what is the gut microbiome? 

The microbiome is the trillions of microorganisms (also called microbes or microbiota) of thousands of different species that live over and inside the surfaces of our body, like a ‘living’ paint, which at a microscopic scale, is teeming with life. These living microorganisms include not only bacteria, but also fungi, parasites, and viruses. 

The largest concentrations of microbes are found in our gut, particularly in our large intestine (although there is growing evidence that these microbe populations are everywhere, including the lung and even the brain). Since 2007, when the massive human microbiome project2 was first launched, research has exploded and we have discovered that these microorganisms (the number of them, types of different ‘bugs’ and the interplay between them) all have a profound effect on our health. In a way, our microbiome could be said to be the most important ‘organ’ in our body.

The organisms in the microbiome can be either helpful or potentially harmful, and even those deemed harmful can react differently in different environments, meaning there is still a lot to learn! Most microbes are symbiotic (both they and our human body benefit from them being there), but some have been identified as being pathogenic (damaging or causing disease). 

These gut microorganisms can produce chemical signals and proteins that interact with our immune system (80% of which, live in our gut),2 our enteric nervous system (a vast nerve network, which connects directly to our brain, via the vagus nerve) and also our gut wall, either improving our health, or creating leaky gut

Many of our gut villains can disrupt the healthy microbiome balance and when this disruption is severe and prolonged, we call it dysbiosis. Dysbiosis is thought to be a root cause of many chronic diseases,3 mental illness, inflammation and multiple health symptoms.  

how does the microbiome develop?

Each person’s microbiome composition is as unique as a fingerprint.4 It begins developing in your mothers’ womb. The first microbiome ‘seeding’ is from your mother, as you pass through the birth canal. This new microbiome is then nourished and supported by breastfeeding and early infant experiences. 

Antibiotics, caesarean section, your mothers’ microbiome health and…


  1. Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project Nature 449, 804–810 (2007). https://doi.org/10.1038/nature06244
  2. G. A. Castro and C. J. Arntzen Immunophysiology of the gut: a research frontier for integrative studies of the common mucosal immune system | American Journal of Physiology-Gastrointestinal and Liver Physiology 1993 265:4, G599-G610 
  3. Clarke TH, Gomez A, Singh H, Nelson KE, Brinkac LM. Integrating the microbiome as a resource in the forensics toolkit Forensic Sci Int Genet. 2017 Sep;30:141-147. doi: 10.1016/j.fsigen.2017.06.008. Epub 2017 Jun 27. PMID: 28728057.
  4. Dunn AB, Jordan S, Baker BJ, Carlson NS. The Maternal Infant Microbiome: Considerations for Labor and Birth . MCN Am J Matern Child Nurs. 2017 Nov/Dec;42(6):318-325. doi: 10.1097/NMC.0000000000000373. PMID: 28825919; PMCID: PMC5648605.