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Background Metabolomics studies hold promise for the discovery of pathways linked to disease processes.In clinical practice, many cases often cause disruption of the gut microflora.The aim of this work was to evaluate the effects of microflora variations on the body s metabolic profiles.Methods Sprague-Dawley rats received either saline, probiotics, Escherichia coli, Salmonella enteritidis, Gentamicin or MgS02 via daily gavage for 7 days, GC/MS analysis the serum metabolic profiles and intestinal bacteria was studied.Results Probiotics can markedly reduce the content of Alanine , and in the nonpathogenic E.coli group, it significantly increase in alanine;orally administered S.enteritidis caused many of these amino acids (alanine, leucine , isoleucine, serine)significantly reduce;an overall reduction in gut microflora due to orally administered Gentamicin resulted in a meaningful reduction in proline and butyric acid.Conclusion(s) The changed gut microflora have diverse effects on the serum metabolic profiles , especially on the Ammonia.