by Dr Jess Braid

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 bottle feeding can all disrupt this early microbiome and have long-term effects. Throughout life, diet, environmental exposures, stress and medications can all impact the microbiome composition and can either be beneficial to health, or place you at a greater risk of many diseases. 


can I test how healthy my gut microbiome is? 

Yes and no. We can get an overview and snapshot of severe imbalances in the gut microbiome by doing a comprehensive stool test (yes, we test your poo!). There are many of these available (we recommend Genova Diagnostics GI Effects) –  they can look at some of the organisms in your gut, substances produced by the bacteria in your gut, inflammatory markers, enzymes and bile salts. 

Whilst this testing is helpful, when it comes to bacteria, many of the species of bacteria in our gut are anaerobic (they don’t survive in air), so we are only able to see the aerobic bacteria under a microscope when we look at the stool. More recently, newer testing has been developed, where we can also look for the genetic code of bacteria in our gut, identified by PCR testing. 

However, two problems still remain: Firstly, everyone’s microbiome is unique (so much so, that just as police look at fingerprints, in future, the residue of organisms we leave behind from our microbiome might be able to identify people5 who were present at a crime scene). This means although we broadly understand which bacteria are ‘good’ and ‘bad,’ the amount of what level is normal for each person will vary. What we do know is that the amount of bacteria and the number of different types of bacteria is important. Healthier people have a greater volume of bacteria and more different types than an unhealthy person. The sicker we are, the less diverse our microbiome. 

Secondly, for most people the gut microbiome means the bacteria in our gut, however, we are constantly learning about viruses – the human virome (our body’s own viral ecosystem). There are many more viruses than bacteria, and research shows that the viruses in our microbiome are mostly bacteriophages, capable of taking pieces of genetic code out of any bacteria and swapping it with other genes from other bacteria. Think of a bacteriophage as a virus controller, affecting the behaviour of that bacteria. 

This is why many health practitioners now suspect that when we see a lot of symptoms but we can’t find a problem in the gut bacteria, the issue may be lurking in the virome. In diseases like inflammatory bowel disease (IBS or IBD), the bacteria can look normal, yet we see huge changes in the number of viruses,6 and we still don’t know why that is. Have these viruses ‘hijacked’ the bacteria and changed their function?6 

What we should take from this is that microbiome knowledge is constantly growing and evolving (much like our microbiomes!) and that testing should only really be used to provide a broad overview in the context of symptoms.

why doesn’t my doctor talk about my microbiome? 

Although there has been an explosion in research on the microbiome since 2007, when the human microbiome project (a huge research project, to map the organisms in a large number of peoples’ microbiomes), many doctors were not taught about the microbiome in medical school (including Dr Jess)! 

Instead, doctors and the medical profession were taught about microbes as a source of infection, and how to treat those infections. Understanding the complexity of the microbiome, the potential damage from medications, and the microbiome’s impact on health is newer evidence. In mainstream medicine, there is a significant lag between evidence and changes in the teaching of up to 17 years)!7 

Whilst a growing number of progressive healthcare workers are educating themselves in functional medicine, gut health and nutrition, much of the education after medical school is self-guided or taught by pharmaceutical companies, which means that all the newer published microbiome research may not be in your doctors’ awareness. It is also not (yet) a major part of hospital guidelines for the treatment of diseases.

how can we improve our microbiome?

We are learning that many of the tried-and-tested home remedies and natural gut supports that are hundreds to thousands of years old, like fermented food, plant fibres and herbs, all have positive impacts on the microbiome and gut health. Traditional medicines, which were historically based on observation and an understanding of people and individual symptoms didn’t need to understand the microbiome to see what commonly worked to help the gut. 

We know that fibre has a big impact on gut health. The microbiome ferments the fibre in our diets, to create Short Chain Fatty Acids (SCFAs). There are healthy types of SCFA and less healthy types. Butyrate is a very important SCFA8 that balances the health of the microbiome, is anti-inflammatory, reverses gut damage, protects against bowel cancer, helps insulin sensitivity, helps manage weight control and the sensation of feeling full (satiety). It even contributes to nerve health. A diet high in fibre and prebiotics can boost butyrate production. 

It is also true that though we might not understand our microbiome, we can see that it interacts with the environmental microbiome in the plants that we eat, the soil we play in as children and the microorganisms in the world around us. 

As we become more reliant on chemicals of all kinds (from those in our foods, to those in our homes), more stressed and less nature-based, not only is our natural world being damaged, but the destruction of the natural diversity of our planet seems to mirror the decreasing diversity of our microbiome. 

Diversity in the average human microbiome has substantially decreased over time, as we have become Westernised. Even today, indigenous, protected communities have much greater diversity and bacterial numbers9. Something that we can all do is to learn from the way our great grandparents ate and lived, to try and reclaim that diversity. 

eight amazing microbiome facts

  • There are 10 times more microorganisms in our gut, than there are visible stars in the night sky – over 100 trillion microbes.
  • We are 99% microorganism and less than 1% human – the human genome project showed that human cells contain about 20,000 genes,10 but our microbiome contains over 2 million genes.11
  • Most of our individual gut microbiome develops before the age of three and is most affected by our mode of birth and whether we are given antibiotics; not by our genetics. 
  • Around 400BC, Hippocrates famously said: “All disease begins in the gut…”. All ancient cultures and traditional medicines look at food as medicine. We have ‘known’ that gut health is key, for thousands of years.
  • Although most research on the gut microbiome is recent, science has also begun to look at other areas. The lung microbiome has been shown to change in response to air pollution and affect the risk of asthma.12 We have also found that the microbiome in breast tissue is different in people who have breast cancer.13 This is an exciting and game-changing way to look at disease, which has the potential to develop new and life-changing approaches to treatment. 
  • The microbiome can affect our hormones. People with dysbiosis are more likely to have bacteria that produce an enzyme called beta-glucuronidase. This enzyme re-conjugates oestrogen (puts it back together when broken down).14 Instead of eliminating it, the enzyme works to have the body reabsorb it, raising our oestrogen levels and increasing our risk of breast cancer.
  • There are five times as many nerve cells in the gut (our gut enteric nervous system, or ‘gut brain’), as there are in our spinal cord, and four times more information is moving from the gut to the brain, as there is from the brain to the gut (although we don’t yet know what our gut is saying!). We do know that changes in microbes in the gut significantly change these signals.15 
  • Our gut bacteria may control our ability to regulate our weight. Experiments show that taking bacteria from the gut of a mouse that has lost weight after surgery and implanting it in a healthy mouse caused the mouse to lose weight. Human twin studies, where one twin is obese and one is lean, have also taken gut bacteria from the obese twin and transplanted it into a microbe-free mouse. The mouse gained weight.16 The study then transplanted the lean twins’ bacteria into the mouse, which led to weight loss. 

How can I help support my baby’s microbiome?

When babies are born in a normal vaginal birth, they pick up their first microbes from their mother. For babies born by C-section, their microbiome is different, most likely as a result of a lack of skin contact or even the environment of the operating room. To support a healthy microbiome for your baby, if you are having a caesarean talk to your doctor about a vaginal swab (if they are unaware of this research, point them to this article from Nature).17 In a small pilot study, sterile gauze was placed inside the vaginal canal in the hour before a mother was due to have C-section. This swab was then used over the baby’s mouth, face and body within the first two minutes after birth. This seemed to partially restore the baby’s microbiome. 

Once your baby has been born, breastfeeding contributes to a healthy microbiome. From then on, children likely get microbes from all over their environment; from family members, from surfaces, playing in dirt, from pets, from food and from the kinds of foods they eat. 

A child’s gut ecosystem is in a state of fairly flexible development until about age two or three, when it becomes more stable.18 That means that events (especially antibiotics) in those early years could have big consequences for your microbiome decades later. There is a fascinating article in National Geographic,19 which describes the development of the microbiome in children.

So what are these microbiomes doing for me?

Microbiomes are tiny ecosystems that I always imagine to be like a coral reef. They can be vibrant, full of colour and diverse with lots of interacting species and organisms, all coexisting and thriving or they can be like the bleached, damaged and ‘dead’ coral reefs, populated by only a few species. Just as climate change is destroying coral reefs in the ocean, our modern diets and lifestyles are guilty of doing the same to our microbiome. 

Our internal microbiome can be diverse and healthy, packed and teeming with life, and making it hard for harmful bacteria like Clostridium difficile (C-Diff) to move in and make you sick. Or it can be barren and empty, with a lot of room for the ‘bad guys’ to move in and create a problem. 

A healthy and diverse balance of ‘good’ bacteria is shown to help break down your food, produce vitamins, interact with the gut immune system to keep it happy and calm (not angry and inflamed). Some bacteria even help produce beneficial short-chain fatty acids like butyrate, which helps keep the gut wall healthy and prevents bowel cancer. We are rapidly learning that the balance of the microbiome in our gut may be the single most important determinant of our long-term health, so supporting it is the best choice we can make.

You said that even the dirt we play in as kids can have an effect on our microbiome? How?

There is a strong argument that we should encourage children to play in the dirt and soil, as this encourages a diverse microbiome. Every surface you see is covered in bacteria and (healthy) soil is one of the richest and most diverse sources of ‘good’ bacteria. The hygiene hypothesis developed by the scientific community correlates the rising allergies and immune reactions in society with an environment that is too ‘sterile’ (over-cleaning and sanitising everything). The theory is that when our immune system is not exposed regularly to lots of microbes in early childhood, it does not properly develop and we are more at risk of immune issues later. 


  1. Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project Nature 449, 804–810 (2007).
  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.
  5. 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.
  6. Mosca Alexis, Leclerc Marion, Hugot Jean P. Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? Frontiers in Microbiology, Vol7, 2016 P455   
  7. Kristensen N, Nymann C, Konradsen H.Implementing research results in clinical practice- the experiences of healthcare professionals BMC Health Serv Res. 2016;16:48. Published 2016 Feb 10. doi:10.1186/s12913-016-1292-y
  8. McNabney SM, Henagan TM. Short Chain Fatty Acids in the Colon and Peripheral Tissues: A Focus on Butyrate, Colon Cancer, Obesity and Insulin Resistance Nutrients. 2017;9(12):1348. Published 2017 Dec 12. doi:10.3390/nu9121348
  10. Moreno PA, Vélez PE, Martínez E, et al. The human genome: a multifractal analysis BMC Genomics. 2011;12:506. Published 2011 Oct 14. doi:10.1186/1471-2164-12-506
  11. Ravel J, Blaser MJ, Braun J, et al. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 Microbiome. 2014;2:16. Published 2014 Jul 18. doi:10.1186/2049-2618-2-16
  12. Hufnagl K, Pali-Schöll I, Roth-Walter F, Jensen-Jarolim E. Dysbiosis of the gut and lung microbiome has a role in asthma Semin Immunopathol. 2020;42(1):75-93. doi:10.1007/s00281-019-00775-y
  13. Hieken TJ, Chen J, Hoskin TL, et al.The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease . Sci Rep. 2016;6:30751. Published 2016 Aug 3. doi:10.1038/srep30751
  14. Parida S, Sharma D. The Microbiome–Estrogen Connection and Breast Cancer Risk  Cells. 2019;8(12):1642. Published 2019 Dec 15. doi:10.3390/cells8121642
  15. Giuffrè M, Moretti R, Campisciano G, et al. You Talking to Me? Says the Enteric Nervous System (ENS) to the Microbe. How Intestinal Microbes Interact with the ENS  J Clin Med. 2020;9(11):3705. Published 2020 Nov 18. doi:10.3390/jcm9113705
  16. Liou AP, Paziuk M, Luevano JM Jr, Machineni S, Turnbaugh PJ, Kaplan LM. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med. 2013 Mar 27;5(178):178ra41. doi: 10.1126/scitranslmed.3005687. PMID: 23536013; PMCID: PMC3652229.
  17. Dominguez-Bello, M., De Jesus-Laboy, K., Shen, N. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer Nat Med 22, 250–253 (2016).
  18. Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev. 2017 Nov 8;81(4):e00036-17. doi: 10.1128/MMBR.00036-17. PMID: 29118049; PMCID: PMC5706746.
  19. Does Your Microbiological Age Match Your Biological One?