In a 2015 study conducted by Dr. Frederic Bushman and colleagues at the University of Pennsylvania and published in ‘Nature’, the researchers were able to establish that changes in diet and application of antibiotics and/or anti-inflammatories had distinct effects on the gut microbiome in children with Crohns disease.

These are the typical interventions used as the standards of care for the treatment of Crohn’s disease (CD), a subtype of inflammatory bowel disease. One major characteristic of Crohns Disease is an imbalance in the normal composition of the microbiota in comparison to healthy controls.

They looked to systematically separate the effects of these interventions on the gut microbiomes of a cohort of pediatric CD patients.

Each intervention independently affected the microbiome in Crohns patients.

  • In particular, antibiotic use seemed to worsen dysbiosis by reducing the abundances of some microbes, increasing the abundances of fungi or both, and so aggravated the condition.
  • Anti-inflammatories, on the other hand, reduced gut microbiota dysbiosis, thereby potentially supporting recovery from Crohns.
  • Certain defined diets resulted in rapid changes in the gut microbiome suggesting diet may also be an effective treatment for Crohn’s Disease.

Since Crohn’s patients often have higher rates of gut epithelial cell shedding and/or blood in their stool, stool samples can be sequenced to use as an early indicator of this disease, even before occult blood can be detected.

This study suggests that analysis of the microbiome may lead to useful biomarkers for determining the efficacy of standard treatment for Crohns Disease and for providing additional tests for early detection.


Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease. Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD. Nature. 14 October 2015. 18(4): 489-500.