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Background  Metritis is an inflammatory uterine disease found in ~ 20% of dairy cows after parturition and associated with uterine microbiota with high abundance of  Fusobacterium ,  Bacteroides , and  Porphyromonas . Ceftiofur is a common treatment, but the effect on uterine microbiota is poorly understood. Herein, we investigated the short-term impact of ceftiofur on uterine microbiota structure and function in cows with metritis. Eight cows received ceftiofur (CEF) and 10 remained untreated (CON). Uterine swabs were collected for PCR and metagenomic analysis at diagnosis before treatment (5 ± 1 DPP) and 2 days after diagnosis/treatment (7 ± 1 DPP) from the same individuals. Seven CEF and 9 CON passed quality control and were used for 16S rRNA gene sequencing.    Results  Ceftiofur treatment resulted in uterine microbiota alteration, which was attributed to a decrease in relative abundance of  Fusobacterium  and in gene contents involved in lipopolysaccharide biosynthesis, whereas uterine microbiota diversity and genes involved in pantothenate and coenzyme A biosynthesis increased. Ceftiofur treatment also reduced rectal temperature and tended to reduce total bacteria in the uterus. However, other uterine pathogens such as  Bacteroides  and  Porphyromonas  remained unchanged in CEF. The  bla   CTX-M   gene was detected in 37.5% of metritic cows tested but was not affected by CEF. We found that β-hydroxybutyric acid, pyruvic acid, and L-glutamine were preferentially utilized by  Fusobacterium necrophorum  according to metabolic activity with 95 carbon sources.    Conclusions  Ceftiofur treatment leads to alterations in the uterine microbiota that were mainly characterized by reductions in  Fusobacterium  and genes involved in LPS biosynthesis, which may be associated with a decrease in rectal temperature. The increase in pantothenate and coenzyme A biosynthesis indicates microbial response to metabolic stress caused by ceftiofur. Preference of  Fusobacterium  for β-hydroxybutyric acid may help to explain why this strain becomes dominant in the uterine microbiota of cows with metritis, and it also may provide a means for development of new therapies for the control of metritis in dairy cows.    Supplementary Information  The online version contains supplementary material available at 10.1186/s42523-021-00077-5.

Ceftiofur reduced Fusobacterium leading to uterine microbiota alteration in dairy cows with metritis