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Gut mierobiota functions in nutrition, immunity and physiology in the host.Lincomycin (LM) is an antibiotic drug principally used in patients allergic to the penicillins.To understand the dynamic systematic consequence of lincomyein exposure, we analyzed the metabonomic and microbiological response of rats to lincomycin by an integrated approach combining 16S rRNA gene sequencing and 1H NMR-based metabolomics profiling.Lincomycin exposure resulted in decreased levels of hippurate, short chain fatty acids (SCFAs) and primary bile acids and increased levels of choline and oligosaccharides.Levels of Barnesiella and Prevotella decreased sharply, whereas levels of Clostridium leptum and Clostridium cluster XIVa increased slightly.