Background: Rabbit produce two kinds of feces: hard and soft feces, and they have a preference for consuming the latter. Although this habit of rabbits has been reported for many years, little is known on whether this behavior will impact growth performance and metabolism. The RNA-Seq technology is an effective means of analyzing transcript groups to clarify molecular mechanisms. The aim of the present study was to investigate the effects of fasting caecotrophy on growth performance and lipid metabolism in rabbits. Results: Our results indicated that, compared with the control group, the final body weight, weight gain, liver weight, specific growth rate and feed conversion ratio were all decreased in the experimental group (P<0.05). Oil red staining of the liver tissue indicated that fasting caecotrophy resulted in decrease of lipid droplet accumulation. RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads approximately 45.06 Gb of high-quality clean data. The data were mapped to the rabbit genome (http://www.ensembl.org/Oryctolagus_cuniculus). After a five step filtering process, 14964 genes were identified, including 444 differentially expressed genes (P<0.05, foldchange≥1). Especially for remarkable changes of genes related to lipid metabolism, RT-PCR further validated the remarkable decrease of these genes in fasting caecotrophy group, including CYP7A1, PPARG, ABCA1, ABCB1, ABCG1, GPAM, SREBP, etc. KEGG annotation of the differentially expressed genes indicated that the main pathways affected were retinol metabolism, pentose and glucuronide interactions, starch and sucrose metabolism, fatty acid degradation, steroid hormone biosynthesis. Conclusion: In conclusion, the present study revealed that banning caecotrophy reduced growth rate and altered lipid metabolism, our results laid instructive basis for rabbit feeding and production. These data also provides a reference for studying the effects of soft feces on other small herbivores.

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