Enzymes, microbes, and the products that work on digestion — physiology first, because none of it makes sense the other way round.
~13 min read
Swallow a mouthful of food and it has not entered your body. It has entered a tube that runs through your body, open at both ends, and everything in that tube is still on the outside of you. Nothing has come in until it crosses a wall.
That is the shape of the thing, not a metaphor. You are, topologically, a doughnut: one continuous channel about nine metres long, and the space inside it is continuous with the room you are sitting in. The crossing happens mostly in the small intestine, across a lining one cell thick, folded and folded again until the working surface reaches thirty or forty square metres. Three things follow.
Three accessory organs sit outside the tube and empty into it — the liver, making bile; the gallbladder, storing it until fat arrives; and the pancreas, the enzyme factory. The digestive system lesson walks the route organ by organ.
Diagram to come
A simplified body in line art with the digestive tract drawn as ONE continuous open channel from mouth to anus, the lumen shaded in the same tone as the background outside the body so it reads visually as outside — that is the entire point of the drawing and must survive at phone size. One arrow at the small intestine wall marked as the crossing, with a cutaway showing a single-cell-thick lining and villi. The three accessory organs drawn outside the channel with ducts feeding in. A topology diagram, not an anatomy chart: no labels beyond those listed.
An enzyme is a protein folded into a shape with a pocket in it, and what happens in that pocket is catalysis. A reaction must first climb a threshold — the activation energy — before old bonds will break. Starch in water would come apart into sugars eventually, but at body temperature that takes years. An amylase does it in milliseconds, having supplied no energy and changed no destination. It has lowered the hill, and is not used up doing so. The naming convention follows the substrate: protease on protein, amylase on starch, lipase on lipids, lactase on lactose, cellulase on cellulose.
[Proteases](/healer/learn/nutrients/protease) — protein
They cut between amino acids, down to single amino acids small enough to cross. The stomach makes pepsin, the pancreas trypsin and chymotrypsin — all shipped out inactive, since a protease active inside its own cell would digest it.
[Amylases](/healer/learn/nutrients/amylase) — starch
The only digestion that begins in the mouth, which is why a plain cracker held on the tongue turns faintly sweet.
[Lipases](/healer/learn/nutrients/lipase) — fat
Fat sits in droplets in the watery contents of the tube, and a lipase works only at a droplet’s surface. That is what bile is for: bile salts break large droplets into small ones, multiplying the surface available.
[Lactase](/healer/learn/nutrients/lactase) — the sugar in dairy
Made in the wall of the small intestine rather than secreted into it. Production is highest in infancy and in most of the world’s adults falls away after weaning; continued high production into adult life is a variant.
[Cellulase](/healer/learn/nutrients/cellulase) — plant cell wall
You make none. Cellulose is glucose joined by a link no human enzyme opens, so the structural material of every plant you eat passes the whole tube untouched.
Supplemental enzymes have two origins. Animal-derived means pancreatin — a pig’s pancreatic enzymes, tuned like your own for the alkaline small intestine, so they usually need protecting through the stomach. Microbial enzymes are grown by fermenting fungi such as Aspergillus species and stay folded across a much wider band of acidity, so they begin on the meal in the stomach.
The first picture anyone drew of this, in the 1890s, was a lock and a key: a rigid enzyme with a slot, a substrate shaped to fit. It is still the picture most people carry, and it is wrong. An enzyme is not rigid. When the right molecule arrives the pocket closes around it — the induced fit — and the strain that closing puts on the captured molecule is part of the mechanism.
Stranger still, the pocket is shaped to fit not the comfortable substrate but the distorted, half-broken arrangement it passes through on the way over the hill, and by binding that shape most tightly the enzyme lowers the hill itself. Specificity comes from several weak things agreeing at once — the shape of the pocket, where charges sit, where hydrogen bonds form — which is why an amylase in a swamp of protein does nothing, and why the unit that makes sense is a complex rather than one enzyme.
A protein’s fold is held by many weak interactions, a good number involving side chains that carry an electrical charge. Whether a side chain is charged depends on how many hydrogen ions are around it, which is what pH measures. Change the pH, change the charges; change the charges, the fold shifts; shift the fold, and the pocket is the wrong shape.
The scale is steeper than it looks — pH is logarithmic, so a stomach at pH 2 is around a hundred thousand times more acidic than a small intestine at pH 7. Salivary amylase works near pH 7 and gets a few minutes before the acid shuts it down. Pepsin’s band is roughly pH 1.5 to 2, which it requires rather than tolerates. The pancreas then delivers its enzymes with bicarbonate, lifting the duodenum to around pH 6 to 8. An enzyme in the wrong compartment is not weaker: it is the wrong shape. That is why an enteric coating exists, and it is the same obstacle a live organism must get past.
Diagram to come
A horizontal strip representing the tract from mouth to colon with a pH axis beneath it, drawn as a curve that starts near neutral, plunges into the acid range through the stomach and climbs back to mildly alkaline in the small intestine. Above the strip, bars showing where each enzyme is active, each bar starting and stopping where the curve enters and leaves its band — the bars must visibly end rather than fade, so the reader sees that activity stops. Mark the bicarbonate delivery point where the curve climbs. The colon segment carries no enzyme bar, only a marker for bacterial fermentation.
TerraZyme is a digestive enzyme complex, and despite sharing part of its name with the digestive blend it contains no oils. In it are the five enzymes from the last section — protease, amylase, lipase, lactase and cellulase — with two whole botanicals, ginger root and peppermint leaf, as plant material rather than distilled oil.
Read that against an ordinary dinner and the logic of a complex is obvious: protease for the protein, amylase for the bread and rice, lipase for the fat, lactase for the sugar in any dairy, cellulase for the part of every vegetable no human enzyme touches. What may honestly be said of it is what its label says: it supports healthy digestion.
On the panel the enzymes are declared in activity units rather than milligrams — HUT for protease, DU for amylase, FIP for lipase, ALU for lactase, CU for cellulase. Two products with identical milligram figures can differ several-fold in activity. Reading a supplement label takes that apart properly.
When to take it follows from specificity: with the meal, or just before. An enzyme with no substrate in front of it has nothing to do, and it does not wait — it travels down the tube and is itself digested. Which products exist, under which names and with which directions, differs by country; your own pack is the authority.
You carry roughly as many bacterial cells as human ones. The figure everyone repeats is ten to one; that came from a rough estimate made in the 1970s and circulated unchecked for forty years. A careful recount published in 2016 put it close to one to one — and the whole population weighs some two hundred grams.
The stomach holds almost nothing — acid and speed see to that — while the large intestine holds on the order of a hundred billion organisms per gram of content. Almost all are bacteria living without oxygen, and between them they carry several million genes against the twenty thousand or so in the human genome. That gene count is the honest reason they matter: metabolic capability we do not have.
Three things are genuinely established, and worth stating plainly because so much around them is not.
Now the part that is oversold, because a healer who cannot say where the evidence stops is not much use.
Fibre is not one substance. It is the collective name for plant carbohydrate human enzymes cannot break: cellulose and hemicellulose from cell walls, pectin from fruit, inulin and the fructo-oligosaccharides, beta-glucan from oats, resistant starch. All of it reaches the colon as it left the plate, and organisms carrying the right enzymes ferment it. The products are short-chain fatty acids — mainly acetate, propionate and butyrate, roughly sixty, twenty, twenty — plus gas, which is the sign that fermentation is happening.
Butyrate barely leaves: the cells lining the colon take it up straight from the lumen and burn it, and it supplies a large share of their energy. Most cells in the body run on glucose delivered by blood; these run on what the bacteria beside them have just made. Propionate travels in the portal vein to the liver, acetate reaches the general circulation, and the acids lower the pH of the colon contents — so the population is partly shaping its own habitat.
The fermentable fibres are worth knowing by name. Inulin and fructo-oligosaccharides: chicory root, onion, leek, garlic. Resistant starch: cooked potato and rice that has been cooled, green banana, beans. Beta-glucan: oats and barley. Pectin: apples and citrus pith. Most adults fall well short of the twenty-five to thirty grams a day guidelines converge on, and a sudden increase makes for a noisy week, so go up slowly. Which fibre yields which acid, in which person, is not predictable.
Diagram to come
Left to right: named fibre sources as small plant icons feeding into a colon segment in cross-section with bacteria in the lumen. Out of the fermentation, three labelled arrows of visibly different weight showing the roughly 60/20/20 split, each to a different destination — butyrate turning immediately into the cells of the colon wall itself, propionate into a vessel marked to the liver, acetate out into general circulation. A fourth, lighter arrow for gas leaving upward. Bottom strip: a pH marker showing the contents becoming more acidic as fermentation proceeds.
The working definition is a demanding one: live micro-organisms which, given in adequate amounts, do something useful for the host. Alive, enough of them, and a demonstrated effect. A dead culture is not a probiotic.
Then the number. CFU stands for colony-forming unit, and the method explains the word: a sample is diluted, spread across a plate of growth medium and incubated, and the colonies counted, each having grown from one cell alive and able to divide. Not a weight — a count of survivors able to reproduce. The figure printed on a pack is usually a count at manufacture; a label guaranteeing its count at the end of shelf life is making a far harder promise.
Next, delivery. To reach the colon alive an organism must survive two barriers built to destroy incoming micro-organisms: the stomach at pH 1.5 to 3.5, and bile in the duodenum, a detergent that takes bacterial membranes apart.
Tolerant strains
Many lactobacilli come from acidic habitats and survive the passage in far greater numbers than a random bacterium would.
Enteric coating
A polymer film that will not dissolve in acid but does dissolve above roughly pH 5, so the capsule stays sealed through the stomach and opens once bicarbonate has raised the pH downstream.
A capsule inside a capsule
A smaller capsule sits inside a larger one; the outer is spent in the stomach, while the inner — never exposed to acid — carries the culture on before opening.
Last, and most important, the naming. Bacteria are named at three levels — genus, species, strain — and in Lactobacillus rhamnosus GG, everything ever demonstrated about that organism was demonstrated about GG. Two strains of one species can differ across a substantial fraction of their genes.
The strain is the claim
A pack naming only a genus, or a genus and a species, has nothing checkable on it — there is no organism specific enough to look up. A pack that names strains is one you can investigate.
Finally, the word that gets confused with all of this. A prebiotic is not an organism — it is food for the organisms already there. Prebiotic fibre means a carbohydrate you cannot digest that the resident population ferments readily. A probiotic adds; a prebiotic feeds.
Two probiotics sit in the range, both built on the same two genera: Lactobacillus and Bifidobacterium, which account for most of the probiotic world.
PB Assist+
The everyday capsule, and the clearest working example of the capsule-inside-a-capsule delivery above. It also includes a prebiotic fibre, so the organisms arrive with something to eat.
PB Restore
The newer and broader formulation, across a wider set of strains. Where it is available it is generally used as a defined run rather than taken indefinitely — the pack states which.
What this lesson deliberately does not tell you: the strain designations, the CFU count, the directions. Those are on the pack in your hand, and they differ between markets and between formulation revisions.
On when to use which, the honest framing is timescale rather than strength: a supplemented strain stays only as long as you keep supplying it. And one thing applies to no other supplement on the shelf — these are alive, so where you keep them decides how many are left. Heat and moisture kill them: not the bathroom cabinet, not a car in summer.
The third product usually kept alongside those two is not a nutritional supplement at all. ZenGest is doTERRA’s digestive blend — seven culinary plants, four of them seeds — and the softgel is that blend measured into a vegetable capsule.
Why a capsule exists when the same oil is in the bottle beside it comes down to three things, none of them potency: it puts the oil past the tongue, it is a measured amount where a drop is not, and it delivers the formula intact.
The part that belongs here is the category difference. Natural Solutions draws the line: a body is sustained by nutrition and directed by chemistry. An enzyme complex supplies a tool the meal needs; a probiotic supplies organisms and a prebiotic their food. A softgel of ZenGest supplies none of that — no enzyme, no organism, no nutrient. It is a small quantity of aromatic plant chemistry, used for comfort.
Which is why it sits beside the other two rather than competing with them: enzymes for the breaking down, organisms and their food for the last stretch, culinary plants for how the hour afterwards feels. Timing matches the enzymes — with the meal or just after. And a softgel is an internal-use product, which means it is only ever what the label on your own pack says it is.
Three products, three different jobs, and most of the time you do not want all three.
Which of these is the situation?
Pick honestly rather than aspirationally — the answers differ more than you would expect.
Nothing here outperforms chewing
Chew properly and the mechanical work is done and the amylase has had its few minutes. Eat sitting down. Leave a real gap between meals. Eat a wide range of different plants across a week — the most reliable thing anyone has found for the population in the colon is the number of different plants, not of capsules. All four are free, and all four do more than anything named here.
Anything persistent, severe, or new and unexplained belongs with a healthcare practitioner, not a shelf.
Supplements are intended to complement a diet, not to replace food, and nothing here replaces professional medical care. Keep supplements out of reach of children, and keep oils away from eyes and inner ears. If you are pregnant, nursing, under medical care or taking medication, speak to your healthcare practitioner before use. Nothing here is intended to diagnose, treat, cure or prevent any disease.
If one thing survives, make it the first idea rather than any of the products. The tube runs through you and its contents are still outside it.
Lesson 5 of 12 · Nutrition