Bacteria, Bones, and Stones: Managing Complications of Short Bowel Syndrome

Nutr Clin Pract. 2018 Aug;33(4):454-466. doi: 10.1002/ncp.10113. Epub 2018 Jun 21.


Short bowel syndrome (SBS) occurs in patients who have had extensive resection. The primary physiologic consequence is malabsorption, resulting in fluid and electrolyte abnormalities and malnutrition. Nutrient digestion, absorption, and assimilation may also be diminished by disturbances in the production of bile acids and digestive enzymes. Small bowel dilation, dysmotility, loss of ileocecal valve, and anatomical changes combined with acid suppression and antimotility drugs increase the risk of small intestinal bacterial overgrowth, further contributing to malabsorption. Metabolic changes that occur in SBS due to loss of colonic regulation of gastric and small bowel function can also lead to depletion of calcium, magnesium, and vitamin D, resulting in demineralization of bone and the eventual development of bone disease. Persistent inflammation, steroid use, parenteral nutrition, chronic metabolic acidosis, and renal insufficiency may exacerbate the problem and contribute to the development of osteoporosis. Multiple factors increase the risk of nephrolithiasis in SBS. In the setting of fat malabsorption, increased free fatty acids are available to bind to calcium, resulting in an increased concentration of unbound oxalate, which is readily absorbed across the colonic mucosa where it travels to the kidney. In addition, there is an increase in colonic permeability to oxalate stemming from the effects of unabsorbed bile salts. The risk of nephrolithiasis is compounded by volume depletion, metabolic acidosis, and hypomagnesemia, resulting in a decrease in renal perfusion, urine output, pH, and citrate excretion. This review examines the causes and treatments of small intestinal bacterial overgrowth, bone demineralization, and nephrolithiasis in SBS.

Keywords: metabolic bone disease; nephrolithiasis; short bowel syndrome; small intestinal bacterial overgrowth.

Publication types

  • Review

MeSH terms

  • Bacteria / growth & development*
  • Bone Density
  • Bone and Bones / metabolism*
  • Calcium / metabolism*
  • Colon / metabolism
  • Humans
  • Intestinal Mucosa / metabolism
  • Intestinal Mucosa / microbiology
  • Intestine, Small* / metabolism
  • Intestine, Small* / microbiology
  • Kidney / metabolism
  • Kidney / pathology
  • Kidney Calculi / etiology*
  • Kidney Calculi / metabolism
  • Osteoporosis / etiology
  • Oxalates / metabolism
  • Short Bowel Syndrome / complications*


  • Oxalates
  • Calcium