Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)

Abstract

Background: The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.

Results: In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.

Conclusions: Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.

Keywords: 16S rRNA; ADG; Dynamic distribution; Gut microbiota; Ira rabbits.

Fig. 1

Differences in diversities and structures of gut microbiota between weaning and finishing samples. a Observed species index (“W” and “F” represents for weaning and finishing samples, respectively; ***** FDR adjusted p < 0.0001). b Shannon index. c Principal Coordinate Analysis (PCoA) of gut microbial community structures based on Unweighted Unifrac distance. d Unweighted Unifrac distance metric

Fig. 2

The dynamic distributions of gut microbiota at different taxonomic levels. a At phylum level. b At genus level. The IDs on the X-axis with the same number but different letters (“W” and “F”) in the two groups represent the same rabbit at weaning and finishing stage, respectively

Fig. 3

Potential functional capacities of gut microbiota showing different enrichment between weaning and finishing samples. a KEGG Orthologs (KOs). b KEGG pathways

Fig. 4

The 34 OTUs showing significant associations with ADG are shown as Z scores. The coral bar represents for positive association, the blue bar corresponds to negative association, and the text on the bar shows the microbial taxa annotated to the OTU

Fig. 5

Heatmap of predicted KEGG Orthologs (a) and pathways (b) significantly associated with ADG (FDR adjusted p < 0.05, |r| > 0.4). The correlation coefficient was used to plot

Fig. 6

The variation of ADG explained by gut microbiome at different levels of significance