years of our lives. In fact, there is a lot of research to confirm that the first 1000 days of life, or roughly until the age of 3, is when we form our microbiomes.

A baby is first exposed to colonising bacteria during the delivery process. It's the first contact of microbes from a mother's vaginal microbiome, skin and rectum that start the establishment of a baby's microbiome. When a baby is born via C-section these first microbes come from skin and the birthing environment. Research indicates that delivery method has an impact on development of asthma or allergies in children. Other early influences include whether or not a baby is breastfed, exposure to animals, soil and medication early in life.


Whilst the basic structure of the microbiome is established in our early years, the specific  composition will continue to develop throughout our lives and can be influenced by a variety of factors such as:

  • DIET: The diet remains key to defining the structure and diversity of the microbiome. Plant based diets or those with more plants included, have been associated with a healthy and diverse gut microbiota, whereas diets high in processed foods have been associated with a decreased number of beneficial bacteria.

  • ANTIBIOTICS: Antibiotics often destroy both the harmful and the beneficial microbes in our gut. This can lead to an imbalance in our gut bacteria known as dysbiosis, which can lead to digestive disturbance.

  • PROBIOTICS AND PREBIOTICS: On the other hand, our microbiomes can be positively influenced through the use of probiotics and prebiotics. Probiotics are living microorganisms that - when taken appropriately - can increase and support the gut microbes. Prebiotics are selected foods which essentially feed the gut microbes. They are classified by being able to cause beneficial changes in the structure of the gut microbiome.


The gut microbiome has a hugely important role in regulating the functions of your body. It aids the absorption of nutrients, produces enzymes, vitamins, amino acids and short chain fatty acids. When our microbiomes are balanced, our intestinal barrier can perform optimally. Having a strong intestinal barrier, or gut wall, is essential; it regulates nutrient absorption and protects us from organisms that can cause disease – an important factor for not just our gut, but also our immune health.


Research has confirmed the link between the intestinal microbiome and a variety of chronic diseases such as inflammatory bowel disease, type 2 diabetes, cardiovascular disease and colorectal cancer, autoimmune conditions, asthma, behavioural diseases and obesity.

It is becoming increasingly clear that caring for the bacteria within our gut is fundamentally important for our health and for protecting us against disease.

Avershina, E., Storrø, O., Øien, T., Johnsen, R., Pope, P. and Rudi, K., 2013. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiology Ecology, 87(1), Available from: https://pubmed.ncbi.nlm.nih.gov/24112053/

Durack, J. and Lynch, S., 2018. The gut microbiome: Relationships with disease and opportunities for therapy. Journal of Experimental Medicine, 216(1), Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314516/

Hasan, N. and Yang, H., 2019. Factors affecting the composition of the gut microbiota, and its modulation. PeerJ, 7, Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699480/

Jakobsson, H., Abrahamsson, T., Jenmalm, M., Harris, K., Quince, C., Jernberg, C., Björkstén, B., Engstrand, L. and Andersson, A., 2013. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut, 63(4), Available from: https://pubmed.ncbi.nlm.nih.gov/23926244/

Klingensmith, N. and Coopersmith, C., 2016. The Gut as the Motor of Multiple Organ Dysfunction in Critical Illness. Critical Care Clinics, 32(2), Available from: https://pubmed.ncbi.nlm.nih.gov/27016162/

Kristensen, N., Bryrup, T., Allin, K., Nielsen, T., Hansen, T. and Pedersen, O., 2016. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Medicine, 8(1). Available from: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0300-5

Lozupone, C., Stombaugh, J., Gordon, J., Jansson, J. and Knight, R., 2012. Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/

Quraishi, M., Sergeant, M., Kay, G., Iqbal, T., Chan, J., Constantinidou, C., Trivedi, P., Ferguson, J., Adams, D., Pallen, M. and Hirschfield, G., 2016. The gut-adherent microbiota of PSC–IBD is distinct to that of IBD. Gut, 66(2), Available from: https://pubmed.ncbi.nlm.nih.gov/27196590/

Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I. and Tuohy, K., 2017. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition, 57(1), Available from: https://pubmed.ncbi.nlm.nih.gov/28393285/

Thursby, E. and Juge, N., 2017. Introduction to the human gut microbiota. Biochemical Journal, 474(11), Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433529/

Grace Carey-Caton, Nutritional Therapist

Grace Carey-Caton is a Registered & Licensed Nutritionist (mBANT) (rCNHC). Her clinic is London based and she specialises in Gut Health and Female Health.