A speed-run guide to what they are, how to group them, and how they solve root causes behind “complex” diseases.
What is a Biomarker?
Biomarkers are measurable signals from your body that reflect biological state, risk, or response to interventions.
When you categorize them and look for patterns across systems, clusters reveal root causes.
Most chronic conditions boil down to a few connected sources: chronic inflammation, metabolic dysfunction, mitochondrial stress, microbiome imbalance, endocrine disruption, immune dysregulation, and environmental load.
How to Test Your Biomarkers
Functional medicine depends on trustworthy biomarkers. Pick a test that matches your longevity priorities.
2025’s top 3 Biomarker Companies:
- Function Health: 100+ tests with biological age from blood markers; complete at Quest Diagnostics labs across the United States with insights from the worlds’ best doctors.
Function Health · 100+ lab tests & insights from the world’s top doctors - TruDiagnostic TruAge: Kits assess biomarkers and biological age with DunedinPACE (aging speed) through blood spot. Recent 2025 multi omic clocks integrate epigenetics—the way your behaviours and environment can affect the way your genes work.
3. Fountain Life: Uses advanced diagnostics to assess biomarkers, biological age and catch disease at the earliest signs. Epigenetic biological age via DNA methylation, combining methylation, telomere length, and biomarkers for organ specific ages.
Good Biomarkers – The Map
Think in layers. Each layer is a lens; together they build a picture of health.
- Molecular
- Genomic: SNPs, polygenic risk scores
- Epigenetic: DNA methylation age
- Transcriptomic/Proteomic: cytokines, apolipoproteins
- Metabolomic/Lipidomic: ketones, acylcarnitines, ceramides
- Clinical labs
- Inflammation: hs‑CRP, IL‑6, TNF‑α
- Metabolic: fasting insulin, HOMA‑IR, OGTT, HbA1c
- Lipids: ApoB, LDL‑P, Lp(a), TG/HDL ratio
- Liver/Kidney: ALT, AST, GGT, eGFR
- Nutrient status: ferritin, B12, folate, 25‑OH vitamin D
- Thyroid/Adrenal: TSH, free T4/T3, cortisol (AM/PM or CAR)
- Physiological signals
- BP, resting HR, HRV
- Body comp: visceral fat, lean mass, bone density
- Fitness: VO2max, lactate threshold
- Glycemic dynamics: CGM metrics (time in range, GMI, GV)
- Imaging and functional
- Coronary calcium score, carotid IMT
- Liver ultrasound/MRI-PDFF (steatosis)
- Spirometry (FEV1), endothelial function (FMD)
- Microbiome and immune
- Gut microbiome diversity, keystone species, SCFA levels
- Zonulin (permeability proxy), fecal calprotectin
- Autoantibodies where indicated
- Exposome and lifestyle
- Sleep architecture, circadian regularity
- Activity patterns, NEAT, resistance/zone 2 minutes
- Environmental: heavy metals, VOCs, mold markers
- Psychosocial stress indices
How Biomarkers Connect: From Signals to Systems
Single biomarkers mislead. Patterns tell truth. Look for correlated clusters:
Inflammatory cluster
- hs‑CRP + ferritin (high) + low HRV + elevated IL‑6
- Often ties to visceral fat, microbiome endotoxemia, sleep loss
Metabolic cluster
- Fasting insulin ↑, HOMA‑IR ↑, TG/HDL ↑, ApoB ↑, CGM variability ↑
- Root: excess energy intake, low muscle mass, circadian mismatch
Mitochondrial/energy cluster
- VO2max ↓, lactate threshold low, acylcarnitines ↑, ceramides ↑
- Root: nutrient overload + inactivity + oxidative stress
Endocrine–immune crosstalk
- Suboptimal free T3, altered cortisol curve, low D + frequent infections
- Root: chronic stress, sleep dysregulation, micronutrient gaps
Gut–liver axis
- GGT ↑, ALT/AST drift, calprotectin ↑, zonulin ↑
- Root: dysbiosis, alcohol, high fructose, mycotoxins
When 3–5 markers from one cluster move together, suspect a shared driver rather than many separate diseases.
Quick Case Snapshots
The “mystery fatigue” case
- Findings: VO2max low, ferritin borderline low, vitamin D low, HRV low, cortisol flat
- Root pattern: mitochondrial stress + micronutrient deficiency + HPA disruption
- Levers: resistance + zone 2, iron repletion if indicated, D optimization, sleep and light anchoring
The “normal LDL” cardiovascular risk
- Findings: LDL‑C normal, but ApoB and LDL‑P high, TG/HDL ratio elevated, CGM variability high
- Root pattern: insulin resistance driving atherogenic particles
- Levers: energy balance, fiber and protein forward, resistance training, consider pharmacology
The “IBS” that wouldn’t quit
- Findings: calprotectin mildly ↑, zonulin ↑, CRP borderline, sleep fragmented, mold exposure
- Root pattern: gut barrier dysfunction + environmental load
- Levers: remove exposure, targeted antimicrobials or diet, circadian repair, reintroduce fibers slowly
Measurement Cadence and Minimal Viable Panel
Baseline: comprehensive labs across metabolic, inflammatory, thyroid, liver, lipids, nutrients + fitness test + body comp + CGM 14 days
Recheck: 8–12 weeks after intervention for dynamic markers (insulin, ApoB, hs‑CRP, ALT, CGM)
Maintenance: every 6 months, or quarterly if actively changing therapy
Continuous: sleep, HRV, activity from wearables to spot pattern drift early
Minimal stack to catch most roots:
- Fasting insulin, HOMA‑IR or OGTT with insulin
- ApoB, TG/HDL, Lp(a once)
- hs‑CRP
- ALT, GGT
- 25‑OH vitamin D, ferritin, B12
- TSH, free T4, free T3
- VO2max estimate, HRV baseline
- 10–14 days of CGM
Examples of High-Yield Levers
- Metabolic root: protein-forward diet, fiber ≥30 g/day, zone 2 + resistance, earlier eating window
- Inflammatory root: dental care, sleep 7.5–8.5 hours, omega‑3 index optimization, remove ultra-processed foods
- Mitochondrial root: progressive conditioning, creatine, heat/cold dosing if appropriate
- Gut root: elimination and structured reintroduction, targeted prebiotic fibers, reduce alcohol
Bottom Line
Complex disease pictures usually reflect a few connected roots. Categorize biomarkers, look for clusters, pick upstream levers, and track the same markers over time. That is how longevity and healthspan move from guesswork to engineering.
Grow Young with Us!
Love, Marie
