Aim The aim of this study was to gain insight into the microbial diversity of the stool of infants with intestinal failure due to surgical resection from NEC. We also assessed if there was any relationship with bacteria cultured during CLA-BSI and the stool microbiome around the time of the episode leading to the diagnosis of CLA-BSI. Introduction Necrotizing enterocolitis (NEC) is a major predisposing factor for surgical short bowel syndrome (SBS) and intestinal failure in infants. Patients with SBS and intestinal failure are dependent on prolonged parenteral nutrition (PN). The prolonged use of PN and minimal enteral nutrition, although life-saving, are associated with multiple complications including recurrent central line associated blood stream infections (CLA-BSI), small bowel bacterial overgrowth, and increased mortality. CLA-BSI is a significant contributor to the morbidity and mortality of these children. Gut permeability and gut associated bacteria may contribute to CLA-BSI. The aim of this study was to gain insight into the microbial diversity of stool of these infant and assess if there is any relationship with CLA-BSI. Methods A sample size of 10 patients (6 boys and 4 girls were recruited. Diagnosis of NEC with Hx of intestinal resection and dependent on PN for > 90 days Stool samples were collected from these patients at baseline and following a CLA-BSI. A comparison group of 9 age- matched healthy children without any history of intestinal resection were also recruited as controls and they provided a single stool sample. Stools were collected into a sterile container and stored at -80°F until analysis. The institutional review boards of Emory University School of Medicine, Atlanta GA and Cincinnati Children's Hospital Medical Center, Cincinnati, OH approved this protocol Multiplexed Pyrosequencing: DNA was extracted using a chemical and mechanical lysis protocol PCR reactions were performed in duplicate for each specimen Taxonomy-based operational taxonomic units (OTUs) were assembled by grouping sequences Between-group differences in biodiversity, prevalence, and relative abundance of taxonomic OTUs were assessed by non- parametric Kruskal-Wallis tests using the R statistical package. Microbiome data Results Median age of 7 months (range 2-24 months) Residual small bowel length ranged from cm, which represented approximately 20% of expected length of small bowel for age. Broad-range 16S rRNA gene PCR and pyrosequencing was successful in all SBS subjects and controls, with median values of 1052 ( ) and 1251 ( ) pyrosequences generated per subject, respectively (Table 1). The majority of SBS cases (90%) had at least 1 episode of CLA-BSI Organisms cultured in the blood during CLA-BSI were present in the stool of majority of the subjects (Table 2). Klebsiella pneumonia was the most common bacteria cultured (35% of cases). Klebsiella spp. were significantly more abundant in the stools of SBS cases compared with controls (19.7% vs 2.3% relative abundance; p = 0.014) Stool-associated microbiome of infants with surgical short bowel Conrad R. Cole MD, MPH, MSc 1, Charles E. Robertson PhD 2, Daniel N. Frank PhD 2, and Thomas R. Ziegler MD 3 1 Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA, 2 University of Colorado Boulder, Boulder, Colorado 3 Emory University School of Medicine, Atlanta, Georgia, USA Inclusion Criteria Children less than 2 years of age History of SBS due to small bowel resection following the diagnosis of NEC Dependent on PN SBS was defined as dependence on PN for at least 6 weeks with bowel length (measured along the anti- mesenteric border from the ligament of Treitz) of less than 50% of estimated normal small bowel length for age Support by National Institutes of Health grant 1R21DK A1 to Conrad R. Cole 182