Rabbit early life coprophagia effect on the ileum transcriptome

R-scripts used to analyse the data presented in the article
“Coprophagia early in life tunes immune system gene expression in ileum after weaning in rabbit”, Cauquil L., Beaumont M., Schmaltz-Panneau B., Liaubet L., Lippi Y., Bluy L., Poli M., Gress L., Lencina C. , Duranthon V., Combes S.

Background and aims

Coprophagia in suckling rabbits is observed in the first 14 days after birth. This behavior stimulates the maturation of the microbiota and strongly reduces mortality after weaning (Combes et al., 2014; doi: 10.2527/jas.2013-6394). In the current study, we hypothesized that this beneficial effect of coprophagia is immune-mediated at the gut level. We present here the R-script used to analyse the ileal transcriptome using a rabbit 60K microarray platform at day 35 and 49 in rabbits with different coprophagia beahavior in early life.

Experimental design encompassed three groups

• the NF group: ingestion of maternal feces in the nest was prevented (No access to Feces)
• the FF group: pup feces ingestion was enhanced removing the maternal feces from the nest and replacing them with feces from unrelated does (coprophagia)
• the FFab group: pup feces ingestion was enhanced removing the maternal feces from the nest and replacing them with feces from unrelated antibiotic treated does (coprophagia with antibiotic feces).