Risk Factors for Gut Microbial Dysbiosis in Hospitalized Children. Gut microbial diversity and composition play important roles in health. This cross-sectional study was designed to test the hypothesis that high-risk patients (defined as those with cancer, sickle cell disease (SCD), transplantation, and other diseases associated with immune suppression) would have decreased microbial diversity and different species composition compared to low-risk children admitted to the same pediatric unit.

Background: Gut microbial diversity and composition play important roles in health. This cross-sectional study was designed to test the hypothesis that high-risk patients (defined as those with cancer, sickle cell disease (SCD), transplantation, and other diseases associated with immune suppression) would have decreased microbial diversity and different species composition compared to low-risk children admitted to the same pediatric unit. Methods: A stool sample was obtained within 72 hours of admission to a single unit at The Children’s Hospital at Montefiore, Bronx, NY from March 2016 to February 2017 and the microbiome assessed by 16S rRNA sequencing. Clostridioides (C.) difficile colonization was also detected by glutamate dehydrogenase antigen and toxin polymerase chain reaction assays. Results: Stool samples were obtained from 69 high-risk (32 SCD, 19 cancer, 9 transplantation and 9 other) and 37 low-risk patients. There were no significant differences in microbial alpha diversity comparing high-risk versus low-risk patients. Lower alpha diversity, however, was independently associated with the use of proton pump inhibitors or antibiotics, including prophylactic penicillin in patients with SCD. Differences in specific species abundances were observed comparing high-risk, and in particular, children with SCD, to low-risk patients. Low-risk patients had increased abundance of probiotic commensals including Alistipes putredinis, Alistipes ihumii, Roseburia inulinivorans, Roseburia intestinalis and Ruminococcus albus (p < 0.005). Conclusions: Antibiotics and proton pump inhibitors, which were more commonly used in high-risk patients, were identified as risk factors for lower microbial diversity. Low-risk patients had higher abundance of several probiotic species associated with health. Longitudinal studies are needed to determine the clinical significance of these differences in gut microbiome.