The Gut Microbiome and Estrogen

Published on: 09/19/2023

Your gut microbiome is a complex and influential community of microorganisms residing within your digestive system. In this article, we will review what the gut microbiome is, what impacts microbial diversity, and what happens when microbial diversity is low. We will then dive into the fascinating world of how women’s hormones, particularly estrogen, can be impacted by the gut microbiome. Understanding this connection is crucial for achieving and maintaining optimal hormonal health.

What is the Gut Microbiome? 

Imagine your gut as a bustling ecosystem, teeming with life. The gut microbiome is an ensemble of microorganisms, including bacteria, fungi, parasites, and viruses, that call your digestive tract home. Your gut microbiome is uniquely your own; the organisms that make up your microbiome are highly individual.  

 Diversity and balance are vital for intestinal and overall health, as this symbiotic relationship between your body and the gut microbiome impacts everything from digestion to immune function. We can’t live without them, nor they without us.

The colonization of the gut microbiome starts at birth. If you were delivered vaginally, you received some of your mother’s vaginal microbiota, which has been linked to numerous health advantages. Throughout infancy, you continue the process of gut colonization, aided by breastmilk. As you progress through childhood, an array of sources, including the doorknobs you chew on, the dogs that affectionately lick you, and the soil inadvertently ingested, contribute to this colonization. There is intelligent design behind children’s compulsive need to put everything in their mouths, much to mom’s dismay!  About 90% of the bacteria you encounter are harmless, and in fact can be quite beneficial. 

Over the course of your life your gut microbiota is evolving constantly and is influenced by your environment, diet, genetics, and inflammation.

Roles of the Microbiome 

Your body and mind are closely intertwined with your microbiome, influencing numerous aspects of your well-being. It is widely acknowledged that a robust gut microbiome is essential for the health and holds significant sway over various factors, including:

  • Detoxification
  • Mood
  • Mental function
  • Hormone production
  • Immunity
  • Intestinal permeability
  • Digestive function

The gut microbiome plays a pivotal role in shaping nutrition through several mechanisms, including:

  • Breaking down indigestible foods
  • Producing vital nutrients such as vitamin K, vitamin B12, folic acid, amino acids, and short-chain fatty acids
  • Signaling appetite and managing cravings

Factors Affecting Microbial Diversity

Microbial diversity can be compromised by various factors. These factors encompass both early-life experiences and subsequent lifestyle choices.

Early Life Influences

During your early years, a variety of factors can impact your microbial diversity, potentially leading to imbalances and opportunistic infections. These influences arise from both the circumstances of your birth and the choices made in infancy and childhood.

  • Birth and Feeding: The method of your birth, whether via C-section or vaginally, and your feeding pattern, whether breastfed or formula-fed, play roles in shaping your microbial diversity.
  • Hygiene Practices: The level of meticulous cleanliness maintained in your environment during your upbringing can influence the development of your microbiome.
  • Childhood Environment: The extent to which you were exposed to outdoor environments, dirt, and animals during childhood can contribute to the diversity of your microbial community.
  • Antibiotic Usage: Early and frequent use of antibiotics can have a lasting impact on the composition and diversity of your gut microbiome.
  • Dietary Factors: Your dietary habits during early life, including the intake of fiber and the diversity of foods consumed, can influence the establishment of a diverse microbial ecosystem.

Later-Life Considerations

The following factors may diminish microbial diversity:

  • A diet high in processed foods, refined grains, and sugar.
  • Low intake of fiber.
  • Consumption of artificial sweeteners.
  • Antibiotic usage.
  • Regular use of non-steroidal anti-inflammatory drugs (NSAIDs) like ibuprofen (Advil) and naproxen (Aleve).
  • Alcohol consumption.
  • Elevated stress levels.
  • Disruption of circadian rhythms (lack of sleep).
  • Inadequate exercise.
  • Exposure to environmental toxins, including herbicides, pesticides, and heavy metals.
  • For certain individuals, gluten and dairy.

Understanding Gut Dysbiosis

Gut dysbiosis occurs when the microbial diversity in your gut is low, resulting in an imbalance between good and bad bacteria. This can lead to excessive growth of “bad” bacteria and increase the risk of opportunistic infections. When the variety of bacteria in your gut decreases, your chances of developing chronic illnesses such as allergic disorders, obesity, diabetes, cancer, cardiovascular issues, central nervous system disorders, Irritable Bowel Syndrome, and Crohn’s disease can rise.

Common Symptoms of Dysbiosis:

Dysbiosis often manifests through various symptoms, and the most common symptoms include:

  • Digestive issues like gas, bloating, heartburn, constipation, and food intolerances.
  • Fatigue that occurs after meals or generally throughout the day.
  • Brain fog and difficulties with concentration.
  • Cravings for sugary or carbohydrate-rich foods.
  • Persistent anxiety or depression.

Dysbiosis can also cause gynecologic problems and hormone symptoms, such as:

  • Chronic or recurring vaginal yeast and fungal infections.
  • Acne.
  • Estrogen – high or low.
  • Difficulties conceiving.
  • Premenstrual digestive symptoms.

The Microbiome and Estrogen

In women, the microbiome exerts significant influence over estrogen levels. Estrogen, a hormone primarily produced in the ovaries, circulates throughout the bloodstream, interacting with cells all over the body equipped with estrogen receptors and playing a multitude of roles. After its journey through the body, estrogen reaches the liver. Here, it undergoes a series of processes, including breakdown, inactivation, and packaging for elimination. The packaged estrogen then combines with bile and enters the intestines, with the intention of being excreted in the stool.

The Role of the Estrobolome

Within the intestines, estrogen encounters a specialized group of microbes known as the estrobolome. A smoothly functioning estrobolome ensures proper estrogen absorption and excretion, contributing to a harmonious hormone equilibrium. They do so in the following ways:

1. Balancing Elimination and Reabsorption

 The estrobolome oversees the balance between eliminated and reabsorbed estrogen. It accomplishes this by producing an enzyme called beta-glucuronidase, which converts inactive estrogen back into an active form, subsequently reabsorbed into the body.

2. Conversion of Lignans

Additionally, the estrobolome has the ability to convert lignans, compounds found in plant foods such as vegetables, legumes, and seeds, into estrogen-like compounds known as phytoestrogens. Phytoestrogens play a crucial role in estrogen regulation.

  • When estrogen levels are too high, phytoestrogens can block estrogen receptors, protecting the body from the risks of excess estrogen.
  • Conversely, when estrogen levels are low, phytoestrogens can provide enough estrogen-like activity to support hormone balance.

The Consequences of Dysbiosis

When dysbiosis occurs, two scenarios may unfold:

1. Excessive Proliferation

Dysbiosis can lead to the excessive proliferation of estrobolome bacteria, resulting in the production and reabsorption of too much estrogen.

2. Low Microbial Diversity

In cases of low microbial diversity, the estrobolome may struggle to efficiently convert and absorb the body’s estrogen and produce lower levels of estrogen from plant-based lignans, leading to low estrogen levels.

Why High and Low Estrogen Levels Matter

Excessive estrogen can have several adverse effects, including painful and heavy periods, breast tenderness, mood swings, and menstrual migraines. It can also be a trigger or exacerbator of conditions such as endometriosis and fibroids. Over time, elevated estrogen levels may contribute to autoimmune disorders, as well as breast, ovarian, and endometrial cancers, along with hypothyroidism.

On the other hand, low estrogen levels can lead to symptoms such as brain fog, memory problems, depression, headaches, irritability, and low libido. Over the long term, it may result in issues like bone loss (osteoporosis), reduced thyroid function, and urinary tract infections (UTIs).

How to Restore a Healthy Gut Microbiome

I invite you to read my blog post, titled “Nutrition Tips to Restore a Healthy Microbiome”. In this article, I provide valuable insights and practical tips to help you nourish and support your gut microbiome. It’s a must-read for anyone looking to enhance their overall well-being through the power of nutrition.


Your gut microbiome is an incredible force influencing your overall health, especially when it comes to women’s hormonal well-being. From estrogen regulation to immune function and mood, it plays a pivotal role in various aspects of your life.

To explore personalized strategies for optimizing your gut health and hormonal balance, I encourage you to take the next step toward a healthier you. Book an appointment with me, a registered dietitian specializing in women’s hormonal health, and let’s embark on a journey to achieve and maintain your optimal well-being.


Get Started

Book a free discovery call today!

Other Resources

There are so many fascinating resources out there on the gut microbiome. Here are a few to get you started: 

My Microbiome

Their mission is to spread the knowledge about a healthy, unharmed microbiome and to serve as a decision-making tool for customers and profiling tool for brands. Link to their website here.

Gut Microbiota for Health

Their mission is to share knowledge and promote debate regarding gut microbiota. Their goal is to raise awareness and interest on the gut’s bacterial community and its importance for our health and quality of life, both among the scientific and medical community and society in general. Link to their website here.

Dr. Aviva Romm

If you want to learn more about the estrobolome and how your gut influences estrogen, check out this blog post by Dr. Aviva Romm, a physician, herbalist and midwife, specialized in women’s hormonal health. 


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Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7;21(29):8787-803. doi: 10.3748/wjg.v21.i29.8787.

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Romm, A. Hormone Intelligence: The Complete Guide to Calming Hormone Chaos and Restoring Your Body’s Natural Blueprint for Well-Being. HarperOne, 2021.

Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010 Jul;90(3):859-904. doi: 10.1152/physrev.00045.2009.

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Verena writing a blog post on computer

Verena is a Registered Dietitian specializing in women’s hormonal health, fertility, and oncology.  The primary aim of this blog is to offer information that empowers individuals to align their lives with their body’s inherent rhythms. Within these pages, you’ll encounter a blend of evidence-based recommendations grounded in modern medicine, complemented by natural healing approaches and insights from traditional wisdom.

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