If there are two systems that consistently show early signs of dysfunction long before a diagnosis appears, those are the Assimilation and Elimination systems, which together form the foundation of gut health. For countless people in Omaha, this dashboard light has been flickering for years.
Bloating after meals.
Irregular stools including constipation, diarrhea, or both.
Food sensitivities that seem to change overnight.
Reflux, cramps and distention.
Slow motility, sluggish digestion, or incomplete elimination.
Normal labs despite very abnormal symptoms.
Most patients are told these symptoms are harmless or just IBS, but they represent something deeper: a breakdown in how your body digests and absorbs nutrients and eliminates the waste products that shape every aspect of human physiology.
Functional medicine excels here because it does not treat gut symptoms as isolated nuisances. It treats them as the outward expression of upstream imbalance.
“Gut symptoms are never random. They are your body’s most reliable early warning system.”
Let’s dive into why your gut health requires both assimilation and elimination.
Why Gut Health Requires Both Assimilation and Elimination
Assimilation is the process that breaks down foods and absorbs nutrients.
Elimination is the process of moving waste, metabolites, and toxins out.
Poor assimilation and elimination cause a long list of problems.
Digestive Symptoms
• Bloating after meals
• Gas and abdominal distention
• Reflux or heartburn (often from low stomach acid)
• Cramping, discomfort, or pain after eating
• Undigested food in stool
• Floating or greasy stools (fat malabsorption)
• Constipation, sluggish motility, or incomplete evacuation
• Diarrhea or rapid transit
• Alternating constipation and diarrhea (IBS pattern)
• Early fullness or feeling stuffed quickly
Nutrient and Metabolic Consequences
• Fatigue (from poor absorption or toxin recirculation)
• Nutrient deficiencies (B12, iron, zinc, magnesium, folate, fat soluble vitamins)
• Difficulty regulating blood sugar
• Muscle weakness, cramps, or poor recovery
• Weight loss resistance or unintended weight loss
• Difficulty building muscle despite exercise
Hormonal and Detoxification Effects
• Estrogen dominance (impaired hormone clearance)
• Worsening PMS or perimenopause symptoms
• Thyroid symptoms worsened by inflammation or nutrient deficits
• Heightened chemical sensitivity
• Headaches or migraines (toxin buildup)
Immune and Inflammatory Consequences
• Increased food sensitivities
• Chronic low grade inflammation
• Joint pain or stiffness
• Immune dysregulation and recurrent infections
• Skin issues such as acne, eczema, rashes, hives
Neurological and Mood Symptoms
• Brain fog and reduced cognitive clarity
• Morning grogginess
• Irritability, anxiety, or low resilience
• Trouble concentrating or feeling mentally slow
Systemic and Quality of Life Effects
• Bad breath or coated tongue
• Increased body odor
• Nausea or poor appetite
• Bloating even with healthy foods
• Greater sensitivity to stress
• Feeling toxic, heavy, or bogged down
Gut health is a two way system. When either side breaks down, the whole digestive ecosystem destabilizes.
The Most Common Assimilation and Elimination Problems We See at UpStream
When patients search gut health Omaha, they often have a collection of symptoms that cross both systems. Here’s what we see most.
Low Stomach Acid (Often Mistaken for High Acid)
Leading to incomplete digestion, bloating, reflux, and downstream microbial imbalance.
Dysbiosis (Microbial Imbalance)
An overgrowth or deficiency of key bacteria affecting motility, elimination, and inflammation.
Increased Intestinal Permeability (Leaky Gut)
Allowing waste products and food particles to activate the immune system.
Pancreatic or Bile Insufficiency
Driving undigested fats, floating stools, diarrhea, and nutrient deficiencies.
Inflammation of the Gut Lining
Often from stress, NSAIDs, poor sleep, alcohol, infections, or processed foods.
SIBO (Small Intestinal Bacterial Overgrowth)
A major cause of gas, distention, constipation or diarrhea, and post meal fatigue.
Sluggish Motility or Elimination Difficulties
Slow transit leading to constipation, toxin reabsorption, and bloating.
Fast transit leading to diarrhea, malabsorption, and nutrient loss.
Every one of these represents a system level imbalance, not a symptom level event.
Why Conventional Approaches Miss the Bigger Picture
Standard conventional care tends to isolate symptoms and treat them with:
• Acid blockers for reflux
• Laxatives for constipation
• Anti diarrheals for loose stools
• Antibiotics for SIBO
• Fiber supplements for irregularity
These treatments can be helpful in the short term but are downstream tools. They soothe symptoms without repairing the upstream system.
Functional medicine asks deeper questions:
• Why is motility slow or fast?
• Why is the microbiome imbalanced?
• Why is the gut lining inflamed?
• Why is the body reabsorbing waste?
• Why are foods triggering disproportionate immune responses?
• Why is elimination inefficient?
Once we correct the root cause, bowel patterns normalize, inflammation drops, and systemic symptoms resolve.
How UpStream Maps Assimilation and Elimination Using Functional Medicine
UpStream’s START process is designed to uncover not just what your gut is doing, but why.
We analyze:
• Digestive function (acid, enzymes, bile)
• Elimination patterns (motility, transit time, hydration)
• Medication effects (PPIs, NSAIDs, SSRIs, metformin) on both systems
• Stress and cortisol patterns that slow or speed motility
• Microbiome balance
• Inflammatory markers
• System level interactions with defense and repair, energy, biotransformation and structure
This creates the first clear map many patients have ever seen of their digestive system.
The Five Pillars of Gut Repair in Functional Medicine (5Rs)
Remove
Inflammatory foods, dysbiosis, chronic infections, and medication triggers when safe.
Replace
Adequate acid, enzymes, bile flow, and nutrients to restore digestion.
Reinoculate
Microbiome support through targeted probiotics, fiber diversity, and nutritional redesign.
Repair
Healing the gut lining and restoring motility through lifestyle, stress support, and key nutrients.
Rebalance
Nervous system regulation, circadian rhythm, movement, hydration, and elimination optimization.
Why Assimilation and Elimination Affect Other Dashboard Lights
A dysfunctional gut impacts:
• Defense and Repair: 70 percent of immune activity sits here
• Energy: nutrient absorption is required for mitochondrial output
• Biotransformation: toxins must be eliminated, not recirculated
• Structure: cannot be built or maintained with inadequate raw materials
Constipation alone can worsen estrogen dominance, fatigue, headaches, anxiety, and skin issues.
Diarrhea can drive nutrient depletion, electrolyte imbalance, and systemic inflammation.
This is why so many non-gut symptoms resolve when these systems are restored.
Why Omaha Patients Choose Functional Medicine for Gut and Elimination Issues
Gut symptoms are among the most searched health concerns in Omaha. They are uncomfortable, disruptive, embarrassing, and often dismissed.
UpStream provides:
• A systems map
• Time to understand the full story
• Medication expertise
• Nutrition that matches your physiology
• A targeted, evidence informed plan
• Root cause clarity
• A path toward long term stability
Functional medicine doesn’t guess about gut health. It explains it and restores it.
“Gut healing is not about removing foods. It’s about restoring the systems that were supposed to handle them.”
Our promise? Gut healing without guesswork. You deserve that.
The UpStream Promise: Gut Healing Without Guesswork
Your gut does two essential jobs: assimilate what you need and eliminate what you do not. When either job falters, your entire body feels the impact.
UpStream helps patients heal by restoring:
• Digestion
• Absorption
• Microbial balance
• Motility
• Clearance
• Inflammation control
• Nutrient repletion
This is gut health at its highest level, root cause and biologically precise.
