The Mineral Roots of the Microbiome
Before the world fixated on probiotics and prebiotics, minerals quietly built the microbiome itself. Maybe we wouldn’t need so many “gut hacks” if we just restored the minerals first
Since many of the readers who paid to access my book, “From Volcanoes to Vitality” on Substack, will not be buying the final, hardcover version, I figured that if I made any critical “addition” to a previously posted chapter, I would share it with you.
This is one of those times, and I think it will be of great interest to all of you (it was to me).
Recall Chapter 5, “The Enzyme Enigma: The Missing Mineral Keys to Human Metabolism.” In that chapter, I highlighted that, of all enzymes thought to be active in the human body, 91 percent have not been characterized, nor have their critical mineral cofactors been identified.
In the conclusion to that chapter, AI agreed with me that:
“The likelihood that the current ‘essential’ trace mineral list is incomplete—and that a major, beneficial knowledge gap exists in modern biochemical sciences—is extremely high, particularly regarding rare and ultra-trace minerals and their roles in enzymatic function.”
I have since added a new section to the chapter, underscoring once again the importance of mineral-enzyme interactions. Check it out—I guarantee it will be of great interest to all of you “health enthusiasts” who have been obsessing over your microbiomes of late.
Minerals And The Microbiome
Know that a healthy microbiome begins with minerals. Every microbial community in the gut depends on a mineral-rich environment to sustain metabolism, redox balance, and structural stability.
Among all gut organisms, Bifidobacterium stands out as the keystone genus most closely tied to mineral availability. It thrives only when fermentable fibers and ionic minerals coexist—fiber provides its fuel, but minerals activate the enzymes that make fermentation possible.
Bifidobacteria operate one of the most mineral-dependent metabolic programs in the human gut. Their carbohydrate-active enzymes (CAZymes) require zinc, magnesium, and manganese as cofactors to break down inulin, fructooligosaccharides (FOS), and other prebiotic fibers.
Let’s drill down on FOS (no, not “full of shit”) in more depth here. FOS are long or branched chains of fructose molecules that Bifidobacterium can’t absorb directly. They must first be enzymatically cleaved by the bacterium’s enzymes which require mineral cofactors (especially Mg²⁺, Zn²⁺, and Mn²⁺) for stability and function.
Once FOS are broken down into simpler sugars, Bifidobacterium uses those fragments as fuel through fermentation pathways that produce acetate and lactate.
The accumulation of these fermentation acids—and the lowered local pH—then favors further bifidobacterial growth while discouraging pathogens. In other words, breaking down FOS not only feeds Bifidobacterium, it also creates the ecological conditions that reinforce its dominance in the gut.
Thus, without these ionic minerals, fermentation slows, short-chain fatty acid (SCFA) output collapses, and the entire downstream microbial network—including butyrate producers—falters.
Just as crucial, sulfate ions sustain the mucosal environment where Bifidobacterium flourishes: they structure the protective mucin layer, support anaerobic redox cycling, and maintain the oxygen-free niche required for bifidobacterium growth.
In essence, minerals are the quiet architects of the gut ecosystem. They power microbial enzymes, stabilize mucosal structure, and govern the redox chemistry that determines whether beneficial species like Bifidobacterium can persist.
The more diverse and bioavailable the mineral complex, the more resilient the microbiome becomes—proving that gut health begins not with probiotics or fiber alone, but with the minerals that make microbial life itself possible.
See more here pierrekorymedicalmusings.com
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