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Gut Bacteria and the microbiome may not be the first things you would think of when treating infertility, but recent research shows us this is an extremely important area to consider.

Our bodies are not made up of individual parts, we are holistic and connected beings and one of the keys to getting everything working in balance is (believe it or not!) our bacteria & microbes.

Microbial cells actually outnumber human cells by 10 to 1 and contain thousands of different strains of bacteria.

The microbiome, the term that describes the ‘community’ of these microbes, have a great many influences over our health, from digestive function and nutrient absorption to immunity and inflammation. When we start to look into these roles, applications for fertility become very apparent.


Causes of DYSBIOSIS – the imbalance of ‘good’ (beneficial) and ‘bad’ (pathogenic) flora

We call DYSBIOSIS the ‘Invisible Intervention’.  As we go about our daily lives, invisible to us are the many influences that are impacting our microbial balance.

Such as;

  • Poor nutrition: Consumption of high sugar, low fibre, processed food products, junk food and alcohol
  • Herbicides and pesticides on our food (designed to KILL microbes!), other environmental and everyday household chemicals
  • Medications: antibiotics, antacids, anti-inflammatories, oral contraceptive pill, steroids
  • Stress!!
  • Inflammation and oxidative stress (free-radicals caused by inflammation)

The over-use of antibiotics is of particular concern. This is having major implications on our microbiomes with the most affluent countries in the world now showing the least diversity in their gut flora. This is mostly due to antibiotic use but also from stress and the modern diet!


Importance of healthy and robust digestive and reproductive tract flora

Research into the microfloras’ role in health is a relatively new field of science but what we do know is they are involved in many essential metabolic and physiological processes, such as;

  • Digestion and assimilation of food (including energy extraction)
  • Normal gastro-intestinal motility
  • Availability and production of many essential nutrients
  • Optimal immune function including direct and first line defense against pathogens
  • Weight metabolism
  • Mood management
  • Insulin and blood glucose regulation
  • Lipid (fat) regulation
  • Inflammation regulation


Applications for Fertility Management

Research has shown the microbiome has direct links to Fertility applications, including;

Optimising Nutritional status

Some nutrients are actually made by bowel flora. Some B Vitamins and Vitamin K are produced by specific microbes in the bowel and are then available for the body to use. Bowel flora are also involved in metabolizing bile acids, plant sterols (helpful) and getting rid of xenobiotics (harmful environmental toxins that can mimic estrogen in the body and contribute to infertility).

Addressing digestive issues

Proper digestive function is key to overall health and vitality and the ‘mucosal gut barrier’ (the lining along the inside of the gastrointestinal tract – GIT) is our first line of defense against pathogens and infection. The same ‘invisible intervention’ that causes dysbiosis, effects the integrity of the gut lining and can contribute to a condition of increased permeability known as ‘Leaky Gut’. Leaky Gut makes us more susceptible to infections, food intolerances and allergies. It also triggers an immune response and inflammation, and if left untreated can cause Auto-immune disease.

Addressing dybiosis is a key factor to optimizing digestive function and ensuring a robust and well functioning gut barrier. Constipation, diarrhoea, bloating, wind, stomach pains, food intolerances, foggy brain, poor memory, mood disturbances and autoimmune conditions are all signs that your digestive system is compromised and there is some level of increased permeability that needs to be addressed.

Microbes in the reproductive organs

Until recently it was believed the site of conception (uterus and fallopian tubes) was sterile and the first exposure to microbes was during birth. We now know that the reproductive organs (including the uterus, fallopian tubes, follicular fluid, testes, seminal fluid etc) are all rich with bacteria particularly the Lactobacillus genus. Researchers have suggested that these microbes have influence over everything from ovulation, embryo maturation, sperm number and motility to implantation and overall IVF outcomes (1) (2) (3)

Reducing bacterial infections

Infections of any kind can put pressure on the immune system and other organs causing problems for fertility. But infections in reproductive organs are even more concerning.

  • Bacterial Vaginosis (BV)

    • is a common infection characterized by a lack of Lactobacilli (beneficial flora) and an overgrowth of pathogenic bacteria, triggering localised inflammation.  Researchers have identified high rates of BV infection in IVF patients and have attributed abnormal vaginal microflora to be associated with reproductive failure and adverse pregnancy outcomes, ranging from early pregnancy loss to late miscarriage and preterm birth (2) (4)
  • Staph aureus

    • is one of the most common infective bacteria found in seminal fluid infections and has direct implications on sperm motility and viability (5) (6)
  • Chronic yeast infection Candida albicans (Thrush)

    • although not bacterial, is a common infection that can drive inflammation and contribute to dysbiosis in the gut and reproductive tract. Candida also allows the pathogenic bacteria Staph Aureus (a key bacterium identified in infertility) to adhere to it – protecting it from control by our immune system and encouraging pathogenic bacterial overgrowth (7).

 Modulating the immune system

Having a strong and robust gut flora with plenty of beneficial ‘probiotics’ as opposed to an overgrowth of ‘pathogenic’ bacteria has many positive effects on the overall function of the immune system, contributing to optimal fertility.

  • Ensures healthy and well functioning GIT mucosal barrier
  • Greatly reduces chances of pathogenic infection
  • Direct induction of immune cells (Secretory IgA) via Peyer’s Patches in the small intestine
  • Reduces localized and systemic inflammatory responses including allergic responses

 Reducing Inflammation and oxidative stress

Acute inflammation is an important part of our normal immune response, but chronic or hypersensitive inflammation is a sign that our immune system is dys-regulated. Chronic inflammation is a driver of many conditions that can contribute to infertility and pregnancy complications. (8), (9), (10)

  • Endometriosis, adenomyosis, PCOS, uterine fibroids, thyroid problems, other autoimmune conditions & PID
  • Pregnancy complications including pre-eclampsia and Pre-term births
  • Inflammation also effects ovulation and hormone production (eg amenorrhea & estrogen dominance) and can alter endometrium receptivity (8)
  • Oxidative stress is the bi-product of inflammation and causes damage to cellular DNA, membrane lipids & cell replication – all of which are important mechanisms in fertility!

Optimising sperm count and motility

Male infertility is estimated to contribute to 40-50% of infertile couples, and seminal fluid infections have shown direct effects on sperm count and motility. Recent research has suggested a strong correlation between seminal bacterial communities and semen quality, with researchers concluding Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas (pathogenic bacteria) (11) (12)


How do we ensure a healthy, robust Microbiome?

Our microbiome begins its colonization in utero, is further impacted by delivery method and continues its development during breast feeding. An infant’s microbiome is fully established by the time it is 3 years old.

To protect and nurture our own microbiome we need to avoid the ‘invisible intervention’ as much as possible;

  • Only take medications and antibiotics when absolutely necessary – and always take a quality probiotic concurrently – and then for at least a month after (ideally 3 months). It can take up to 2 years for your microbiome to re-establish after just one course of antibiotics. And some strains will never recover. (13)
  • Avoid environmental toxins as much as possible
  • Address stress and ensure good sleeping patterns

We need to eat a nourishing ‘microbiome diet’

  • Avoid processed sugars and carbohydrates
  • Limit gluten containing foods and alcohol
  • Eat lots of pre & pro-biotic rich foods
  • Eat a pre-dominantly plant-based diet – aim for 40 serves of different plant foods a week
  • Take the RIGHT probiotic supplement


What is the RIGHT probiotic supplement?

The most essential thing to understand here is that not all probiotics are created equal.

TGA (Therapeutic Goods Association) in Australia only specifies probiotics to be labeled with the Genus and species – this is a major problem as the benefit and effectiveness of a probiotic is only (and completely) determined by the STRAIN.

Let me give you an example you would’ve all heard of;

Genus – Lactobacillus, Species – Acidophilus

There are literally thousands of strains of Lactobacillus Acidophilus but only a few of them have been scientifically studied to be effective and beneficial. Unless the probiotic has the STRAIN identified on the bottle – you may be taking any old L. Acidophilus that is not guaranteed to be effective.

The other thing that is very important to understand is that different strains have varying roles in the body. We liken this to dogs and differing breeds. All dogs are animals (genus), canines (species), but the different breeds (strains) have completely different characteristics. You wouldn’t use a Chihuahua as guard dog if you could get a German Shepherd!!

It is also very important to get a good quality probiotic, as (due to cutting corners in processing) many of the over-the-counter brands don’t even contain live bacteria!

It’s important to get the advice of a professional when choosing your probiotic, this ensures you are getting the right product for your needs. Make sure it has research to prove it is effective, appropriate and the best choice for you. As a general rule of thumb if the strain is not identified on the bottle don’t buy it!

When you do get pregnant there is a well- researched strain that has been isolated from human breast milk (rather than bowel flora) that is very beneficial during pregnancy and breastfeeding,

Lactobacillus Fermentum CECT5716.

As you can see the microbiome has an important role to play in our health, vitality AND to optimize fertility outcomes. Please contact a health professional to get advice on how a probiotic may help you on your fertility journey.




(1) Pelzer ES, Allan JA, Waterhouse MA, Ross T, Beagley KW, et al. (2013) Microorganisms within Human Follicular Fluid: Effects on IVF. PLoS ONE 8(3): e59062. doi:10.1371/journal.pone.0059062

(2) Reid G et al (2015) Microbes central to human reproduction. Am J Reprod Immunol 2015; 73: 1–11

(3) Ido Sirota et al, 2015 Potential Influence of the Microbiome on Infertility and Assisted Reproductive Technology Semin Reprod Med. 2014 January; 32(1): 35–42.

(4) Verstraelen,, H & Senok AC: Vaginal lactobacilli, probiotics, and IVF

Reprod. Biomed 2005 Dec;11(6):674-5).


(5) Gupta S, Vijay P (2012) Human Sperm Interaction with Staphylococcus aureus: A Molecular Approach Journal of Pathogens Volume 2012 Article ID 816536 doi:10.1155/2012/816536

(6) Momoh, A et al 2011 Pathogenic bacteria-a probable cause of primary infertility among couples in Ekpoma J. Microbiol. Biotech. Res., 2011, 1 (3): 66-71


(7) Kong E, Jabra-Rizk MA (2015) The Great Escape: Pathogen Versus Host. PLoS Pathog 11(3): e1004661. doi:10.1371/journal.ppat.1004661

(8) Weiss et al 2009. Inflammation in reproductive disorders Reprod Sci Feb;16(2):216-29. doi: 10.1177/1933719108330087


(9) Mengheri E, 2008 Health, Probiotics, and Inflammation JClinGastroenterol 2008;42:S177–S178


(10) Isolauri et al 2001 Probiotics: a role in the treatment of intestinal infection and inflammation? Gut 2002;50:iii54-iii59 doi:10.1136/gut.50.suppl_3.iii54


(11) Roseenfeld, Y & Shai, Y 2006. Lipopolysaccharide (Endotoxin)-host defense antibacterial peptides interactions: Role in bacterial resistance and prevention of sepsis BBA Volume 1758, Issue 9, Pages 1513–1522


 (12) Wend et al 2014 Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality. PLoS One. 2014 Oct 23;9(10):e110152. doi: 10.1371/journal.pone.0110152. eCollection 2014.


(13) Jernberg C1, Löfmark S, Edlund C, Jansson JK 2007 Long-term ecological impacts of antibiotic administration on the human intestinal microbiota.

ISME J. 2007 May;1(1):56-66.