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Background: Intestinal epithelial integrity is influenced by short-chain fatty acids (SCFAs) and is of critical importance for children with intestinal failure (IF) given the known devastating infectious and gastrointestinal complications. The composition of the microbiome in IF represents an important variable in the physiology and prognosis of this disease.Aim: We sought to compare the intestinal microbiome and SCFA concentration of children who require parenteral nutrition (PN) with that of children with short-bowel syndrome (SBS) who have discontinued PN and with age-matched controls, using high-throughput sequencing to investigate host-microbe interactions.Methods: Fifty-three samples were submitted over 6-15 months. Six children with SBS + IF submitted 34 samples, and 6 children with SBS with discontinued PN submitted 15 samples; these were compared with samples from 5 control children. Fecal samples were analyzed by 16S ribosomal RNA partial gene sequencing using the MiSeq Illumina sequencer. SCFAs were measured in stool samples by mass spectrometry.Results: Butyrate quantity was near absent in children with IF compared with that in controls (median 0.37 nmol/mg vs 10.92 nmol/mg; P < .0001). Similarly, commensal anaerobes known to produce SCFA, including Ruminococcaceae and Lachnospiraceae, were reduced in those with SBS. SBS + IF enteric samples demonstrated a 168-fold increase in the relative abundance of the Escherichia genus seemingly attributable to the species Escherichia coli.Conclusion: The reduced relative abundance of butyrate-producing Clostridia as well as decreased intestinal butyrate concentration in children with IF support further investigation in therapeutic options that target butyrate-producing bacterial communities or butyrate supplementation. [ABSTRACT FROM AUTHOR]