Genetic determinism of rabbits’ cecal microbiota

Rabbit cecum harbors a complex microbial ecosystem whose members constantly interact between them and with their host to ensure homeostatic balance maintenance. Our objective was to estimate heritability of rabbit cecal microbiota in order to assess whether interactions with the host also occur at genetic level. 16S rDNA amplicon MiSeq sequencing was conducted on cecal samples collected from 425 kits. These rabbits were bred in two experimental farms and fed with the same diet, supplemented or free of antibiotics, but under different intake levels (ad libitum/restricted). Bioinformatics analysis of the paired-end sequences was performed with R package “dada2”. Taxonomic assignment of the sequence variants inferred was based on Greengenes database gg_13_5_otus. We used Bayes Factor and Deviance Information Criterion to test the existence of host’s genetic determinism on phyla Euryarchaeota, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, Tenericutes and Verrucomicrobia normalized relative abundances and on four microbial alpha-diversity indexes computed at 5,000 contigs. The joint consideration of both model choice criteria evidenced the existence of a certain host genetic determinism on all indexes and phyla abundances; except on Bacteroidetes. Nevertheless, heritability estimates were low for phyla composition, e.g., Tenericutes and Verrucomicrobia 0.08 (0.07), Firmicutes 0.09 (0.08) and Euryarchaeota 0.13 (0.08). Microbial richness indexes showed higher heritability (observed OTUs 0.17 (0.13) and Chao1 0.18 (0.13)) than diversity indexes (Shannon 0.11 (0.09) and inverse Simpson 0.11 (0.08)).  Large estimation errors disclose a large number of animals is needed to accurately estimate heritabilities of the studied traits, which nonetheless seem to be low.