Digestion Part 9: Gut Microbiome


The microbiome is the name given to the trillions of bacteria that live on, and in, our bodies.

Your microbiome has 10 times as many cells as our whole body, and over 100 times the number of different genes. Different humans will share 99% of their genes, but their respective microbiomes will share only 10% of their DNA. These factoids should give you an impression of the size and diversity of the human microbiome.

These microbiota, or bacteria, are grouped based on their location. This post is interested in the gut microbiome, but there are also oral, genital, faecal (seriously) and respiratory microbiomes.

Prior to 2000 there was little research on the microbiome. Today it is a hot topic, but we are still only scratching the surface of what these trillions of bacteria can do (for better or worse).

That said having unbalanced gut flora has been shown to have a deleterious impact on the immune system, risk of major disease (e.g. IBD, diabetes and cancer), mental health, weight gain, and gene expression. For example, we can predict with 60% accuracy whether someone is obese by looking at their DNA. Using an individual’s gut microbes we can be 99% confident. Your gut bacteria can also act like hormones, sending information to your brain which then controls your body’s response to insulin, or how full you feel after eating.

We get these bacteria from food, from our environment, and from our mothers. Individuals born from C section and/or who don’t breast-feed have significantly different gut flora from those that do. Assuming that these factors are now beyond our control, if we want to improve our gut flora that leaves us with diet and environment.

Certain foods, and medications, can harm your gut flora. Gluten, sugar, high fructose corn syrup, GM foods, and anything doused in agricultural chemicals are all harmful, as are antibiotics, protein pump inhibitors, and NSAIDs.

To improve your microbial diversity, eat fermented foods on a regular basis, e.g. pickled veggies, kombucha, kimchi and sauerkraut. These foods are “probiotics”. A probiotic is a food or dietary supplement containing live bacteria that replace or add to the beneficial bacteria normally present in the gastrointestinal tract. A “prebiotic” is a non-digestible food which promotes the growth of beneficial bacteria. Prebiotics are like food for probiotics. Useful foods considered prebiotics include asparagus, artichokes, onions, garlic, oats, and beans.

Finally, soap and water now and then are fine, but by depending on hand-sanitizer at multiple points every day we may be denying our bodies exposure to a wide assortment of microbes, many of which could actually do us good. I’ve been a fan of the hygiene hypothesis for a while, and this gives a pathway through which it could work.


If you want to find out more about the gut microbiome there are several TED talks that discuss it, you can find them here, here, and here. You could also read more on Mark’s Daily Apple. If you want to know more about how the gut microbiome affects weight gain, UBiome have a free PDF available here.

P.S. If you are really committed you can get your microbiome analysed by UBiome. UBiome will tell you what kinds of bacteria you have in your gut, what they are associated with and how similar your gut flora is to other populations (e.g. people of a similar age or nationality). In addition you’ll be helping to further science as your data will become part of a larger dataset which can be tested in future.