Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery from Salmonella enterica subsp. Serovar Typhimurium Infection in Neonatal Chickens.

Enrofloxacin is an important antibiotic used for prevention and treatment of infection in poultry in many countries. However, oral administration of enrofloxacin may lead to the alterations in the microbiota and metabolome in the chicken intestine, thereby reducing colonization resistance to the infection. To study the effect of enrofloxacin on in the chicken cecum, we used different concentrations of enrofloxacin to feed 1-day-old chickens, followed by oral challenge with subsp. serovar Typhimurium ( Typhimurium). We then explored the distribution pattern of Typhimurium in cecum contents and analyzed the microbial community structure of cecum contents using microbial 16S amplicon sequencing. Untargeted metabolomics was used to explore the gut metabolome on day 14. and , which are closely related to the chicken intestinal metabolome, were screened using a multi-omics technique. The abundance of Typhimurium was significantly higher in the enrofloxacin-treated group than in the untreated group, and Typhimurium persisted longer. Moreover, the cecal colony structures of the three groups exhibited different characteristics, with reaching its highest abundance on day 21. Notably, Typhimurium infection is known to affect the fecal metabolome of chickens differently. Thus, our results suggested that enrofloxacin and infections completely altered the intestinal microbiota and metabolism of chickens. In this study, we examined the effects of Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent Typhimurium infection.