Enterotypes, network and functional profiling of rabbits’ cecal microbiota

Complex but little studied interactions between members of rabbits’ cecal microbial communities take place. Aiming to unravel these interactions, we performed a first network study combined with an enterotype-like clustering analysis in rabbit. Microbiota of cecal samples collected from 357 rabbits fed with the same diet supplemented with antibiotics under different intake levels: ad libitum or restricted, was assessed by means of Illumina sequencing of 16S rRNA gene amplicons. After quality control and chimeras removing, 963 OTUs were detected using QIIME software. Three enterotype-like clusters (R1, R2 and R3) were identified. The cluster classification resulted significantly associated with average daily gain (ADG) showing the animals belonging to R3 the lowest ADG. This R3 had a higher relative abundance of genera Adlercreutzia, Akkermansia, Bacteroides, Coprobacillus and Desulfovibrio compared to R1 and R2, but a lower one of genera Butyrivibrio, Coprococcus, Dorea and Faecalibacterium. A network was inferred at genus level and, in agreement with the enterotypes genera composition, a strong co-abundance patterns was observed between Akkermansia, Bacteroides and Coprobacillus (R3) as well as a strong co-exclusion between them and Dorea and Coprococcus. Prediction of rabbits’ cecal functional microbiota was done by using PICRUSt at KEGG Orthologs (KO), Clusters of Orthologous Groups (COG) and Carbohydrate-active enzymes (CAZy) levels.  Diversity analysis at OTU and CAZy levels revealed that R3 had significantly lower alpha-diversity and richness than R1 and R2. Intriguingly, opposite patterns were observed at KO and COG functional levels showing R3 the highest alpha-diversity and richness.  Pathways related to the activation of immune system (retinol and riboflavin metabolism and lipopolysaccharide, sphingolipid and bile acid biosynthesis) as well as pathways associated with gut dysbiosis (ascorbate and aldarate, sulfur and galactose metabolism) resulted overrepresented among R3 what may explain the low ADG of these animals as a possible consequence of a subclinical digestive disorder.