Probiotic treatment vs empiric oral antibiotics for managing dysbiosis in short bowel syndrome: Impact on the mucosal and stool microbiota, short-chain fatty acids, and adaptation

JPEN J Parenter Enteral Nutr. 2022 Nov;46(8):1828-1838. doi: 10.1002/jpen.2377. Epub 2022 Apr 30.


Background: Infants and children with short bowel syndrome (SBS) are presumed to be at risk of gut microbial dysbiosis with potential sequelae of bacterial overgrowth that include sepsis, d-lactic acidosis, mucosal inflammation, and malabsorption. In neonatal piglets with SBS, we compared intestinal microbial composition, short-chain fatty acids (SCFAs), and adaptation given probiotic (PRO) treatment (Lactobacillus and Bifidobacterium spp) vs oral metronidazole (MET).

Methods: Following 75% distal small intestinal resection, piglets were allocated to PRO (500 mg twice a day, n = 7), MET (15 mg/kg twice a day, n = 8), and placebo (PLA) (500 mg twice a day, n = 8). After 10 days of parenteral and enteral nutrition, 16S ribosomal RNA gene amplicon sequencing (colon tissue and stool) was undertaken and SCFA analysis (stool and colon effluent) was performed using gas chromatography.

Results: In colon, Shannon diversity was higher for PRO compared with MET and PLA (P = 0.002). PRO and PLA increased abundance of Bacteroidetes species (eg, Bacteroides fragilis) compared with MET (P < 0.001). PRO, compared with PLA, increased abundance of Firmicutes species (eg, Lactobacillus fermentum) (P < 0.001). MET increased abundance of Proteobacteria members, predominately Enterobacteriaceae, compared with PRO (P = 0.004). In stool, microbial findings were similar and SCFA (butyrate) concentrations were highest for PRO (P = 0.003) compared with MET.

Conclusion: In pediatric SBS, the empiric use of oral antibiotics, such as MET, is common for presumed clinical consequences of microbial dysbiosis. In this study of SBS piglets, that approach was associated with decreased microbial diversity and increased abundance of potentially inflammatory Proteobacteria. In contrast, a PRO treatment using Lactobacillus and Bifidobacterium spp increased both diversity and SCFAs.

Keywords: enteral nutrition; life cycle; microbiome; nutrition; parenteral nutrition; pediatrics; probiotics; research and diseases; sepsis; short bowel syndrome; surgery.

MeSH terms

  • Animals
  • Anti-Bacterial Agents / therapeutic use
  • Dysbiosis / complications
  • Dysbiosis / drug therapy
  • Fatty Acids, Volatile
  • Feces / microbiology
  • Gastrointestinal Microbiome* / genetics
  • Lactobacillus
  • Microbiota*
  • Polyesters
  • Probiotics* / therapeutic use
  • Proteobacteria
  • Short Bowel Syndrome* / complications
  • Short Bowel Syndrome* / drug therapy
  • Swine


  • Anti-Bacterial Agents
  • Fatty Acids, Volatile
  • Polyesters