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Overlooked Causes of Miscarriage

May 16, 2025

For many women trying to conceive, experiencing a miscarriage can be an incredibly heartbreaking and confusing event. Even more challenging is when the cause of the pregnancy loss remains unknown. While many miscarriages occur due to chromosomal abnormalities, there are several overlooked causes that may contribute to pregnancy loss, particularly in the first trimester. This article focuses on overlooked causes of miscarriage and is not a complete list of possibilities.

what causes miscarriage

 

Overlooked Causes of Miscarriage

  1. Low Vitamin Levels Nutritional deficiencies, particularly low levels of vitamin D, have been linked to recurrent pregnancy loss. Vitamin D plays a critical role in immune modulation and endometrial receptivity, both of which are essential for maintaining a healthy pregnancy. It influences the activity of immune cells such as T regulatory cells, which help prevent an overactive immune response that could harm early pregnancy. Additionally, vitamin D enhances endometrial receptivity by promoting the expression of implantation-related genes and supporting the vascular development of the endometrium. Without adequate levels, the body may struggle to support early implantation and fetal development. Research indicates that women with vitamin D deficiency may face increased difficulty in sustaining a pregnancy.

     
  2. Gut Dysbiosis An imbalanced gut microbiome can lead to systemic inflammation and disrupt the delicate hormonal balance necessary for pregnancy. The gut microbiome varies throughout the gastrointestinal (GI) tract, influencing immune cell production such as secretory IgA. This antibody supports mucosal immunity and helps regulate inflammation. Disruptions in the gut microbiota can affect hormone production, including progesterone, and create an environment less conducive to pregnancy.

     
  3. Vaginal Infections Conditions like bacterial vaginosis (BV) are often overlooked but can increase the risk of miscarriage. BV disrupts the normal vaginal flora, leading to inflammation and an environment that may hinder early pregnancy. Research has demonstrated a link between BV and infertility, emphasizing the importance of assessing and treating this condition.

     
  4. Low Progesterone Often referred to as the "pregnancy hormone," progesterone is essential for maintaining the uterine lining and supporting the early stages of pregnancy. Low levels can result from not eating enough to support hormonal health. Inadequate caloric intake or nutrient deficiencies can impair progesterone production, making it difficult to sustain a pregnancy. Additionally, research has shown that sleep disturbances can reduce progesterone levels, highlighting the importance of restorative sleep. Progesterone and estrogen levels also influence the vaginal microbiome, with imbalances potentially contributing to an environment that supports conditions like BV.

     
  5. Undiagnosed Autoimmune Conditions Autoimmune conditions such as antiphospholipid syndrome, Lupus (SLE) or Hashimoto's Thyroiditis can contribute to pregnancy loss by creating an inflammatory or hostile immune environment. These conditions are frequently undiagnosed until multiple miscarriages occur.

  6.  Poor Sperm Health Male factors, such as high DNA fragmentation in sperm, play a significant role in miscarriage risk. DNA fragmentation can lead to poor embryo quality, even if fertilization occurs. High levels of DNA fragmentation are associated with impaired embryo development, disrupted blastocyst formation, and reduced implantation potential. This fragmentation compromises the integrity of genetic material critical for early fetal development and increases the likelihood of early pregnancy loss. Addressing male fertility with targeted nutrition and lifestyle changes is critical for improving outcomes.

 

 

Testing to Identify Hidden Causes

 To uncover the root cause of a miscarriage, functional medicine emphasizes a thorough investigation. Testing may include:
 
man semen analysis DNA fragmentation
  • Bloodwork: Checking for vitamin D levels, progesterone, thyroid function, and markers of autoimmune conditions such as antinuclear antibodies (ANA), antiphospholipid antibodies, and thyroid peroxidase antibodies.

  • Inflammatory Markers: Measuring high-sensitivity C-reactive protein (hs-CRP) to assess systemic inflammation and other antibody markers relevant to immune health.

  • Hormonal Testing: Including cortisol levels to evaluate stress response and its impact on reproductive hormones.

  • Stool Testing: Identifying gut dysbiosis, inflammation, or infections that may impact overall health and fertility. Specific markers to consider include secretory IgA, calprotectin, and zonulin.

  • In-Depth Semen Analysis: Assessing sperm count, motility, morphology, and DNA fragmentation. Elevated DNA fragmentation can impair embryo quality and increase the risk of pregnancy loss.


 

Lifestyle and Environmental Factors

 In addition to physiological causes, several lifestyle and environmental factors can increase the risk of miscarriage:
 
 

 

 

Inflammation, the Immune System, and Gut Health

The immune system’s role in pregnancy is complex. A balance between pro-inflammatory and anti-inflammatory states is necessary for successful implantation and fetal development. Dysregulated immune cells, such as an imbalance in CD4 and CD8 T-cells, can disrupt this balance, increasing the risk of pregnancy loss. Markers like hs-CRP and antibody levels can provide insight into underlying inflammation or immune dysfunction.

gut health what causes miscarriage

  The gut microbiome plays a crucial role in immune regulation and hormone production. Variations in the microbiome throughout the GI tract influence the production of immune cells, including IgA, which helps maintain mucosal immunity and reduces systemic inflammation. A disrupted microbiome may negatively affect progesterone levels, further complicating early pregnancy maintenance. Microbial metabolites, such as short-chain fatty acids (SCFAs), play a key role in modulating hormonal pathways and immune responses. These metabolites can influence hormone receptors, such as estrogen and progesterone receptors, and regulate inflammation through pathways like the NF-κB signaling. Dysbiosis, or an imbalance in microbial composition, may impair SCFA production, leading to inflammation and hormonal disruptions that interfere with early pregnancy success.

 

Stress and Cortisol’s Role in Fertility

 

Underlying health issues, including chronic inflammation or hormonal imbalances, often contribute to increased stress. This, in turn, elevates cortisol levels—the body’s primary stress hormone. Cortisol plays a dual role in fertility: while it’s essential for managing acute stress, chronically high levels can interfere with reproductive hormones such as luteinizing hormone (LH) and progesterone. Prolonged stress can disrupt ovulation and metabolic health, increase inflammation, and exacerbate gut dysbiosis. Managing stress by addressing root causes and through practices such as mindfulness, yoga, and adequate sleep can help regulate cortisol levels and improve fertility outcomes.

 
 

Functional Medicine Approaches to Care 

A natural and functional medicine approach focuses on optimizing overall health and addressing root causes of miscarriage. Key strategies include:

 

  • Nutritional Support: Ensuring adequate intake of vitamins and minerals through a diet rich in whole foods, including leafy greens, fatty fish, seeds, and legumes. Targeting specific deficiencies, like vitamin D, through diet and supplementation when necessary.

  • Gut Health Restoration: Incorporating probiotics, fermented foods, and a diverse diet to support a healthy microbiome. Treating underlying infections with herbal therapies can also help to balance gut microbiome.

  • Addressing Vaginal Infections: Using natural remedies, such as probiotics and antimicrobial herbs, under the guidance of a healthcare professional. Companies like Evvy offer vaginal microbiome testing.

  • Hormone Balance: Supporting progesterone levels through lifestyle changes, stress reduction, and, if needed, bioidentical progesterone therapy.

  • Reducing Toxin Exposure: Switching to non-toxic cleaning products, avoiding plastic containers, and prioritizing organic foods to minimize exposure to harmful chemicals.

  • Male Fertility Support: Encouraging a nutrient-dense diet, stress reduction, and lifestyle changes to improve sperm quality.

woman walking what causes miscarriage

 

Checklist for Women Experiencing Miscarriage

 

If you’ve experienced a miscarriage, consider discussing the following with your healthcare provider:

 
  • Vitamin D and 7 DPO progesterone testing

  • Comprehensive thyroid panel (TPO, TGA, TSH, FT3, FT4, RT3, iodine)

  • Screening for autoimmune markers (e.g., ANA, antiphospholipid antibodies)

  • Gut health evaluation (e.g., stool testing for secretory IgA and calprotectin)

  • Vaginal microbiome assessment

  • Advanced semen analysis for your partner including DNA fragmentation

  • Inflammatory marker testing (e.g., hs-CRP, ESR)

  • Environmental toxin exposure and ways to reduce it

     

Closing Thoughts

Understanding the overlooked causes of miscarriage can empower women to take charge of their reproductive health. By addressing potential root causes through a functional medicine approach, it is possible to improve the likelihood of a healthy pregnancy. If you’ve experienced a miscarriage and feel you lack answers, know that there is hope in uncovering and addressing these hidden factors.

 
 

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