Diversity and Co-Occurrence Pattern Analysis of Cecal and Jejunal Microbiota in Two Rabbit Breeds

Abstract

This study aimed to evaluate the productive performance and microbiota variation in the jejunum and cecum of two rabbit breeds with different growth rates. This study was carried out on Native Middle-Egypt Breed (NMER) and Giant Flanders (GF) rabbits from 5 weeks to 12 weeks of age. Twenty NMER (NM) and GF male rabbits were slaughtered, and the jejunum and cecum tracts were collected to assay gut microbiota composition via 16S ribosomal RNA (rRNA) gene sequencing and histology examination. At 12 weeks of age, daily weight gain, villus height in the jejunum, total protein, and albumin were higher in GF rabbits than in NMER rabbits. Also, the jejunal villi of GF were well arranged in their dense borders. The microbiota between the jejunum and cecum was significantly different in terms of Beta-diversity. A significant correlation between Enterococcus (jejunum NM samples) and Lactobacillus (cecum GF samples) with body weight and weight gain was found (p < 0.05). Moreover, Escherichia-Shigella in the cecum of NM was significantly correlated with weight gain (p < 0.05). The most abundant genera identified in the jejunal and cecal contents of GF were generally beneficial microbiota. They may also play a role in reducing the pathogenic effects of Escherichia coli in these rabbits.

Keywords: 16S rRNA gene sequencing; Giant Flander breed; NMER breed; breeds; cecum; growth; jejunum; microbiota; rabbits.

Figure 1

Blood biochemical parameters in GF and NM rabbits. Means and standard deviations (SD), and the differences were considered significant at p < 0.05.

Figure 2

Comparing the histological morphometric parameters between GF and NM rabbits in the cecum and jejunum. Means and standard deviations (SD), and the differences were considered significant at p < 0.05.

Figure 3

SEM photographs of villi of the cecum and jejunum in NM and GF breeds. (A,C) photographs showed the villi in the cecum of NM. (B,D) photographs showed the villi on the cecum of the GF breed. (E,F) photographs of the villi on the jejunum of the NM and GF breeds, respectively. Scale bars: (A,B) 50 µm; (C,D) 100 µm; (E,F) 500 µm.

Figure 4

Boxplots of alpha-diversity estimations (PD whole tree metric) for rabbit breeds and organs separated. Each point represents a sample, whereas the median value is in the red line.

Figure 5

Principal Coordinate Analysis (PCoA) plots derived from unweighted UniFrac distances comparing the two breeds and organs separately. In the plots, each point represents a sample, colored according to the experimental group. Ellipses represent the 95% SEM-based confidence, and the p-values reported are those deriving from the “adonis” test on the distance matrices. The second and third principal coordinates are plotted.

Figure 6

The Co-Occurrence patterns among the bacterial genera in the cecum and jejunum in NM and GF breeds, separately. Patterns here depict the significant (p < 0.05) correlations among the bacterial genera for the four experimental classes. Node size is proportional to the average abundance of the genera in the experimental condition, and the fill color follows the taxonomic classification of the genera. The edges size is proportional to the strength of correlation, whereas the edges color is blue for negative correlations and red for positive correlations.

Figure 7

Heatmap of the Spearman’s correlation between the top twenty most abundant genera, the body weight, and the weight gain in the experimental classes. Blue is for negative correlations, red for positive correlations, and “★” indicates significant (p < 0.05) correlations.

Figure 8

The functional prediction of gut microbiome in rabbit breeds NM and GF, separated by 0.008 organs (cecum and jejunum). (A) Signaling and cellular processes; (B) Genetic information processing; (C) Cellular processes; (D) Metabolism.