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

We’ve evolved alongside our microbiome over millennia, and it’s an essential and integral part of human health and fertility, and while we haven’t always appreciated this. The widespread use of antibiotics since the 1950s has coincided with a change in our relationship with our microbiome, our health and fertility. Taking preconception antibiotics reduces fertility, which varies with the type taken, but can reduce conception rates by 40%. i 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 testicles, 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

There’s increasing evidence that repeated miscarriages and unexplained IVF failures can be due to abnormalities in the microbiome of the vagina and uterus iii Premium membership brings access to specialised tests for gut or sexual microbiome and specific fertility probiotics, 

The vaginal microbiome of healthy women is usually dominated by Lactobacillus species which produce lots of hydrogen peroxide that 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 and 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 (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 significantly 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 semen sample microbiomes. The semen samples of most men have predominantly Lactobacillus dominant communities, and this helps sperm cope better 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 reduce their partner’s fertility.

Creating a healthy microbiome


  1. Antibiotics for non-life-threatening conditions or infections as they aren’t selective in their actions and kill “good” bacteria along with the “bad”. This encourages the growth of moulds and fungi that disturb the microbiome throughout the body, and take probiotics alongside and after them if they have to be taken. Antibiotics profoundly impact the immune system: a cancer study has shown that oral antibiotics before immunotherapy significantly reduces survival times for all cancer types, but the expected life expectancy 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 can help prevent this. x
  3. Diet quickly alters the microbiome; reduce refined sugar, artificial sweeteners and trans-fats (in things like pastries) as they inhibit “good” bugs.
  4. Alcohol irritates the gut and reduces the number of healthy bacteria; 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. “Resistant starch” is great for the microbiome, so increase foods high in it, 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 resembles 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, with some clinics transferring the mother’s microbial culture 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 consider avoiding 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 a core issue, and by supporting our microbiome, we can improve our fertility and our children’s health.

i Mikkelsen EM, et al.,  Preconception use of antibiotics and fecundability: A Danish prospective cohort study, Fertility and Sterility (2023), doi: https://doi.org/10.1016/j.fertnstert.2023.04.030.
iReduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children’ Dae-Wook Kan, et al. (2013) PLoS ONE 8(7): e68322. doi:10.1371/journal.pone.0068322
ii “Reproductive tract microbiome in assisted reproductive technologies” Franasiak JM, Scott RT Jr. Fertil Steril. 2015 Dec;104(6):1364-71.
iii“Vaginal lactobacilli, probiotics, and IVF” Hans Verstraelen,  Abiola C Senok Reproductive BioMedicine Online 2005 Volume 11, Issue 6, Pages 674–675 x
iv“Bacterial vaginosis and infertility: cause or association?” Salah RM, Allam AM, Magdy AM, Mohamed ASH. Eur J Obstet Gynecol Reprod Biol 2013; 167:5963.
v “Association between Polycystic Ovary Syndrome and Gut Microbiota” Yanjie Guo et al. (2016) PLoSONE11(4): e0153196
vi“Optimal uterine anatomy and physiology necessary for normal implantation and placentation.” de Ziegler D1, Pirtea P2, Galliano D3, Cicinelli E4, Meldrum D5. Fertil Steril. 2016 Apr;105(4):844-54.
vii “Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality” Weng SL et al. PLoS One. 2014 Oct 23;9(10):e110152
viiihttps://www.theguardian.com/society/2019/sep/12/antibiotic-use-before-cancer-treatment-cuts-survival-time-study. https://jamanetwork.com/journals/jamaoncology/article-abstract/2749683
ix‘Disturbance in the Mucosa-Associated Commensal BacteriaIs Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics?’ Sohei Arase et al. (2016)
xHighlights Regarding Host Predisposing Factors to Recurrent Vulvovaginal Candidiasis: Chronic Stress and Reduced Antioxidant CapacityAkimoto-Gunther L, et al. PLoS One. 2016 Jul 14;11(7):e0158870.
xBacterial vaginosis: a review on clinical trials with probiotics” Paola Mastromarino, Beatrice Vitali, Luciana Mosca. NEw MICRoBIoLogICA, 36, 229-238, 2013
xii Dominguez-Bello MG, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America. 2010;107:11971–11975. [PubMed] Shows that infants have largely undifferentiated microbiota across multiple anatomic sites immediately after birth, and that delivery mode determines the types of bacteria that are the earliest colonizers of the infant microbiome
xiii Robinson CJ, Young VB. Antibiotic administration alters the community structure of the gastrointestinal micobiota. Gut microbes. 2010;1:279–284. [PMC free article] [PubMed]
xivWlodarska M, et al. Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis. Infection and immunity. 2011;79:1536–1545. [PMC free article] [PubMed]