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The Hormone Clarity Guide
In my last post, we explored the importance of preserving beneficial gut microbes—species like Akkermansia, Bifidobacteria, and Faecalibacterium—and how to feed them with prebiotics and microbial-accessible foods.
We’ve also talked about probiotics:
What they can (and can’t) do, and how to choose them wisely.
Today, we’re turning to the dark side of the microbiome: the bad bugs that can set up camp in your gut.
When harmful microbes enter the gut, a healthy biome should be resilient enough to crowd them out. But if the beneficial community is depleted, these “bad bugs” can overgrow and take up residence.
This imbalance is called dysbiosis.
Unfortunately, many labs and practitioners focus almost exclusively on the “bad” microbes—sometimes prescribing harsh antimicrobial protocols that wipe out both the harmful and beneficial species. That’s not true healing.
In my clinic, I often meet people who worry about parasites or candida. These do show up, but much more often I see persistent communities of problematic bacteria that quietly drive inflammation, pain, and gut dysfunction.
Certain bacteria produce LPS endotoxins (lipopolysaccharides). These molecules slip through the gut lining into the bloodstream, where they trigger widespread inflammation.
High levels of LPS are linked to:
Common LPS-producing bacteria include E. coli, Salmonella, and Klebsiella.
When these overgrow in the small intestine, it’s known as SIBO (small intestine bacterial overgrowth).
Tip: LPS producers should make up <4% of your biome—ideally less than 1%.
Bacteria like Desulfovibrio and Bilophila wadsworthia produce hydrogen sulfide gas. A little H₂S is normal—but too much becomes toxic to the gut lining.
Excess H₂S is linked with:
Symptoms include:
Diet connection: H₂S producers thrive on fatty animal protein, eggs, dairy fat, coconut oil, and saturated fat because they feed on bile and sulfur amino acids.
Technically not bacteria, these microbes are classified as archaea. We call them methanogens because they produce methane gas.
While not as inflammatory as LPS or H₂S producers, methanogens are stubborn and difficult to reduce.
The first step is always assessment. You need to know which populations are overgrowing before you can address them.
When we identify hydrogen producers, methanogens, or LPS-producing bacteria, the goal is to lower their populations selectively—not carpet-bomb the whole ecosystem.
That’s why in my practice we avoid harsh botanicals like berberine or oregano oil, which can wipe out good species along with the bad. Instead, we use:
Healing dysbiosis is both an art and a science. The goal is to move from imbalance (dysbiosis) back into symbiosis—where beneficial bacteria thrive, inflammation quiets down, and the “pesky bugs” fade out.
Ready to find out if dysbiosis is behind your symptoms?
Do you have any questions about this article or about root cause functional medicine?
Dr. Laura Paris is a women’s health specialist who provides integrative, holistic Functional Medicine care and Acupuncture at her two clinics in Capitola and Monterey, California. She also works with women remotely in the United States through telehealth appointments.
Her unique approach to root-cause medicine includes a whole-body view including hormones, digestion, microbiome and gut health, nutrition, autoimmunity and inflammation, blood sugar regulation, and energy metabolism. Learn more about Dr Laura Paris here, and message her directly here.
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