​You And Your Microbiome

Words: Laura Tilt

Think your gut bacteria simply help digest food? Think again. New research suggests the balance of microbes living in your gut influence everything from immune function to body weight. So how can you maintain a healthy balance?

Picture a sea of 40 trillion bacteria weighing more than the human brain… say hello to your microbiome – the personal blueprint of bacteria living in your body.

First used by Nobel Prize winning biologist Joshua Lederberg in 2001, the word “microbiome” is used to describe the trillions of bacteria (and the genes they code) that share our body space1.

Our understanding of the human microbiome is still fairly new, but scientists have known about the link between the microbiome and health since the 1700’s, when they found that the types of bacteria in the mouths and stools of people who were healthy and sick were different2.

Fast-forward 300 years and the big picture of the microbiome and health is emerging, with research suggesting the number and species of bacteria in our guts affect far more than digestion.

Microbiome 101

Although bacteria live all over the body (including skin and body fluids) the vast majority of them are found living in our digestive tract1 (also called the ‘gastrointestinal tract’ or ‘gut’).

Within 24 hours of birth, the gut becomes home to trillions of bacteria that live throughout it’s length (running from mouth to bottom, including the food pipe, stomach, small intestine and large intestine). A single gram of stomach contents (a quarter of a teaspoon) houses between 10 and 103 bacteria, with this number increasing to 1000 bacteria per gram by the time you reach the large intestine3.

During the first few months of life, the landscape of our gut bacteria changes dramatically, with the start of breast or formula feeding, and with each new food added to our diet. Our environment (where we live), the foods we eat, and even the microbiome of our mum plays a role in how our own bacteria develop.

It’s no surprise then, that the microbiome is truly personal. Although we are virtually identical to each other in terms of our genes (around 99% of our genetic makeup is similar), we can be up to 80-90% different from each other in terms of the communities of bacteria in our guts. And that’s where it really gets interesting… because it’s this personal blueprint of bacteria that seems to influence our health risk.

The healthy microbiome

Scientists estimate there are around 1000 species of different bacteria that can live our guts3. In the MetaHIT study (a 4 year EU funded project looking at the links between gut bacteria and health) researchers found that on average, adults carry about 160 of those species4.

Together these bacteria (and the genes they code) carry out up to 19,000 jobs in the body. Bacteria in the small and large intestine break down sugars in the foods we eat, and harvest energy from fibre and resistant starches (a type of carbohydrate) that the body can’t digest. This process (called fermentation) transforms undigested carbohydrates and fibres into compounds known as short chain fatty acids (SFCAs), which have anti-inflammatory effects 3, and may even play a role in how satisfied we feel after eating.

Remarkably, the bacteria in our guts also provide us with vitamin K (important for blood clotting and bone health) and most of the family of B vitamins5, which help transform carbohydrates into energy.

A second vital job of the microbiome is supporting the immune system. From an early age gut bacteria train the immune system to respond properly to antigens – substances that can trigger allergic reactions. The bacteria lining your gut also protect against disease by acting as a barrier between your body’s internal organs and tissues and harmful bacteria from the external environment.

Dysbiosis and disease

Given the number of important jobs that the microbiome carries out, it’s no surprise that changes to the balance of bacteria can have a knock on effect on our health.

Two main “families” of bacteria dominate a healthy microbiome – the Bacteroidetes (mainly found in the large intestine) and Firmicutes (mainly found in the small intestine)6. Studies suggest that a change in the balance of these groups (termed ‘dysbiosis’) can alter immunity, increasing our risk of developing conditions like irritable bowel syndrome (IBS) and potentially even diabetes and inflammatory conditions.

Although the exact cause of IBS (a condition where gut function changes, triggering symptoms like stomach pain, bloating and diarrhoea) isn’t clear, people with the condition show a 2-fold increase in the ratio of Firmicutes to Bacteroidetes in the gut. Similarly, changes in the number and diversity of the microbiome have been seen in inflammatory bowel disease.

The balance of these bacterial communities may even affect how easily we gain body fat. Comparisons of obese and lean mice show that they have different numbers of Bacteroidetes and Firmicutes. When lean mice are transplanted with gut bacteria from obese mice, they become hungrier, and start to ‘harvest’ more energy from food, leading to an increase in body fat7. Similarly, transplanting obese mice with Bacteriodetes (nicknamed the ‘lean’ microbes2) leads to weight loss and changes in the way they metabolise food.

The F word

When it comes to your microbiome, diet plays an important role in maintaining a good balance of bacteria. In fact, studies show that changing the amounts of protein, carbohydrate and fat can alter the microbiome in as little as a day.

In one 2014 study8, healthy adults switching from a plant-based diet (consisting of cereal for breakfast and meals of vegetables, rice, lentils and fruit for snacks) to a completely animal based diet (of meat, eggs and cheeses) showed a decrease in the diversity of their gut bacteria in just one day. The meat and cheese diet also resulted in lower levels of short chain fatty acids (SFCAs), thanks to a lack of fibre.

In another diet-switch study, researchers saw reductions gut bacteria and SFCAs after switching adults from a high fibre, low fat diet to a high fat low-fibre western-style diet. As well as less bacterial diversity, they saw changes linked with inflammation, similar to those seen in inflammatory bowel disease9.

Regardless of whether you’re a meat eater or vegetarian, it seems eating plenty of fibre is crucial – Italian researchers found levels of SCFAs were linked with the amount of fruit, vegetables, pulses and fibre regularly consumed, regardless of diet – with highest levels were found in those consistently following a Mediterranean-style diet10.

Latest guidelines from SACN – the UK government’s scientific advisory board – recommend that we aim for 30 grams of fibre a day, which is a good target if you’re looking to keep a healthy balance of bacteria in your gut. However, this might not be realistic for people with conditions like IBS, because they can experience more symptoms with an increase in fibre intake.

What about probiotics?

Outside of diet, there’s been growing interest in the use of probiotics (also known as beneficial bacteria) as a way of maintaining a healthy microbiome11.

Probiotics can be described as specific strains of beneficial bacteria that encourage the growth of other good bacteria in the gut. They aren’t a new invention – they’ve existed for thousands of years in fermented foods like yoghurt, cheese and drinks like kombucha (a type of fermented tea) – but it’s only in the last few decades that they’ve become available as dietary supplements.

Because stress, alcohol, diet and antibiotics can change the balance of gut bacteria (research shows it can take up to four years for some species to be restored after antibiotic treatment2), using probiotics to help keep the microbiome healthy is an attractive option.

While it’s still early days in terms of studies, one common condition that seems to have some potential for probiotic therapy is irritable bowel syndrome (IBS). In one study carried out in 2012, researchers at Kings College University in London tested the effects of Symprove (a live, water-based multi-strain probiotic) on IBS symptoms such as bloating and gas.

During the study, 186 adults with IBS were randomly placed in one of two groups and given either a daily dose of Symprove, or a liquid placebo – a dummy supplement13. After 12 weeks, the participants in the Symprove group experienced a 63.3% drop in the severity of their symptoms, versus a 28.3% drop in the placebo group.

Getting to the gut

Although there is a long way to go before we understand the potential for probiotics to manage health conditions, one factor experts agree on is that a probiotic must survive digestion and settle in the gut in meaningful amounts for it to be effective.

Interestingly, this isn’t as straightforward as it seems. In an independent study carried out in 2014, researchers from University College London12 tested eight of the top probiotic brands (including Actimel, Symprove, Biobalance, Probio7, Yakult and VSL#3) to see how they fared against digestion.

As well as looking at whether the supplements contained the numbers of bacteria they claimed, they also tested which were able to survive the acidic conditions of the stomach, by simulating an environment similar to the human gut.

Surprisingly, results showed that only the liquid based products (Actimel, Yakult and Symprove) contained as many bacteria as the label stated, with freeze dried products (capsule or powders) containing far fewer.

As the tests continued, only two products (Symprove and VSL#3) survived the acidic conditions of the gut in meaningful numbers and only two (Symprove and VSL#3) went on to grow in meaningful amounts over a period of 10 hours.

Although this might seem disheartening for the majority of brands, it highlights the importance of optimizing both the dose and delivery method, to ensure consumers can be confident that they are investing in an effective product.

Despite these challenges, the potential for probiotics to have a positive impact on health remains an exciting prospect, and one that will no doubt continue to grow.


1. The NIH HMP Working Group. The NIH Human Microbiome Project. Genome Res. 2009;19(12):2317-2323. doi:10.1101/gr.096651.109.

2. Luke K Ursell, Jessica L Metcalf, Laura Wegener Parfrey and RK. Defining the Human Microbiome. NIH Manuscripts 2013;70(Suppl 1):1-12. doi:10.1111/j.1753-4887.2012.00493.x.Defining.

3. Bull MJ, Plummer NT. Part 1: The Human Gut Microbiome in Health and Disease. Integr. Med. (Encinitas). 2014;13(6):17-22. doi:26770121.

4. Ehrlich D. Metagenomics of the Human Intestinal Tract.; 2010. Available at: http://www.metahit.eu/index.php?id=234.

5. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Curr. Opin. Biotechnol. 2013;24(2):160-168. doi:10.1016/j.copbio.2012.08.005.

6. Brown K, DeCoffe D, Molcan E, Gibson DL. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 2012;4(8):1095-1119. doi:10.3390/nu4081095.

7. Turnbaugh PJ, Ley RE, Mahowald M a, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444(7122):1027-31. doi:10.1038/nature05414.

8. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014;505(7484):559-63. doi:10.1038/nature12820.

9. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8:51. doi:10.1186/s13073-016-0307-y.

10. De Filippis F, Pellegrini N, Vannini L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut 2015:gutjnl-2015-309957. doi:10.1136/gutjnl-2015-309957.

11. Hemarajata P, Versalovic J. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap. Adv. Gastroenterol. 2013;6(1):39-51. doi:10.1177/1756283X12459294.

12. Fredua-Agyeman M, Gaisford S. Comparative survival of commercial probiotic formulations: tests in biorelevant gastric fluids and real-time measurements using microcalorimetry. Benef. Microbes 2015;6(1):141-51. doi:10.3920/BM2014.0051.

13. Sisson G, Ayis S, Sherwood RA, Bjarnason I. Randomised clinical trial: A liquid multi-strain probiotic vs. Placebo in the irritable bowel syndrome – A 12 week double-blind study. Aliment. Pharmacol. Ther. 2014;40(1):51-62. doi:10.1111/apt.12787.

Popular Stories

Sourdough Loaf

There’s always a real sense of excitement in the office when our colleague Amy brings in some of her amazing sourdough … Read More…

Vitamin D and How it Supports a Healthy Gut Microbiome

Toral Shah, nutritional scientist, functional medicine practitioner and founder of The Urban Kitchen is here to talk to us about the … Read More…

Tomato, Courgette and Ricotta Tart

Serves 4 A wonderfully easy back-to-school recipe, that’s perfect for a quick weeknight dinner, with any leftovers ideal for lunch boxes. … Read More…


It looks like you are located in the US, would you like to go to our dedicated US website?