Eating to Support a Healthy Microbiome and Fertility

Version For Professionals

Maintaining a healthy diet is crucial for improving fertility, and one of the best ways to do this is by eating a variety of foods. A diverse diet, especially one rich in plant-based foods, supports reproductive health, provides essential nutrients, and reduces the risk of conditions that could affect fertility.

Why Microbiome Diversity Matters for Fertility

The gut microbiome is a complex community of trillions of microorganisms, including bacteria, viruses, fungi, and other microbes. These tiny organisms are essential for digestion, immune function, and overall health. A diverse microbiome is especially beneficial because it:

  • Improves Digestion: Different bacteria help break down various types of fiber and complex carbohydrates, aiding in nutrient absorption, which is important for reproductive health.
  • Supports the Immune System: A diverse microbiome helps regulate the immune system, making the body better at fighting infections and reducing inflammation, which can affect fertility.
  • Balances Hormones: Research suggests that a healthy microbiome can influence hormone levels, which are crucial for reproductive health.
  • Boosts Mental Health: Studies show that a diverse gut microbiome can positively affect mood and mental functions, contributing to overall well-being.

In summary, eating a wide range of plant-based foods can support a healthy gut microbiome, which in turn can enhance fertility and overall health.

How to enhance the diversity of the gut microbiome

  1. Eat a Diverse Range of Foods

To promote a diverse microbiome, it is crucial to consume a variety of plant-based foods. Studies show that eating at least 30 different plants per week introduces different fiber and polyphenols that nourish distinct microbial species, contributing to a balanced microbiome:

  • Incorporate a variety of fruits, vegetables, whole grains, nuts, seeds, and legumes into your diet.
  • Aim for different colours and types to provide a wide range of nutrients and fiber.
  1. Consume Fermented Foods:

The gut-immune axis is a two-way communication channel where the gut microbiota and the immune system continually influence each other. Fermented foods, by altering the gut microbiota, also affect immune cell signalling and cytokine production. A balanced immune response is essential for successful implantation and pregnancy maintenance. Autoimmune reactions can lead to fertility issues; thus, the modulation of immune responses through diet can be a strategic approach to managing fertility-related problems.

Studies show key positive findings from consuming fermented foods such as: 

  1. Reduction of Inflammation:
    1. Mechanisms: Inflammation in reproductive disorders like endometriosis and PCOS is often mediated by cytokines such as IL-6. These cytokines can disrupt follicular development, affect ovarian steroidogenesis, and alter the endometrial environment, making it less conducive to implantation. Fermented foods, through their bioactive compounds and probiotics, can modulate the gut-immune axis, leading to decreased production and release of pro-inflammatory cytokines like IL-6.
    2. Research Evidence: Studies have shown that certain probiotics found in fermented foods can reduce the expression of nuclear factor kappa B (NF-κB), a key regulator of inflammation, thus directly reducing the levels of IL-6 and other inflammatory mediators.
  2. Immune System Regulation:
    1. Pathways: The immune system’s role in infertility is complex, involving both innate and adaptive immunity. Dysregulation can lead to conditions like recurrent pregnancy loss or implantation failure. Fermented foods introduce beneficial microbes that can modulate immune responses by affecting T-helper cells balance and regulatory T cell activities, reducing overactive immune responses.
    2. Specifics: Probiotics can influence cytokine profiles, reducing IL-10 in overactivated immune states, and balancing Type 1 vs. Type 2 immune responses. This modulation helps prevent autoimmune reactions and enhances the body’s ability to support a pregnancy.
  3. Gut Health and Hormonal Balance:
    1. Interactions: The gut microbiota can directly and indirectly influence hormonal regulation via the “gut-brain axis” and “gut-liver axis.” By improving gut health, fermented foods aid in the more efficient metabolism of estrogens through the enterohepatic circulation, preventing estrogen dominance.
    2. Biochemical Links: The microbiome can produce and modulate bioactive compounds that mimic hormonal activity or influence hormonal pathways, such as short-chain fatty acids (SCFAs) that have been shown to influence insulin sensitivity and steroid hormone levels.
  4. Stress and Oxidative Stress Reduction:
    1. Biochemical Pathways: Oxidative stress can damage DNA in gametes, impairing fertility. Fermented foods, rich in antioxidants and anti-inflammatory compounds, can reduce oxidative stress markers. They can also influence stress hormones like cortisol through the gut-brain axis.
    2. Clinical Implications: Regular consumption of fermented foods has been associated with improved antioxidant capacity in the body and a reduction in biomarkers of oxidative stress, such as malondialdehyde (MDA) levels, thus protecting reproductive tissues and functions.
  5. Nutrient Absorption:
    1. Mechanisms: A healthy gut microbiota enhances the absorption of key nutrients by improving the integrity of the gut lining and facilitating active transport mechanisms. This is vital for the bioavailability of micronutrients like folic acid, zinc, and selenium, which are essential for DNA synthesis and repair in gametes and for supporting early embryonic development.
    2. Impact on Fertility: Enhanced nutrient absorption ensures optimal levels of these nutrients, which are critical for oocyte maturation, sperm motility, and overall reproductive health. For instance, zinc is vital for sperm motility and testosterone production, while selenium is necessary for preventing oxidative damage in sperm
  6. No Increase in Pathogenic Microbes:

Studies did not report any increase in pathogenic microbes, suggesting that the consumption of fermented foods did not introduce harmful bacteria into the participants’ microbiomes.

Include fermented foods like yogurt, kefir, sauerkraut, kimchi, miso, tempeh, and kombucha in your diet. These foods contain live beneficial bacteria that can enhance your gut microbiota. However, if patients you are undergoing any medical treatment or have specific health concerns, consult your healthcare provider before making dietary changes. Pay particular attention to unpasteurized versions of fermented foods, which may not be appropriate at certain stages of treatment or during pregnancy.

  1. Increase Fiber Intake

The Impact of Dietary Fiber on Gut Mucus Layer and Pathogen Susceptibility

Fiber is a crucial nutrient for gut bacteria, promoting a healthy and diverse microbiome. A lack of dietary fiber has profound implications for the gut microbiota and the structural integrity of the intestinal mucus layer, which plays a critical role in maintaining gut health and preventing infections:

  1. Mucus Layer Function and Composition: The mucus layer in the intestines serves as a protective barrier that separates the gut microbiota from the epithelial cells lining the intestine. This layer is primarily composed of mucins, glycoproteins produced by goblet cells, which form a gel-like matrix that traps pathogens and facilitates their removal from the gut.
  2. Impact of Dietary Fiber on Mucus Layer: Dietary fiber is not digestible by human enzymes but can be fermented by certain beneficial bacteria in the gut, such as Bifidobacteria and certain Lactobacilli. The fermentation process produces short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate. These SCFAs provide energy to colonocytes (the cells lining the colon) and stimulate them to produce more mucins, thus thickening the mucus layer and enhancing its protective function.
  3. Consequences of a Fiber-Free Diet: In contrast, a fiber-free (FF) diet leads to a decrease in the production of these beneficial SCFAs. The reduction in SCFA levels results in less stimulation for mucin production by goblet cells, leading to a thinner mucus layer. Moreover, some gut bacteria, in the absence of fiber, may start to degrade the mucins directly to obtain nutrients, further thinning the mucus layer. This process involves an increase in mucus-degrading enzymes, such as glycosidases and proteases, which break down the carbohydrate and protein components of mucins.
  4. Vulnerability to Pathogens: A thinner mucus layer means that harmful bacteria, such as Citrobacter rodentium (Cr), can more easily reach and adhere to the epithelial cells of the intestine. Cr is a model pathogen used to study gut infections and inflammation, similar to how certain pathogenic E. coli strains operate in humans. Once these pathogens adhere to or invade the epithelial cells, they trigger an immune response, leading to inflammation, a condition known as colitis.
  5. Implications for Gut Health: Chronic inflammation in the gut, especially when driven by recurrent infections due to a compromised mucus barrier, can lead to a range of disorders. This includes not just acute infections but also long-term conditions like inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and increased risk for colorectal cancer.
  6. Nutritional Recommendations: Given these findings, it’s clear that maintaining a diet rich in diverse fiber is essential for supporting a healthy mucus layer and, by extension, a robust gut microbiota. This helps prevent pathogen invasion and the subsequent inflammatory responses, thereby protecting against gastrointestinal disorders.

How to eat more Fiber

Foods high in fiber include fruits, vegetables, legumes, and whole grains. For example, apples, carrots, beans, and whole wheat bread are excellent sources of dietary fiber. Incorporating a variety of these foods into your diet can support gut health and overall well-being.

Additionally, consider including sources of resistant starch, which acts similarly to fiber by resisting digestion in the small intestine and fermenting in the large intestine. Resistant starch can be found in foods like green bananas, oats, and potatoes that have been cooked and then cooled. This cooling process increases the resistant starch content, making these foods even more beneficial for gut health.

By diversifying fiber sources, it is possible to introduce different types of fiber and polyphenols that nourish distinct microbial species in the gut, contributing to a balanced and healthy microbiome. This approach not only supports digestion but also plays a role in reducing inflammation and improving metabolic health.

  1. Avoid Highly Processed Foods

The consumption of highly processed foods, artificial sweeteners, and high-fat diets can significantly impact gut health by altering the microbiota and increasing inflammation. These changes have profound effects on fertility, highlighting the importance of a balanced diet rich in natural, unprocessed foods for maintaining both gut health and reproductive function.

  1. Impact of Processed Foods on Gut Health and Fertility:
    • Mechanisms: Highly processed foods are generally low in fiber and high in unhealthy fats, refined sugars, and artificial additives. The lack of fiber means that beneficial gut bacteria receive fewer substrates for fermentation, leading to decreased production of short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate. These SCFAs are crucial for maintaining the integrity of the gut barrier and modulating immune responses.
    • Research Evidence: Studies have demonstrated that diets rich in processed foods lead to a reduction in microbial diversity and an increase in the abundance of pathogenic or pro-inflammatory microbes such as Proteobacteria. This shift can cause increased gut permeability (often referred to as ‘leaky gut’) and systemic inflammation, which has been linked to conditions like endometriosis and polycystic ovary syndrome (PCOS).
  2. Artificial Sweeteners and Fertility:
    • Biochemical Impact: Artificial sweeteners, despite being non-caloric, can disrupt the gut microbiota balance. They may inhibit the growth of beneficial bacteria while promoting pathogenic strains, altering the overall composition of the microbiome. This disruption can lead to dysbiosis, a condition marked by an imbalance in the microbial community.
    • Fertility Implications: The alteration in gut microbiota due to artificial sweeteners can impair glucose metabolism, leading to insulin resistance and metabolic syndrome. These conditions are closely linked to fertility issues, particularly in women with PCOS, where insulin resistance plays a significant role in hormonal imbalances and ovulatory dysfunction.
  3. High-Fat Diets and Fertility:
    • Microbial and Immune Responses: Diets high in saturated and trans fats can reduce the diversity of the gut microbiota and increase the prevalence of pro-inflammatory bacteria. This change in the microbiome can trigger the release of inflammatory cytokines such as IL-6 and TNF-alpha, which contribute to systemic inflammation.
    • Fertility Consequences: The inflammation and metabolic dysregulation resulting from a high-fat diet can affect hormonal balance and reproductive health. For instance, in females, inflammation can impact the ovarian follicle development and ovulation, while in males, it can affect sperm quality and motility.
    • Empirical Findings: Research indicates that diets rich in unhealthy fats are associated with poorer reproductive outcomes, including lower sperm quality in males and reduced embryo quality in females undergoing fertility treatments.

Opt for Whole, Unprocessed Foods to Support Fertility

To support a healthy gut microbiome and enhance fertility, it is advisable to opt for whole, unprocessed foods. These foods are rich in natural fiber, vitamins, and minerals that promote the growth of beneficial bacteria and enhance gut health. Whole foods such as fruits, vegetables, whole grains, nuts, seeds, and lean proteins provide the nutrients necessary for maintaining a balanced and diverse microbiota, which is crucial for reproductive health.

Tips to avoid highly processed foods:

Reduce intake of processed foods, artificial sweeteners, and high-fat diets which can negatively impact gut diversity. Opt for whole, unprocessed foods instead, avoiding processed foods can significantly improve gut health and enhance fertility. Here are some practical tips to help reduce the intake of processed foods and choose healthier alternatives:

1. Cook at Home

  • Plan Meals: Take time to plan meals for the week. This helps to control the ingredients and avoid the temptation of processed convenience foods.
  • Cook from Scratch: Prepare meals using whole, fresh ingredients. Cooking from scratch avoids additives and preservatives found in processed foods.
  • Batch Cooking: Prepare larger quantities of food and freeze portions for later. This ensures healthy, homemade meals ready whenever they are needed.

2. Read Labels

  • Check Ingredients: When buying packaged foods, read the ingredient list. Avoid products with long lists of unfamiliar or artificial ingredients.
  • Choose Whole Foods: Opt for products with simple, natural ingredients. The fewer the ingredients, the better.
  • Watch for Hidden Sugars: Be aware of added sugars hidden under different names like high fructose corn syrup, dextrose, or maltose.

3. Shop Smart

  • Stick to the Perimeter: Focus on the outer aisles of the grocery store where fresh produce, meats, and dairy are usually located. Avoid the inner aisles filled with processed snacks and convenience foods.
  • Buy Frozen: Choose frozen fruits and vegetables over processed options. Frozen fruits and vegetables are often picked at peak ripeness and retain their nutrients.
  • Opt for Whole Grains: Select whole grain options such as brown rice, quinoa, and whole wheat bread instead of refined grains like white rice and white bread.

4. Snack Wisely

  • Healthy Snacks: Prepare healthy snacks like sliced vegetables, fresh fruits, nuts, and seeds. These are excellent alternatives to processed snack foods.
  • DIY Snacks: Make homemade snacks, like trail mix or granola bars, to avoid the additives and preservatives found in store-bought versions.

5. Limit Processed Meats

  • Choose Fresh Meat: Opt for fresh, unprocessed meats over processed options like sausages, hot dogs, and deli meats.
  • Plant-Based Proteins: Incorporate plant-based proteins such as beans, lentils, and tofu into the diet to reduce reliance on processed meats.
  1. Prebiotics

Prebiotics are a type of dietary fiber that serve as food for the beneficial bacteria in the gut. Unlike probiotics, which are live bacteria introduced into the digestive system, prebiotics help to nourish and support the growth of these good bacteria already present in the intestines. Found naturally in various foods like fruits, vegetables, and whole grains, prebiotics play a crucial role in maintaining a healthy and balanced gut microbiome. They work by promoting the growth of beneficial bacteria, which in turn helps improve digestion, boost immune function, and reduce inflammation, contributing to overall health and well-being.

Types of Prebiotics

Prebiotics are mostly found in various carbohydrate groups, particularly oligosaccharide carbohydrates (OSCs). However, prebiotics are not limited to carbohydrates alone. Here is a breakdown of different types of prebiotics:

1. Fructans

Fructans include inulin and fructo-oligosaccharides (FOS). These are chains of fructose molecules linked together. Inulin can have up to 60 fructose units, while FOS has fewer than 10.

  • Inulin and FOS: These have been shown to selectively stimulate the growth of lactic acid bacteria, such as Bifidobacteria. However, the length of the fructan chain can influence which bacteria can ferment them, affecting gut health.

2. Galacto-Oligosaccharides (GOS)

GOS are derived from lactose (milk sugar) and come in two main types:

  • GOS with extra galactose units: These are connected at different points on the molecule.
  • Trans-Galacto-Oligosaccharides (TOS): Made from lactose through a special process, resulting in a mix of sugars with various linkages.
  • GOS Benefits: They are particularly effective at stimulating Bifidobacteria and Lactobacilli, essential for a healthy gut. These prebiotics are especially beneficial for infants.

3. Starch and Glucose-Derived Oligosaccharides

Some starches resist digestion in the upper gut and are known as resistant starch (RS). These starches are important because they produce butyrate, a substance that promotes gut health.

  • RS and Health: They are particularly good at promoting Firmicutes, a group of beneficial bacteria. Studies show that RS is broken down by specific bacteria like Ruminococcus bromii and Bifidobacterium adolescentis.

4. Polydextrose

Polydextrose is a synthetic fiber made from glucose. It has a complex structure with many branches.

  • Polydextrose Benefits: Some evidence suggests it can stimulate Bifidobacteria, although this is not yet fully confirmed.

5. Other Oligosaccharides

Pectic oligosaccharides (POS) are derived from pectin, a substance found in many fruits.

  • POS Varieties: These can be based on galacturonic acid or rhamnose, with various sugars and acids attached to their structure. The source of POS can affect their specific structure and benefits.

6. Non-Carbohydrate Oligosaccharides

Although most prebiotics are carbohydrates, some compounds that aren’t carbohydrates can also act as prebiotics.

  • Cocoa-Derived Flavanols: These compounds from cocoa have been shown to stimulate beneficial lactic acid bacteria in the gut.

Common Sources of Prebiotics

Prebiotics are found in many everyday foods:

  • Vegetables: Asparagus, garlic, onions, leeks, and chicory.
  • Fruits: Bananas and tomatoes.
  • Grains: Wheat, barley, rye, and whole grains.
  • Legumes: Soybeans, peas, and beans.
  • Other Sources: Honey, coco, human and cow’s milk, seaweeds, and microalgae.
  1. Hydration and Its Impact on the Microbiome

Proper hydration plays a critical role in maintaining a healthy and balanced gut microbiome. The gut microbiome consists of trillions of microorganisms that thrive in the digestive tract, and their health is closely linked to the overall well-being of the host. Here is how hydration affects the microbiome:

  1. Promotes Gut Motility

Adequate hydration ensures proper gut motility, which is the movement of food and waste through the digestive tract. Water helps to soften the stool and promote regular bowel movements, preventing constipation. Constipation can lead to the overgrowth of harmful bacteria and a reduction in beneficial bacteria, disrupting the balance of the microbiome.

  1. Supports Mucosal Barrier Function

Hydration helps maintain the mucosal lining of the intestines, which serves as a barrier to pathogens and harmful substances. A well-hydrated mucosal layer supports the growth of beneficial bacteria while preventing the colonization of harmful microbes. This barrier function is essential for maintaining gut health and preventing inflammation.

  1. Enhances Nutrient Absorption

Water is vital for the dissolution and absorption of nutrients in the digestive system. Proper hydration ensures that nutrients, including those that feed beneficial gut bacteria, are effectively absorbed. These nutrients are crucial for the growth and function of a healthy microbiome.

  1. Dilutes Toxins and Waste Products

Water helps to dilute and flush out toxins and waste products from the body. This detoxification process prevents the buildup of harmful substances in the gut, which can negatively impact the microbiome. Hydration supports the removal of metabolic by-products that could otherwise disrupt microbial balance.

Influences Microbial Composition

The composition of the gut microbiome is highly responsive to various dietary and environmental factors, including hydration levels. Proper hydration supports a diverse and balanced microbial community, while dehydration can lead to dysbiosis, an imbalance between beneficial and harmful bacteria. 


To support a healthy gut microbiome and enhance fertility, it is important to encourage a diverse diet. This helps improve digestion, immune function, hormone balance, and mental health. Including fermented foods can reduce inflammation and support reproductive health by improving nutrient absorption and reducing oxidative stress.

To further boost microbiome diversity, focus on eating whole, unprocessed foods and increasing fiber intake. Avoid highly processed foods, artificial sweeteners, and high-fat diets to prevent negative impacts on gut bacteria and inflammation. Also, incorporate prebiotics from sources like vegetables, fruits, grains, and legumes to nourish beneficial bacteria. Finally, ensure proper hydration to maintain gut health and balance.