Systems Deep Dive: The Digestive System & the Microbiome

The Root of Health in Horses, Dogs, and People

They say “all health begins in the gut” — and they’re right.The digestive system is where true wellness takes root. It’s not just a pathway for food to travel through — it’s an ecosystem, a communication hub, and a reflection of balance (or imbalance) throughout the body.

Across species — horse, dog, or human — the digestive system and the microbiome are intimately linked with immunity, hormones, mood, energy, and even how we respond to stress. When this system thrives, every other system does too.

1. Anatomy & Function: Designed by Nature

Horses – The Hindgut Fermenters

A horse’s digestive system was built for near-constant motion and near-constant grazing. Their small stomach secretes acid continuously — whether they’re eating or not — and depends on a steady trickle of fibrous forage to buffer that acid. Once food passes into the hindgut (cecum and colon), microbial fermentation takes over. Billions of bacteria and protozoa break down cellulose, creating short-chain fatty acids (SCFAs) that supply slow, steady energy.

When horses are fed grain, high starch feeds, or go too long between meals, pH in the hindgut drops, killing beneficial microbes. The result? Gas, colic, ulcers, laminitis, and systemic inflammation.In other words — when the microbiome is disrupted, the horse’s whole system feels it.

Dogs – The Monogastric Carnivores

Dogs are designed for meat. Their short digestive tracts and highly acidic stomachs are built to break down raw proteins, fat, and bone quickly. In the wild, a canine diet would include not just muscle meat, but organs, fat, fur, and partially digested plant matter from prey — a natural prebiotic source that supported microbial balance.

Modern kibble diets — full of starches, grains, soy, and synthetic additives — flip that design upside down. They feed yeast and unwanted bacteria, dull enzyme activity, and contribute to skin allergies, hot spots, anal gland issues, and chronic inflammation. A dog’s microbiome thrives on whole, species-appropriate food — not processed fillers.

People – The Omnivorous Bridge

Humans sit between the two: omnivorous, yet microbiome-dependent. The small intestine absorbs most nutrients, but the colon — home to our densest microbial population — ferments fiber into SCFAs that feed colon cells and regulate immunity.Modern stress, antibiotics, pesticides, and ultra-processed diets have led to massive microbial loss, correlating with autoimmune issues, hormonal imbalances, and mental health struggles.

Our digestive tracts may look different, but the principle is universal: nature intended diversity, simplicity, and balance.

2. The Microbiome – Our Hidden Organ

The microbiome is not just a cluster of bacteria; it’s a living organ influencing metabolism, immunity, and even gene expression. These microorganisms:

• Produce vitamins (B-complex, K)

• Generate short-chain fatty acids that regulate inflammation

• Train the immune system to recognize friend from foe

• Detoxify harmful compounds and metabolize hormones

When in balance, they form a protective community. When disrupted (a state called dysbiosis), harmful species overgrow, and the barrier lining the gut becomes “leaky.” This allows endotoxins (like lipopolysaccharides) to escape into the bloodstream, igniting inflammation throughout the body.

For horses, that may look like laminitis or stocking up.For dogs, chronic ear infections or hot spots.For people, bloating, fatigue, brain fog, or autoimmune flares.

Different bodies. Same story.

3. Dysbiosis: When the Gut Loses Its Rhythm

Several factors can shift a healthy microbiome off course:

• Processed feeds & diets high in starch, soy, or refined carbs

• Antibiotics, dewormers, and NSAIDs that wipe out beneficial microbes

• Stress (yes, emotional stress alters gut motility and microbial composition)

• Toxins in water — chlorine, fluoride, and heavy metals

• Lack of natural diversity — sterile environments, limited diet variety

Once disrupted, microbial communities become less diverse, digestive enzymes falter, and inflammation begins. Many “mystery” symptoms — from behavioral changes to skin issues — trace back to gut imbalance.

4. Restoring Harmony – Root-Cause Healing

Herbal medicine excels here because herbs are food first, medicine second. They feed, soothe, and rebalance rather than suppress.

For Horses

• Slippery Elm & Marshmallow Root – coat and protect the GI lining

• Chamomile & Fennel – reduce gas, ease tension, and calm the nervous system

• Dandelion Root & Burdock – support bile flow and liver detoxification

• Prebiotic Fiber from Forage – encourages beneficial hindgut microbes

• Mineral Balance – supports microbial enzyme function

And above all: a forage-first diet with clean water and salt access at all times.

For Dogs

• Slippery Elm & Plantain Leaf – gentle mucilaginous protectors

• Ginger & Licorice Root – soothe nausea and inflammation

• Gentian & Dandelion – act as natural bitters to stimulate digestive juices

• Raw or Lightly Cooked Whole Foods – the foundation for microbial diversity

• Probiotic-rich foods like kefir or fermented vegetables (in moderation)

For People

• Digestive Teas – peppermint, fennel, and chamomile support peristalsis

• Bitters – gentian, orange peel, and angelica to “wake up” digestion

• Adaptogens – ashwagandha or holy basil to ease stress-related sluggishness

• Fermented Foods – yogurt, kimchi, miso, and sauerkraut for natural probiotics

• Prebiotic Herbs – chicory root, burdock, and artichoke feed healthy flora

Healing begins when we support the terrain — not when we chase the symptoms.

5. The Mind–Gut Connection

The gut has its own nervous system — the enteric nervous system, often called the second brain. It communicates directly with the brain through the vagus nerve, influencing mood, heart rate, and even immunity.

When stressed, blood flow to the digestive tract decreases; motility slows or speeds up; enzymes reduce; and beneficial microbes suffer.For horses, this looks like ulcers and tension.For dogs, appetite loss or diarrhea.For people, IBS or emotional eating.

Activating the parasympathetic state — through calm feeding routines, slow breathing, and mindful presence — is just as healing as the right herbs.Peaceful environments feed the gut as much as food does.

6. Whole-Being Integration

When we talk about the digestive system, we’re really talking about how we process life.Are we allowing nourishment in? Are we holding on to what needs to be released?For horses, that means freedom to move and graze.For dogs, connection to their pack and instinct.For people, slowing down, chewing thoroughly, and trusting the body’s rhythms.

When body, mind, and spirit align — digestion flows.Because in the end, gut health isn’t only about food. It’s about balance, environment, and emotional peace.

🌿 In Harmony

Healing the digestive system isn’t about a quick fix — it’s a lifelong relationship with the way we nourish ourselves and those we love.Feed the body what it was designed for support the microbes that support life.And remember: the root of wellness always begins in the gut.

With Love, Herbs & Harmony,

~Debbi, Wholehearted Harmony

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