Complete Microbiome Map: Deep Dive - Methanobrevibacter
Methanobrevibacter smithii is a microbe that plays a unique role in human digestion, one that made perfect sense thousands of years ago, but can create problems in today’s world of abundant food, chronic stress, and hormonal imbalances.
It appears elevated in people struggling with bloating, constipation, and hormone-related concerns such as endometriosis.
Methanobrevibacter smithii is not a bacteria - it is an archaea. This is important to note, because archaea behave differently to bacteria, respond differently to treatment strategies, and play a unique role in digestion. Unlike bacteria which produces hydrogen gas, Methanobrevibacter smithii produces methane gas, which has a direct and powerful effect on slowing down gut motility.
Methanobrevibacter smithii has lived alongside humans for tens of thousands of years.
From an evolutionary perspective, its presence made perfect sense. Early humans did not have regular access to food, and long periods of scarcity were common. In this environment, slowing digestion was not a problem - it was a survival advantage.
By slowing digestion, methane-producing archaea allowed food to remain in the gut for longer, increasing the amount of energy and nutrients that could be extracted from each meal. This helped prevent nutrient loss and supported survival during times when food was limited or unpredictable. It essentially helped humans get more calories and nutrients from less food.
The problem?
Methanobrevibacter smithii has not evolved, but our food environment has. It still behaves as though food scarcity is the norm, except we now live in an era of constant food availability. When levels become elevated, excess methane production occurs, digestion slows excessively, and this is where symptoms begin.
What Happens When Methane Is Too High?
Methane gas has a direct slowing effect on gut motility. Unlike hydrogen, which can speed up transit time, methane acts like a brake on the intestines. Excess methane leads to all of the typical constipation symptoms - straining, hard and dry stools, incomplete evacuation, and overall sluggish digestion.
It is important to note that constipation is never “just constipation”. Chronic constipation sets off a cascade of downstream effects - especially for hormone health.
Sluggish Motility Alters the Microbiome
Sluggish motility changes the entire gut environment. When stool sits in the bowel too long:
• Fermentation increases → more gas, bloating, pressure
• Microbial balance shifts → more opportunistic, pro-inflammatory species
• Bacterial byproducts accumulate → Certain bacteria thrive in a slower, more stagnant environment → more inflammatory by-products.
This creates a gut environment that feeds inflammation, which then impacts all systems in the body:•
• Skin - congestion, acne, flares
• Mood - irritability, low mood, anxiety
• Pain sensitivity
• Hormone metabolism and clearance
Estrogen Recirculation & the Estrobolome
One of the most significant consequences of slow transit time — particularly for women — is oestrogen reabsorption.
Within the gut lives what we call the estrobolome — the collection of microbes involved in:
• Breaking down oestrogen
• Reactivating or recycling oestrogen
• Regulating how much oestrogen remains in circulation
In a healthy system, oestrogen is metabolised in the liver, conjugated (packaged for removal), sent into the bowel via bile, and eliminated efficiently in stool.
But when constipation is present, that process shifts.
Oestrogen lingers in the bowel. Certain bacteria produce enzymes (notably beta-glucuronidase) that deconjugate it - essentially reactivating it - allowing it to be reabsorbed back into the bloodstream. Over time, this can contribute to relative oestrogen excess.
Clinically, this pattern is associated with:
• Endometriosis
• PMS
• Acne
• Fibroids
• Heavy or painful periods
Another layer we frequently see is methane overproduction. Methane-dominant patterns are strongly associated with slowed motility and significant abdominal distension. This is particularly relevant in the classic “endo belly” presentation - where bloating worsens as the day progresses and does not resolve with dietary changes alone.
Straining, Pelvic Floor & Period Pain
Chronic constipation often leads to repeated straining, which places ongoing stress on the pelvic floor muscles. Over time, this can cause the pelvic floor to become overactive and unable to fully relax. This constant tension is often overlooked but can play a significant role in menstrual pain and pelvic discomfort.
An overactive pelvic floor may contribute to:
Increased period pain
Difficulty fully emptying bowels
Pelvic, hip, or lower back discomfort
In many cases, pelvic floor dysfunction does not begin in the pelvis itself, but as a downstream consequence of long-term gut dysfunction.
It’s important to emphasise that Methanobrevibacter smithii is a normal resident of the human gut microbiome. It is not a pathogen, and complete eradication is not the goal.
The aim is regulation rather than elimination. The challenge is that modern diets, stress, disrupted circadian rhythms, low fibre intake, and frequent antimicrobial exposure continuously encourage methane dominance.
Supporting gut motility, reducing excessive fermentation, and restoring microbial balance allows Methanobrevibacter smithii to return to ta proportionate role within the gut ecosystem - rather than dominating it.
