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Microbiome and Fertility

The microbiome is the tens of trillions of bacteria and other organisms (viruses, retroviruses, fungi and archaea) that live on and in us. The gut alone has 1.5–2kg of microbes, and they digest food, producing essential enzymes, anti-inflammatories and vitamins (including the B’s and K) we can’t make ourselves.

We’ve evolved alongside our microbiome over millennia, and it’s an essential and integral part of human health and fertility. We haven’t always appreciated this, and the widespread use of antibiotics since the 1950s has coincided with a change in our relationship with our microbiome and our health.

Research into the human microbiome started in earnest in 2007, and in that short space of time, we’ve learned the microbiome is crucial for a wide range of health issues, including:

  • Weight
  • Skin health and function
  • Autism i
  • Dementia
  • Immunity
  • Cancer
  • Fertility:
      • Inflammation of the uterus lining
      • Inflammation of the cervix
      • Bacterial vaginosis
      • Implantation failure
      • Miscarriage
      • Tubal factor infertility
      • Male fertility
      • Couple fertility


We have a complex and changing relationship with the microbes that live on and in us, and while the traditional view was that bacteria are “bad” for us, there’s been a radical rethink! The microbiome extends way beyond our gut into areas of the body (such as the brain) that were previously thought sterile, and microbes colonise both the male and female reproductive tracts. They live in the vagina, uterus, Fallopian tubes and ovaries, and even the follicular fluid that surrounds the egg, with differences in the follicular fluid microbiome affecting IVF treatment outcomes. ii

The microbiome is a lot more complicated than a “soup” of microbes that live on or in us as they can form 3-dimensional structures, lattices and “biofilms” that extend across and from our cells. These have a range of functions, including protecting bacteria from antibiotics, but they also alter the state of our immune and hormonal systems.

Female fertility and the microbiome

Fertility levels, the health of pregnancies and chances of miscarriage are affected by the microbiomes of the:

  • Vagina
  • Womb
  • Fallopian tubes
  • Ovaries
  • Digestive tract

Membership of morefertile brings access to specialised tests for gut or sexual microbiome and specific fertility-based probiotics. There’s increasing evidence that repeated miscarriages and unexplained IVF failures may be due to abnormalities in the microbiome of the vagina and uterus. iii

Lactobacillus species usually dominate the vaginal microbiome in healthy women, and they produce lots of hydrogen peroxide, which inhibits the growth of other bacteria and moulds that can cause Candida or Bacterial Vaginosis (BV). BV is a relatively common (and often undetected) infection that reduces fertility, which is a particular concern for women with unexplained infertility or PCOS: iv

Groups of women BV infection rates
Fertile women with no symptoms 15.4%
Women with unexplained infertility 37.4%
Women with PCOS 60.1%


The microbiome in the gut affects the health of the microbiome throughout the body, and diet is the critical factor for the gut microbiome, as microbes rely on dietary fibres to thrive. The good news is that adjusting diet can bring significant improvements in the microbiome in just two weeks.


In a PCOS study (OK with rats), they transplanted Lactobacillus and faecal matter from normal microbiomes to rats with PCOS and remarkably, all the PCOS rats improved their menstrual cycles plus 75% of them regained normal ovary shape and lower male hormone levels. This dramatic change shows that an abnormal gut microbiome is a cause of PCOS development and that changing the microbiome is a realistic treatment option for reversing the condition. v

Chronic inflammations of the womb are difficult to detect, as obvious symptoms are rare. Despite this, we know the condition reduces fertility, and there’s a close link to an abnormal uterine microbiome which makes the womb less friendly to sperm or implantation. vi

Male fertility and the microbiome

The microbiome also affects male fertility, and men with low fertility are more likely to have abnormal microbiomes in their semen samples. The semen samples of most men have predominantly Lactobacillus dominant communities, and they cope best in challenging female environments. vii Because sex involves exchanging fluids, microbes are passed between partners (infections like Chlamydia prove this), and the sexual microbiome is a crucial aspect of couple fertility health as one person’s unhealthy microbiome can make their partner less fertile.

Creating a healthy microbiome


  1. Taking antibiotics for non-life-threatening conditions or infections as antibiotics aren’t selective in their action. They kill “good” bacteria along with the “bad” and encourage the growth of moulds and fungi that disturb the microbiome throughout the body. If you have to take them, take probiotics alongside and after them. Antibiotics profoundly impact the immune system, and a cancer study has shown that oral antibiotics before immunotherapy significantly reduces survival times for all cancer types, but the expected life expectancy of patients with lung cancer fell from 26 months to 2.5 months viii
  2. Stress profoundly alters the body’s balance, and Crohn’s disease, ulcerative colitis and IBS are stress-related digestive conditions. Stress triggers changes to the lining of the gut, the microbiome, and the release of enzymes to digest food. Long-term stress increases levels of “bad” bacteria and increases the likelihood of Candida infections, ix but improving the microbiome with probiotics can help prevent this x
  3. Diet quickly alters the microbiome, and do all you can to avoid refined sugar, artificial sweeteners and trans-fats (in things like pastries) as they reduce “good” bugs
  4. Alcohol irritates the gut and reduces the number of healthy bacteria; in fact, antiseptic wipes are alcohol-based, so keep alcohol to a minimum when supporting the microbiome


  1. Fermented foods such as sauerkraut, live yoghurt, kefir, miso, natto, tempeh and live cheeses
  2. Saturated fats (olive and other cold-pressed oils), whole foods, and vegetables support the growth of “good” bugs
  3. Good quality probiotics (viable strains that survive stomach acids and bile salts) regularly and oral probiotics positively alter both the gut and genital microbiome xi
  4. All food that’s high in “resistant starch” is great for the microbiome, especially green bananas, oatmeal, lentils, white beans, pearl barley, corn starch, peas, parsnip, cold potato, sweet potato and cold pasta. Also include apple, leek, artichokes (both), chicory, radish, asparagus, ginger, garlic, onions, inulin, FOS and psyllium husks to increase variety.

Inheriting a microbiome

There’s growing evidence that mothers play essential roles in microbiome development as a baby’s microbiome is very similar to their mother’s vagina and breast milk (mainly Lactobacillus). xii This has raised the question of how Caesarean sections and other interventions affect this natural transfer, so some clinics transfer the microbial culture of the mother’s vagina onto the baby after birth. The baby’s skin microbiome is important, and babies do a lot of sucking, where Lactobacillus is transferred from the skin to the gut, so it’s best to avoid bathing babies daily.

Diet, environmental exposure and developmental stages (such as teething) all play important roles in microbiome growth, and it’s known that early life antibiotics produce major shifts in microbiome development. xiii xiv Research into the microbiome and human health and fertility is relatively new, but it’s clearly a core issue, and by supporting our microbiome, we can improve our fertility and our children’s health.