A Healthy Microbiome for Better Gut Health, Immune Health, and Mood Health

Roles of the Microbiome


The ‘microbiome’ is a popular topic at the moment for anyone interested in their health and well being, but what exactly it is? You may have heard about the good bacteria living in your digestive system, and might have thought about taking a probiotic to support them. Your body contains an internal community of a massive 38 trillion microbes (not just bacteria), and this community is referred to as your commensal microbiome, or microbiome for short. The guts of it is, when your microbiome is healthy it helps make you healthier, and when it is unhealthy it makes you less healthy.

When healthy and balanced, your microbiome has a range of wide-reaching effects on your health, such as creating important vitamins you need, helping to control and boost your immune system, assisting with waste elimination through healthy bowel functions, and even affecting your mood and mental state.1

However, diet, lifestyle and other factors can reduce both the number and the diversity of these organisms in our gut. This can create an environment where pathogenic (disease causing) organisms have the opportunity to establish themselves and ‘take over’ parts of your digestive system. This state of imbalance is termed ‘dysbiosis’, and often results in a broad range of health issues, including digestive problems, nutrient deficiencies, or a compromised immune system (which can lead to food intolerances, allergies, or frequent infections).

The following are the most common diet and lifestyle factors that can have a negative impact on the health of your microbiome.

Five Ways You can Upset Your Microbiome

  1. Eating a low fibre diet: as your gut microbes rely on the fibre in your food for fuel, a low fibre diet leads to a reduction in the diversity of your microbiome.(Evidence shows that those who eat more than 30 different types of plants/vegetables each week have a much more diverse microbiome compared to those who consume 10 or fewer types.2
  2. Alcohol intake: the consumption of alcohol can result in dysbiotic changes in your intestinal microbiome, and also triggers gastrointestinal inflammation.3 (If you’re consuming more than one standard drink per day, your microbiome’s probably keen for you to abstain a bit more often.)
  3. Unmanaged stress: when you are stressed, the release of the stress hormone cortisol plus adrenaline sensitises your body to inflammation, including gut inflammation.4 This disrupts the gut environment, compromising the conditions your beneficial microbes need to flourish.
  4. Leading a sedentary lifestyle: lack of exercise has also been linked to reduced microbial diversity in the gut (another good reason to get your body moving).
  5. Antibiotic use: a round of antibiotics leads to some of the core commensal organisms being destroyed. Antibiotics are designed to kill off bacteria, but unfortunately many of the good ones are destroyed as well. This leaves the gut susceptible to microbiome imbalances and dysfunction.

Improving Your Microbiome

Avoiding or addressing the diet and lifestyle factors mentioned above is important for improving the health and diversity of your microbiome. However, perhaps the most important thing you can do to help, is to consume a diet rich in plant based fibres, which will provide a great food source for the beneficial organisms to flourish.

Microbiome Foods Table

Figure 1: Foods that Feed Your Microbiome

If ‘bad’ (pathogenic) bacteria and other organisms have established in your gut and are creating dysbiosis, there are specific natural products to correct this. For example, antimicrobial herbal medicines can be used, including pomegranate (Punica granatum),5 nigella (Nigella sativa),6 and myrrh (Commiphora myrrha).7,8 These herbs work to eliminate unwanted organisms in the gut.

Then, to regenerate and rebuild the health and diversity of your microbiome, specific probiotic strains can be used. Some of these include

  • Lactobacillus rhamnosus (LGG): one of the most studied probiotic stains in the world, research shows taking LGG promotes the growth and function of key core commensal bacteria.
  • Saccharomyces cerevisiae (boulardii) (SB): multiple investigations have shown that boulardii reduces antibiotic-associated loss of bacteria, whilst also supporting the rapid restoration of the microbiome after antibiotic use.9
  • Lactobacillus acidophilus (NCFM)10 and Bifidobacterium animalis lactis (Bi-07): are two strains also highly indicated to protect and support a healthy microbiome.11

So even though diet, lifestyle or antibiotic use can upset your microbiome, there are plenty of natural medicines and diet options to restore it’s health as well, and improve the wellbeing of your whole body.

Free Assessment

If you have any digestive or immune problems, or want to improve your mood or general health and well being, we offer a free Comprehensive Assessment, to establish what is going on in your body, what is causing the problem, and the best way to sort it out. (Terms and conditions- the Assessment is a completely free service, with no obligations whatsoever.) Please call us on 3376 6911 if you have any questions at all, or ring or book online if you would like to make an appointment.


The above table and much of the information in this article is from a Metagenics blog titled ‘5 Ways You Might Upset Your Gut Microbiome and What to Do About It’.

1. D’Argenio S. The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta. 2015;451(Part A):97-102.

2. Buschman H, Bright D. Big Data from World’s Largest Citizen Science Microbiome Project Serves Food for Thought. [Internet]. San Diego (CA): UC San Diego School of Medicine. 2018 [cited 2018 July 05]. Available from: https://health.ucsd.edu/news/releases/Pages/2018-05-15-big-data-from-worlds-largest-citizen-science-microbiome-project-serves-food-for-thought.aspx

3. Engen PA, Green SJ, Voiqt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res. 2015;37(2):223-36.

4. Guilliams TG. The role of stress and the HPA axis in chronic disease management. Point Institute, Stevens point (WI). 2015;80.

5. Abdel-Haffez E, Ahmed A, Abdellatif M, Kamal A, Toni N. The efficacy of pomegranate (Punica granatum) peel extract on experimentally infected rats with blastocystis spp. J Infect Dis Preve Med. 2016;4(1):1-6.

6. Salem EM, Yar T, Bamosa AO, Al-Quorain A, Yasawy MI, Alsulaiman RM, et al. Comparative study of Nigella sativa and triple therapy in eradication of Helicobacter pylori in patients with non-ulcer dyspepsia. Saudi J Gastroenterol. 2010 Jul;16(3):207.

7. Fathy FM. Effect of mirazid (Commiphora molmol) on experimental giardiasis. J Egypt Soc Parasitol. 2011 Apr;41(1):155-77.

8. Basyoni MM, El-Sabaa AA. Therapeutic potential of myrrh and ivermectin against experimental Trichinella spiralis infection in mice. Korean J Parasitol. 2013 Jun;51(3):297-304. doi: 10.3347/kjp.2013.51.3.297.

9. Moré M, Swidsinski A. Saccharomyces boulardii CNCM 1-745 supports regeneration of the intestinal microbiota after diarrheic dysbiosis – a review. Clinical and Experimental Gastroenterology. 2015;8:237-55.

10. Anderson JM, Barrangou R, Hachem MA, Lahtinen SJ, Goh YJ, Svensson B, et al. Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM. PLos ONE. 2012;7(9):e44409.

11. Mäkeläinen H, Saarinen M, Stowell J, Rautonen N, Ouwehand AC. Xylo-oligosaccharides and lactitol promote the growth of Bifidobacterium lactis and Lactobacillus species in pure cultures. Benef Microbes. 2010 Jun;1(2):139-48.



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