Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

Abstract

BackgroundNecrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predictive biomarkers to guide prevention are lacking. We analyzed banked stool and urine samples collected prior to disease onset from infants <29 weeks gestational age, including 11 infants who developed NEC and 21 matched controls who survived free of NEC. Stool bacterial communities were profiled by 16S rRNA gene sequencing. Urinary metabolomic profiles were assessed by NMR.ResultsDuring postnatal days 4 to 9, samples from infants who later developed NEC tended towards lower alpha diversity (Chao1 index, P = 0.086) and lacked Propionibacterium (P = 0.009) compared to controls. Furthermore, NEC was preceded by distinct forms of dysbiosis. During days 4 to 9, samples from four NEC cases were dominated by members of the Firmicutes (median relative abundance >99% versus <17% in the remaining NEC and controls, P < 0.001). During postnatal days 10 to 16, samples from the remaining NEC cases were dominated by Proteobacteria, specifically Enterobacteriaceae (median relative abundance >99% versus 38% in the other NEC cases and 84% in controls, P = 0.01). NEC preceded by Firmicutes dysbiosis occurred earlier (onset, days 7 to 21) than NEC preceded by Proteobacteria dysbiosis (onset, days 19 to 39). All NEC cases lacked Propionibacterium and were preceded by either Firmicutes (≥98% relative abundance, days 4 to 9) or Proteobacteria (≥90% relative abundance, days 10 to 16) dysbiosis, while only 25% of controls had this phenotype (predictive value 88%, P = 0.001). Analysis of days 4 to 9 urine samples found no metabolites associated with all NEC cases, but alanine was positively associated with NEC cases that were preceded by Firmicutes dysbiosis (P < 0.001) and histidine was inversely associated with NEC cases preceded by Proteobacteria dysbiosis (P = 0.013). A high urinary alanine:histidine ratio was associated with microbial characteristics (P < 0.001) and provided good prediction of overall NEC (predictive value 78%, P = 0.007).ConclusionsEarly dysbiosis is strongly involved in the pathobiology of NEC. These striking findings require validation in larger studies but indicate that early microbial and metabolomic signatures may provide highly predictive biomarkers of NEC.

Human milk and infant intestinal mucosal glycans guide succession of the neonatal intestinal microbiota

“…This genetic variation in glycosyltransferase genes within the infant manifests as distinct differences in glycosylation of the infant intestinal mucosa. Such dissimilarities are consistent with differences in gut colonization and differential risk of enteric inflammatory disease (36).…”

“…Perhaps individual variation in HMOS directs colonization by specific bacteria, leading to systematic differences in microbiota. If so, this phenomenon could contribute toward the differential risk of disease that has been observed in breastfed infants of genetically distinct mothers (36). This genetic variation in glycosyltransferase genes within the infant manifests as distinct differences in glycosylation of the infant intestinal mucosa.…”

“…Of these, most prevalent are differences in expression products of fucosyltransferase 2. In populations of European, Asian, and African ancestry, 15-25% can be homozygous recessive for expression of the FUT 2 gene; they are nonsecretors, that is, unable to secrete α1,2-linked fucosylated glycans in their secretions, including milk (36). Specific α1,2-fucosylated HMOSs, including 2′-fucosyllactose, inhibit binding by specific pathogens to their host target.…”

“…Altered gut microbiota, with concomitant abnormal communication between bacteria in the gut and the mucosal immune system, seems to underlie inflammatory bowel disease, that is, Crohn's disease or ulcerative colitis (38). A strong risk factor for necrotizing enterocolitis, a severe gut inflammation most common in premature infants, is early dysbiosis (36). Unregulated inflammation and cell turnover can eventually lead to colorectal cancer, the third most common cause of cancer mortality (39).…”

Patterned progression of bacterial populations in the premature infant gut

“…Studies of gut bacteria in preterm infants have been limited in subject and/or sample numbers (24,28,29), have used cross-sectional comparisons (30), or did not stratify extensively by gestational age at birth or age postconception (30)(31)(32)(33)(34)(35)(36). Our intensive and extensive dataset suggests that limited sampling in premature neonates is problematic because of very frequent alterations in population structure.…”