Gastroenterology & Nutrition & Internal Medicine & Family Medicine
Malabsorption
Malabsorption is a clinical and biological syndrome resulting from a deficiency in the intestinal absorption of macronutrients (fats + carbohydrates + proteins) and/or micronutrients (vitamins + minerals + trace elements), leading to progressive nutritional deficiencies and a deterioration of general health. It is distinct from maldigestion—a defect in the luminal digestion of food (exocrine pancreatic insufficiency + achlorhydria + bile salt deficiency)—although the two mechanisms often coexist. Malabsorption can result from damage to the intestinal lining (celiac disease + Crohn's disease + villous atrophy), a reduced absorptive surface area (short bowel syndrome after resection + gastric bypass), maldigestion (exocrine pancreatic insufficiency—EPI—+ bile salt deficiency), infectious causes (Giardia + Whipple's disease + SIBO—small intestinal bacterial overgrowth), lymphatic causes (intestinal lymphangiectasia), or vascular causes (chronic mesenteric ischemia). The classic clinical presentation of severe malabsorption includes fatty diarrhea (steatorrhea—bulky, pale, oily, floating, foul-smelling stools), progressive weight loss, and multiple deficiencies (iron + folate + B12 + fat-soluble vitamins A, D, E, K + calcium + magnesium + zinc). Evaluation involves targeted laboratory tests, functional tests (Sudan III stain + fecal elastase + glucose or lactulose breath test for SIBO), and colonoscopy and upper endoscopy with duodenal biopsies.
Pathophysiology and Classification of Malabsorption Causes
- Pathophysiological mechanisms of normal and deficient intestinal absorption: Normal intestinal absorption: lipids: digestion by pancreatic lipase in the intestinal lumen → micelle formation thanks to bile acids → transcellular absorption into the enterocyte → chylomicron formation → transport via lymphatics (lacteals) → general circulation → carbohydrates: digestion by amylases (salivary + pancreatic) + brush border disaccharidases (lactase + sucrase + maltase) → monosaccharide absorption → proteins: digestion by gastric pepsins + pancreatic proteases (trypsin + chymotrypsin + elastase) → amino acid + small peptide absorption → micronutrients: iron → duodenum + proximal jejunum → B12 → terminal ileum (B12-intrinsic factor complex + cubilin receptor) → folates → jejunum → fat-soluble vitamins A D E K → with lipids → calcium → duodenum (vitamin D-dependent) + jejunum → malabsorption deficit mechanisms: 1/ reduced absorption surface: villous atrophy (celiac disease) + or intestinal resection (short bowel) + 2/ luminal digestion defect: exocrine pancreatic insufficiency (EPI) → insufficient lipase + proteases + bile salt deficiency (cirrhosis + biliary obstruction + ileal bile salt malabsorption = radiation enteropathy + ileal resection) + 3/ bacterial competition in the small intestine: SIBO (small intestinal bacterial overgrowth) → bacteria consume vitamin B12 + deconjugate bile salts → steatorrhea + 4/ lymphatic obstruction: intestinal lymphangiectasia → protein loss (exudative enteropathy) + 5/ enterocyte damage: Whipple's disease (Tropheryma whipplei) + Giardia + HIV + giardiasis
- Etiologic classification and clinical presentation: Mucosal causes: Celiac disease (most common in the West): villous atrophy + anti-tTG IgA + anti-EMA + duodenal biopsies + ileal Crohn's disease → loss of ileal absorption surface + Whipple's disease (rare): Tropheryma whipplei + PAS-positive + duodenal macrophages + migratory arthritis + lymphadenopathy + eosinophilic enteritis → ileum and jejunum affected + giardiasis (Giardia intestinalis) + HIV (HIV enteropathy) + radiation (radiation enteritis) + pancreatobiliary causes: exocrine pancreatic insufficiency (EPI): chronic pancreatitis (alcoholism +++) + cystic fibrosis + pancreatic cancer + pancreatic surgery → insufficient lipase + proteases + amylase → massive steatorrhea + fat-soluble vitamin deficiency → fecal elastase 100 cm) + causes of surface reduction: short bowel syndrome: extensive resection >200 cm + or loss of functional small intestine → long-term parenteral nutrition → gastric bypass (Roux-en-Y) → reduced absorption surface + selective malabsorption: lactase deficiency: hypolactasia + osmotic diarrhea after milk → lactose H₂ breath test + clinical presentation of global malabsorption: fatty diarrhea (steatorrhea) + weight loss + profound asthenia + bloating + deficiencies: mixed anemia (iron + B12 + folate) + hemorrhagic syndrome (vitamin K deficiency) + osteomalacia (vitamin D + calcium deficiency) + neuropathy (B12 + E deficiency) + xerophthalmia (vitamin A deficiency) + tetany (hypocalcemia + hypomagnesemia) + dermatitis (zinc + niacin)
Diagnosis and treatment according to etiology
| Etiology / appearance | Diagnostic Approach and Treatment | References and recommendations |
|---|---|---|
| Diagnostic workup for malabsorption Biological assessment of deficiencies - celiac anti-tTG IgA total IgA - fecal elastase IPE - Sudan III test steatorrhea - glucose breath test SIBO - upper endoscopy duodenal biopsies - fecal calprotectrin - entero-MRI - albumin prealbumin - CBC iron folate B12 - fat-soluble vitamins |
Diagnostic approach to malabsorption: First-line biological workup: Complete blood count (mixed anemia or microcytic +/- macrocytic) + ferritin + serum iron + transferrin saturation + serum folate + B12 + albumin + prealbumin (nutritional status) + calcium + phosphorus + magnesium + PT-INR (vitamin K) + 25-OH vitamin D + zinc + liver function tests Immunological workup: Anti-tTG IgA + total IgA (IgA deficiency can give false positive anti-tTG) + anti-EMA + if IgA deficient -> anti-tTG IgG + anti-DGP (deamidated gliadin peptides) Functional tests: Fecal elastase (single stool sample): <200 mcg/g = moderate to severe pancreatic exocrine insufficiency (PEI) + 7 g/day = pathological steatorrhea 75g glucose H2 breath test: early rise in H2 ( Celiac disease PAS+ macrophages -> Whipple's disease Inflammatory cells -> Crohn's disease Upper gastrointestinal endoscopy (EGDS) + colonoscopy if IBD is suspected Fecal calprotectin: IBD vs IBS Enteric MRI or CT enterography: evaluation of the small intestine (Crohn's disease + lymphangiectasia + tumor) Wireless capsule endoscopy: small intestine not accessible by conventional endoscopy | Rubio-Tapia 2010 — Clinical Gastroenterology and Hepatology: celiac disease + biopsy + reference + Dominguez-Munoz 2011 — Gut: EPI + fecal elastase → reference + Gasbarrini 2009 — Alimentary Pharmacology and Therapeutics: SIBO + breath test + Rome Consensus + Hammer 2005 — Neurogastroenterology and Motility: SIBO + tests + Lindkvist 2013 — Pancreatology: EPI + diagnosis → CCDA (Canadian Celiac Association) + SCGE (Société canadienne de gastroentérologie) + INESSS Québec + RAMQ: anti-tTG + duodenal biopsy + fecal elastase + endoscopies → reimbursed |
| Etiological treatment — celiac, EPI, SIBO and Crohn's Celiac gluten-free diet — Creon IPE pancreatin — SIBO rifaximin — Giardia metronidazole — Crohn's mesalamine — enteral nutrition — parenteral nutrition short bowel — fat-soluble vitamin supplementation — Whipple's disease doxycycline — bismuth — cholestyramine — bile salts UDCA |
Etiological treatment of malabsorption based on the cause: celiac disease: strict lifelong gluten-free diet (GFD) → elimination of wheat + rye + barley + contaminated oats → mucosal healing within 6–24 months + initial supplementation with iron + folate + B12 + vitamin D + calcium → monitoring of healing: anti-tTG + biopsy at 1–2 years + exocrine pancreatic insufficiency (EPI): exogenous pancreatic enzymes (pancreatin + lipase) — CREON (gastroresistant pancreatin): 25,000–75,000 IU of lipase per meal + 10,000–25,000 IU per snack → take during meals → adjust based on clinical response (resolution of steatorrhea) → supplementation with fat-soluble vitamins A + D + E + K → proton pump inhibitors (PPIs): optimize the action of pancreatic enzymes (acidic pH degrades enzymes in the duodenum) → SIBO (Small Intestinal Bacterial Overgrowth): rifaximin 550 mg × 3/day × 14 days: non-absorbable antibiotic → local action in the small intestine → possible relapse → treatment of the underlying cause (motility disorders + adhesions + diverticula) → or metronidazole 400–500 mg × 3/day × 7–10 days if rifaximin is unavailable → Giardia intestinalis: metronidazole 250 mg × 3/day × 5–7 days + or tinidazole 2 g single dose → Whipple’s disease: doxycycline 100 mg × 2/day + hydroxychloroquine × 12 months → ceftriaxone 2 g/day IV × 2 weeks if severe forms → ileal Crohn’s disease: Crohn’s treatment (budesonide + biologics) + IM B12 supplementation (if ileal resection or extensive disease) → exclusive pediatric enteral nutrition + short bowel syndrome: long-term parenteral nutrition if residual small intestine is insufficient + progressive enteral nutrition as tolerated + teduglutide (GLP-2 analog — Revestive) → stimulates growth of the residual mucosa → reduction in parenteral dependence → lactase deficiency: low-lactose diet + tolerated yogurts → exogenous lactase (Lactaid) PO + cholestyramine if bile salt malabsorption (ileal resection <100 cm) | Rubio-Tapia 2013 — Gastroenterology (ACG guidelines): celiac disease + RSG + reference + Dominguez-Munoz 2014 — United European Gastroenterology Journal: IPE + enzymes + treatment + Pimentel 2020 — NEJM: SIBO + rifaximin -> reference + Jain 2019 — Journal of Clinical Gastroenterology: Whipple disease + doxycycline + hydroxychloroquine + Jeppesen 2012 — NEJM: teduglutide + short bowel syndrome -> reduction of parenteral nutrition + SCGE + CCDA + Pancrease Canada + INESSS Québec + RAMQ: CREON + rifaximin + metronidazole + teduglutide + B12 IM + fat-soluble vitamins -> reimbursed according to criteria |
| Correction of nutritional deficiencies and support Iron IV IronInject - B12 IM - folates - fat-soluble vitamins A D E K - calcium - magnesium IV PO - zinc - osteoporosis DXA bisphosphonates - adapted diet - dietitian - enteral nutrition - parenteral nutrition - biological monitoring - B12 neuropathy emergency treatment |
Correction of nutritional deficiencies in malabsorption: Iron: If severe intestinal malabsorption, IV iron (iron carboxymaltose - Ferinject or iron sucrose - Venofer) is preferred. Complete iron studies (ferritin + saturation) before. Oral iron is possible if mild malabsorption: ferrous sulfate tablets 300 mg twice to three times daily, away from meals. B12 (cobalamin): If ileal involvement or ileal resection or celiac disease with severe involvement: cyanocobalamin 1,000 µg IM once weekly for 4 weeks, then once monthly. Intramuscular B12 bypasses deficient ileal absorption. Do not use oral B12 if there is ileal malabsorption. B12 neuropathy: urgent treatment to prevent irreversible damage. Folates: Folic acid 5 mg/day PO for 3-6 months, after excluding B12 deficiency (risk of masking B12 deficiency with neuropathy). Fat-soluble vitamins (A + D + E + K): Absorption is impaired if lipids are malabsorbed. Vitamin D3 1,000-4,000 IU/day PO or IM if severe steatorrhea. Vitamin K1 (phytonadione) 5-10 mg/day if prolonged PT. Vitamin A palmitate if night blindness. Vitamin E if neuropathy or ataxia. Calcium: 1,000-1,500 mg/day PO. Magnesium: If malabsorption (short bowel + Crohn's + EIM), magnesium citrate 300-400 mg/day PO, or IV if severe malabsorption. Zinc: Zinc sulfate 220 mg twice daily PO. DXA if chronic malabsorption: Osteoporosis is frequent. Bisphosphonates if T-score ≤ -2.5. Professional dietary follow-up is mandatory. Complete nutritional assessment and adapted meal plan. | Green 2005 — Gastroenterology (ACG): celiac + deficiencies + supplementation → Rubio-Tapia 2013: SG + deficiencies → supplementation + Bernstein 2012 — Journal of Clinical Gastroenterology: Crohn's + nutritional deficiencies + Holick 2011 — NEJM: vitamin D + malabsorption → CEBC + CDDA + Dietitians of Canada + INESSS Quebec + RAMQ: IV iron + IM B12 + vit D + bisphosphonates + magnesium → reimbursed according to indications + enteral nutrition + parenteral nutrition → reimbursed if documented indication |
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Celiac disease is the most common cause of malabsorption in the West. Its diagnosis is based on anti-tTG IgA, total IgA, and duodenal biopsies, and its treatment is a strict lifelong gluten-free diet. Exocrine pancreatic insufficiency is diagnosed by fecal elastase (<200 µg/g) and treated with pancreatic enzymes (CREON) taken during meals. B12 deficiency with neuropathy is a therapeutic emergency—IM B12 bypasses deficient ileal absorption. Always rule out B12 deficiency before supplementing with folate.
Situations requiring urgent care
Known malabsorption + progressive lower limb neuropathy + or ataxia + cognitive disorders + serum B12 <150 pmol/L + or in the gray zone with elevated homocysteine or elevated MMA Severe vitamin B12 deficiency with neuropathy → B12 IM 1,000 µg x 1/day x 7 days → then x 1/week x 4 weeks → then x 1/month → delayed treatment leads to irreversible neurological damage → DO NOT wait for oral regimen.
Patient with severe malabsorption (steatorrhea + weight loss >10% of body weight + albumin <25 g/L) + effusions (ascites + pleural effusion) and/or significant lower extremity edema Severe protein-energy malnutrition with hypoalbuminemia + exudative enteropathy → hospitalization + urgent enteral and/or parenteral nutrition + complete etiological workup + IV albumin if symptomatic severe hypoalbuminemia + nutrition and gastroenterology consultation.
Patient with known short bowel syndrome or post-bariatric surgery + massive watery diarrhea (>3 L/day) + dehydration + severe muscle cramps + very low calcium or magnesium Severe malabsorption + electrolyte imbalances → emergencies → IV hydration + electrolyte correction (calcium + magnesium) + oral rehydration with appropriate oral rehydration solutions + reassessment of parenteral nutrition + teduglutide if eligible.
Consult at Clinique Omicron
Clinique Omicron physicians prescribe a complete malabsorption workup (CBC + iron + B12 + folate + albumin + calcium + vitamin D + anti-tTG + total IgA + fecal elastase + SIBO breath test), refer for upper endoscopy with duodenal biopsies, initiate urgent nutritional corrections (IV iron + IM B12 + fat-soluble vitamins), prescribe pancreatic enzymes (CREON) if EPI, a gluten-free diet if celiac, and rifaximin if SIBO, and ensure multidisciplinary follow-up with a dietitian and gastroenterologist. Consultations are available at several service locations in Quebec and via telemedicine. To book an appointment, visit cliniqueomicron.ca.
The content of this page is for informational purposes only and is not a substitute for the advice of a doctor, gastroenterologist, or dietitian. Malabsorption is often a chronic and multifactorial condition requiring thorough investigation and professional nutritional follow-up. Never supplement with folate without first checking for and correcting a possible vitamin B12 deficiency.
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