The Mineral Roots of the Microbiome: The Missing Link in Gut Health

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% 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.

More recently, I came across this study:

They used Deep-sea water (DSW), defined as water from depths greater than 200 m, with high mineral content and low temperature. They described is as mineral-rich, apparently “hard water” with high mineral/hardness content compared to the “soft” mineral water used as control. However, the exact mineral composition (e.g., which specific minerals and concentrations) was not fully detailed, but the key is that the beverage is enriched with trace minerals sourced from deep-sea water.

Without going into the granular details, their 12-week clinical trial found that drinking refined deep-sea water (RDSW) improved gut health more than standard mineral water (so, keep in mind, the “control” group got mineral water!.

Nearly all participants with constipation improved on RDSW (94% vs. 60% controls), and their levels of beneficial gut metabolites—short-chain fatty acids (SCFAs)—significantly increased, while harmful microbial by-products like phenol decreased.

Markers of gut immune stress (sIgA) also dropped, and the ability of gut bacteria to process plant nutrients (isoflavones) tended to rise.

Overall, the study suggests that mineral-rich deep-sea water can meaningfully shift gut microbial activity toward a healthier profile, supporting digestion, reducing irritation, and enhancing metabolic signaling. However, the trial was short, involved healthy adults, and the authors emphasize that larger, longer studies are needed to understand long-term and therapeutic implications.

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.

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P.S. If interested in reading “From Volcanoes to Vitality”, you can read it for free as a paid subscriber (an oxymoron, I know). The Table of Contents is here.

Upcoming Book Publications

Yup — not one, but two books are dropping from yours truly. At the same time? What?

1. From Volcanoes to Vitality: if, instead of (or in addition to) this Substack version, you prefer the feel of a real book—or the smell of paper—or like to give holiday gifts, pre-order my grand mineral saga, shipping before Christmas.

2. The War on Chlorine Dioxide: if you want to read (or gift) another chronicle of suppression, science, and survival, grab the sequel you didn’t see coming—shipping mid-January. On this one, I say: “Buy it before they ban it.” Hah!

© 2025 Pierre Kory. All rights reserved.

This chapter is original material and protected under international copyright law. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of the author.