Microbiome: Tending Your Bacterial Garden

one boy with 3 companions planting a medicinal plant

Bacteria- we’re made of them! Well, not completely of course, but more than you might think. Approximately 2kg of our weight is made up of microbial organisms. For every human cell in our body, there is a bacterial cell. There are over 1000 species of bacteria in the gut alone! Not only are there more bacteria than we thought, but we are learning an astonishing amount about how exactly our bacteria shape every part of our lives. The bacteria which make up our particular body’s colony are our individual microbiome. A lot of these (75%) live in our gut, but also on our skin, and on every mucosal surface including our sinuses.


Everyone’s microbiome is different. Not only is our bacterial ‘garden’ different from everyone else’s, it can also change over time and is influenced by many factors. Our particular bacterial makeup is influenced by many things including our genetics, our environment, our diet, where we live in the world, our exposure to chemicals and our state of health.


But we have some things in common. Healthy people have about 80% of bacterial strains in common, known as the ‘core’ strains. We also know that diversity is associated with good health, so the more different strains you have, the better. Gardens are the same- monocrops (like whole fields of just corn for example) are more vulnerable to disease! Diversity in the microbiome is increased when you’re a hunter/gatherer, and decreased when you live in a city and eat lots of processed fast food.


Things we know the microbiome has an influence on:

  • Metabolic function- cholesterol, insulin resistance, inflammation
  • Appetite regulation
  • Immune development and function
  • Vitamin synthesis
  • Digestion (obviously) and disorders of the digestive system
  • Reducing the overgrowth of pathogens- unwanted bacteria etc
  • Producing Short Chain Fatty Acids (SCFAs) such a butyrate, an important anti-inflammatory compound and immune modulator
  • Detoxification (the gut bacteria detoxify at least as much as the liver!)
  • Neurotransmitter synthesis (yep, they can make us feel good…or not)


Dysbiosis is the name for when bacteria is out of balance. You can see from the list above that a poor bacterial balance will have many potential negative consequences for our health. Sometimes weeds can get really out of control in any garden. A weed, remember, is just a plant in the wrong place at the wrong time. In regards to your gut, this may be an overgrowth of Candida albicans or Helicobacter pylori, or it may be that the bacteria is just in the wrong part of your gut, as is the case in SIBO (Small Intestinal Bacterial Overgrowth). Sometimes supporting your immune system and using targeted probiotic treatments are enough, but other times some serious weeding is needing! Natural botanical extracts do this very effectively when properly prescribed.


Probiotics. We know enough now about our microbiome to know that taking probiotic supplements (or fermented foods) is not simply ‘putting back the good bacteria’. It’s not just planting seeds in our gut that we hope will grow! Specific strains of probiotic or ‘beneficial bacteria’ have specific functions in the gut and act as catalysts for a whole range of things to happen. For example, Lactobacillis rhamnosus (LGG) and Sachromyces cerevisiae (boulardii) can specifically help to rebuild the ‘core’ bacteria we discussed earlier. A specific Lactobacillus acidophilus (NCFM) has been shown in studies to reduce pain for those with Irritable Bowel Syndrome (IBS), perhaps because of its effects on increasing natural opioid (pain relief) receptors in the mucosal layer of the gut.


Enhancing your microbiome- tending your bacterial garden! So the right balance of bacteria can mean we have a better chance of really good physical and mental health. But how to achieve this? Here are some simple steps to take to lovingly tend your microbiome:

  • Avoid fast foods, fried foods, processed foods: Just 10 days on a fast food diet can decrease your microbial diversity by 40%!
  • Since 70% of our bacteria are in our colon, getting your poo right really does make a difference! This starts with fibre…
  • Fibre is the first food choice of our gut bacteria. Without it, they will start to eat the natural mucus barrier in our guts. This can’t be good right? It increases inflammation and can lead to further issues in the gut. Increasing the different plants in your diet can double your microbial diversity.
  • Special foods include those containing FOS (fructo-oligo-saccharides) and Inulin, key prebiotics that feed bacteria: garlic, leeks, onions, Jerusalem artichokes, asparagus, banana, barley, honey.  
  • ..and those containing Resistant Starch: cooked cold potatoes, bananas, white beans, lentils, raw rolled oats
  • ..and those containing polyphenols: blueberries, strawberries, peaches, plums, tea, cocoa, chocolate (yep, it’s a health food, but you knew that didn’t you?)
  • ..and also other fibre rich foods and those containing prebiotics such as: beetroot, kiwifruit, fennel bulb, green peas, snow peas, sweetcorn, chickpeas, kidney beans, soy beans, cashew nuts, flaxseeds, dried fruits
  • Avoid the use of antibiotics unless absolutely necessary (for more on this read about Microbial Resistance here). If you do need to take them be sure to take the right kind of probiotic supplement to help replenish core bacteria, along with plenty of fibre!
  • Exercise increases your microbial diversity
  • Stress, lack of sleep, and lack of time outdoors in green spaces can all have negative impacts on your microbiome.
  • Talk to your natural health practitioner about addressing any dysbiosis and eliminating any unwanted weeds.


Tending your microbial garden is just like tending the one you have outside- doing a little bit every day makes a big difference and leads to less work later on. Identify weeds, nourish the soil, feed your plants and enjoy the harvest of a healthy, balanced body and mind.


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