The Gut Microbiome and Sex Hormones: What’s the Connection?

The microbiome is healthiest when it is abundant. As we touched on at the end of the last post, women’s microbiomes change in our middle years. Microbe communities tend to become less plentiful and diverse than when we were younger. While the reasons for this are not entirely within the grasp of science yet, we know hormone changes and microbiota changes go hand in hand. It’s not so much that one shift causes the other. It’s that hormones and microbes act as a whole, like two notes harmonizing into one during a song. 

Gut dysbiosis happens when the gut microbiome gets perturbed – the composition of microbes becomes less diverse and less plentiful. Dysbiosis comes from the Greek dys, meaning bad or difficult, and biosis, meaning mode of life. Dysbiosis, then, means difficult mode of life, which tells us something about how central the gut microbiome is for our own quality of life. 

Every day, we become more convinced about the vital need to care for and nurture the gut microbiome as a practice to support our wellbeing. In this post, though, we offer insights into the interplay of the microbiome and sex hormones. Our hope is that what follows will spark curiosity about nurturing your microbiome as a friend and partner during the menopause transition and beyond. If you don’t yet feel the inner stirrings of the menopause transition, we hope it will intrigue you all the same. All of us benefit from a healthy microbiome. 

Microbes and Estrogen


Estrogen levels decline as we near menopause and fall off sharply in the first year or two after that. Since estrogen is involved in so many functions across the body – not only our monthly cycles – that fall-off brings about effects nearly everywhere. A healthy microbiome can counter some of those fall-off effects. 

Why? For estrogens to be available in active form across the body, they need to become ‘unbound’. Microbes produce active compounds that do just that. They unbind estrogens. 

When the microbiota becomes less plentiful and diverse, levels of ‘bound’ estrogens go up. These bound estrogens are not usable by the body. Studies have correlated a link between these bound estrogens and the incidence of estrogen-related cancers – breast, cervical, uterine, and ovarian. 

There’s something beautiful about this dance between microbes and hormones. As microbes ‘unbind’ estrogens, the unbound estrogens help microbes proliferate. The newly unbound estrogens nurture a healthy and diverse microbiota. The healthy microbiota and unbound estrogen dance, in turn, fosters properties against those estrogen-related cancers.  

There’s even support for the idea that hormone replacement therapy (HRT) could be safer and more effective with the addition of probiotics to feed the microbiome. Estrogen and gut microflora may also act together to regulate weight and fat distribution, bone health, cardiovascular health, memory, concentration, and mood.  

Microbes and Progesterone


We don’t know as much about the interplay between the microbiome and progesterone as we do about microbes and estrogen. We often wonder if this gap has to do with the prevailing view that insists menopause is about estrogen deficiency. There’s more research emphasis on estrogen. Progesterone is just as important. Together, they harmonize and help coordinate the menstrual cycle. Progesterone is also critical for creating a healthy lining of the uterus. 

Progesterone is a calming hormone. When levels are low, we’re likely to feel irritable and edgy, which helps explain PMS and mood changes during and after the menopause transition. Progesterone levels are at their lowest just before our periods. And the closer we get to menopause, the lower progesterone tends to go. Like estrogen, progesterone falls off sharply in the first year or two after menopause.

The gut microbiome helps regulate progesterone. Progesterone also fosters the proliferation of certain microflora. One, in particular, is a family of friendly bacteria called Bifidobacteria. You may have seen this genus of bacteria listed on probiotics’ bottles. Younger women tend to have higher counts of Bifidobacteria. As we get older and progesterone declines, we tend to have less. Bifidobacteria produce calming and feel-good hormones. When their counts decline, we are more likely to experience anxiety and irritability, or depression. 

You can see how intertwined Bifidobacteria are with progesterone and moods. With both on the decline in midlife and beyond, it becomes clearer why our moods might be affected. We can glimpse at the benefits of feeding the microbiome with a good probiotic to support our moods. We’ll explore probiotics later. For now, we hope what’s coming into view is a new way of relating to the microbiome as a partner in the menopause transition and afterwards, too.  


Microbes and Other Hormones

Gut microbes also support healthy insulin signaling. Insulin is necessary for glucose (sugar) metabolism. As we age, cells become less sensitive to the actions of insulin. A healthy microbiome helps to counter that resistance. Gut dysbiosis, on the other hand, can disrupt insulin signaling and contribute to weight gain and even obesity.

There are truly countless ways the microbiome supports hormones across the body. In the next part of this series, we explore microbes and mood and energy hormones. 

Gateway to Vibrant Wellbeing

  1. If you were surprised about the interplay between gut microbes and sex hormones, what, in particular, struck your curiosity?
  2. What touched a personal note or stirred a bit of wonder about your body and menstrual cycle or menopause?

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gut health for menopause transition

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  1. Baker, JM, Al-Nakkash, L, Herbst-Kralovetz, MM. Estrogen-gut microbiome axis: Physiological and clinical implications. Maturitas 2017;103:45-53.
  2. Bitzer, J. Progesterone, progestins and psychosomatic health of women. Horm Mol Bio Clin Inv. 2010;3(3):477-480.
  3. Cani, PD, Delzenne, NM. The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharmaceut Des. 2009;15:1546-1558.
  4. Chen, KL, Madak-Erdogan, Z. Estrogen and microbiota crosstalk: Should we pay attention? Trends Endocrinol Metabol. 2016;27(11):752-755.
  5. Gonidakis, S, Longo, VD. Assessing chronological aging in bacteria. Methods Mol Biol. 2013;965:421-437.
  6. Kim, S, Jazwinski, SM. The gut microbiota and healthy aging. Gerontology. 2018;64(6):513-520.
  7. Markle, JGM, Frank, D, Mortin-Toth, S, et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013;339(6123):1084-1088.
  8. Neuman, H, Debelius, JW, Knight, R, et al. Microbial endocrinology; The interplay between the microbiota and the endocrine system. FEMS Microbio Rev. 2015;39(4):509-521.
  9. Nuriel-Ohayon, M, Neuman, H, Ziv, O, et al. Progesterone increases Bifidobacterium relative abundance during late pregnancy. Cell Rep. 2019;27(3):730-736.e3.
  10. Vrieze, A, Van Nood, E, Holleman, F, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. 2012;143(4):913-916.

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