Background: Cow milk protein allergy (CMPA) is an increasing disease in Neonates and related with allergic diseases in childhood. Emerging evidence has highlighted the involvement of gut microbes and its downstream metabolic pathways in CMPA, but it remains unknown in neonates. Methods: Thirty-one neonates with CMPA were selected as the CMPA group, and 31 neonates matched for demographic and clinical characteristics comprised the control group in a 1:1 ratio. 16S rRNA high-throughput sequencing was used to detect the diversity and composition of the gut microbiome, meanwhile liquid chromatography with tandem mass spectrometry (LC‒MS/MS) non-targeted metabolomics was used to detect its metabolites. Results: There were significant differences in the beta diversity of the gut microbiome at the class and family levels between groups ( p=0.018, 0.03). Clostridium_sensu_stricto_1, Klebsiella, Cutibacterium, Phascolarctobacterium and Bacillus were found with significant disparity between groups. Receiver operating characteristic (ROC) analysis showed the AUC of Clostridium_sensu_stricto_1 was 0.69, which was the highest. Nontargeted metabolomics revealed 214 different metabolites between groups, the enriched pathways mainly included protein digestion and absorption; mineral absorption; tryptophan and galactose metabolism. The ROC analysis indicated that the AUC were both 0.85 for genipic acid and tryptophan. Conclusion: The microbiome Clostridium_sensu_stricto_1 and metabolites genipic acid and tryptophan are related to neonatal CMPA, and combined detection can be used as an early diagnostic marker.
