Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis

Giorgio Casaburi; Jingjing Wei; Sufyan Kazi; Junlin Liu; Kewei Wang; Guo-Zhong Tao; Po-Yu Lin; James C Y Dunn; Bethany M Henrick; Steven A Frese; Karl G Sylvester

doi:10.3389/fped.2022.893059

Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis

Front Pediatr. 2022 Aug 23:10:893059. doi: 10.3389/fped.2022.893059. eCollection 2022.

Authors

Giorgio Casaburi¹, Jingjing Wei^{2

3}, Sufyan Kazi¹, Junlin Liu^{2

4}, Kewei Wang^{2

5}, Guo-Zhong Tao², Po-Yu Lin², James C Y Dunn², Bethany M Henrick^{1

6}, Steven A Frese^{1

6

7}, Karl G Sylvester²

Affiliations

¹ Evolve Biosystems, Inc., Davis, CA, United States.
² Department of Surgery, Stanford University, Stanford, CA, United States.
³ Department of Pediatrics, Shanxi Medical University, Taiyuan, China.
⁴ Department of General Surgery, The People's Hospital of Liuyang City, Liuyang, China.
⁵ Department of Gastrointestinal Surgery, The First Hospital of China Medical University, Shenyang, China.
⁶ Department of Food Science and Technology, University of Nebraska, Lincoln, NE, United States.
⁷ Department of Nutrition, University of Nevada Reno, Reno, NV, United States.

Abstract

Necrotizing enterocolitis (NEC) is a leading cause of premature newborn morbidity and mortality. The clinical features of NEC consistently include prematurity, gut dysbiosis and enteral inflammation, yet the pathogenesis remains obscure. Herein we combine metagenomics and targeted metabolomics, with functional in vivo and in vitro assessment, to define a novel molecular mechanism of NEC. One thousand six hundred and forty seven publicly available metagenomics datasets were analyzed (NEC = 245; healthy = 1,402) using artificial intelligence methodologies. Targeted metabolomic profiling was used to quantify the concentration of specified fecal metabolites at NEC onset (n = 8), during recovery (n = 6), and in age matched controls (n = 10). Toxicity assays of discovered metabolites were performed in vivo in mice and in vitro using human intestinal epithelial cells. Metagenomic and targeted metabolomic analyses revealed significant differences in pyruvate fermentation pathways and associated intermediates. Notably, the short chain fatty acid formate was elevated in the stool of NEC patients at disease onset (P = 0.005) dissipated during recovery (P = 0.02) and positively correlated with degree of intestinal injury (r ² = 0.86). In vitro, formate caused enterocyte cytotoxicity in human cells through necroptosis (P < 0.01). In vivo, luminal formate caused significant dose and development dependent NEC-like injury in newborn mice. Enterobacter cloacae and Klebsiella pneumoniae were the most discriminatory taxa related to NEC dysbiosis and increased formate production. Together, these data suggest a novel biochemical mechanism of NEC through the microbial production of formate. Clinical efforts to prevent NEC should focus on reducing the functional consequences of newborn gut dysbiosis associated metabolic pathways.

Keywords: artificial intelligence; dysbiosis; formate; metagenomics; microbiome; necrotizing enterocolitis (NEC); probiotics.