Microbiota and Metabolite Profiles in the Feces of Juvenile Sika Deer (Cervus nippon) from Birth to Weaning

Abstract

The gut microbiota establishment in young ruminants has a profound impact on their adult production performance. However, the critical phase for the succession of the gut microbial composition and metabolic profiles of juvenile sika deer still needs to be further investigated. Here, we analyzed the fecal microbiota and metabolites of juvenile sika deer during the birth (D1), transition (D42), and rumination (D70) periods based on 16S rRNA sequencing and gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). The results showed that the fecal bacteria and metabolites composition were significantly different in D1 compared to D42 and D70, and the number of OTUs and the Shannon index were significantly higher in D70 than in D1 (p < 0.05). The relative abundances of Lactobacillus, Lactococcus, and Lachnoclostridium showed a significant increase in D1 compared to D42 and D70, whereas the relative abundances of Ruminococcaceae UCG-005, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Christensenellaceae R-7, and Eubacterium coprostanoligenes group were significantly decreased in D1 compared to D42 and D70 (p < 0.05). The amounts of serine, phenylalanine, aspartic acid, ornithine, citrulline, creatine, isoleucine, galactose, and ribose in the feces were significantly higher in D1 compared to D42 and D70. In contrast, the concentrations of cortexolone, resveratrol, piceatannol, fumaric acid, alpha-ketoglutarate, glycerol, uracil-5-carboxylic acid, and maleic acid were significantly decreased in D1. The enrichment analysis showed that amino acid metabolism and carbohydrate metabolism were significantly changed in D1 compared to D42 and D70. The glycine, serine and threonine metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; glyoxylate and dicarboxylate metabolism; citrate cycle; and pyruvate metabolism were significantly enriched across the three periods (p < 0.05). In conclusion, our results suggested that the birth-transition period is a critical phase for the gut bacterial community and metabolic function shift in juvenile sika deer.

Keywords: Lactobacillus; amino acid metabolism; gut development; juvenile sika deer.

Figure 1

Bacterial community composition in the feces of juvenile sika deer in the three age groups. Bacterial profiles at the phylum level (a), family level (b), and genus level (c). D1 = day 1, D42 = day 42, D70 = day 70.

Figure 2

Comparison of the diversity of the fecal microbiota in the juvenile sika deer among the three age groups. (a) Alpha diversity indices in the feces of juvenile sika deer among D1, D42, and D70. * p < 0.05, ** p < 0.01. (b) The PCoA shows the separation of the fecal bacterial community among the three age groups at the OTU level based on the unweighted UniFrac distance and weighted UniFrac distance.

Figure 3

Comparison of the significantly different bacterial genera and functions in the feces of juvenile sika deer among the different age groups. (a) The bar plot shows the significantly different bacterial genera in the feces of juvenile sika deer among the different age groups using the LEfSe based on the KW test (LDA > 4, p < 0.05). * p < 0.05, ** p < 0.01. (b) The PCoA shows the difference in the bacterial functional profiles at KEGG level 3 (relative abundances) based on the Bray–Curits dissimilarity. (c) Heatmap showing the significantly changed pathways at KEGG level 3 among the different age groups (LDA > 2, p < 0.05).

Figure 4

Fecal metabolic profiles of sika deer from birth to weaning. (a) PCA of the fecal metabolites of sika deer. (b) Heatmap showing the significantly different metabolites among the different age groups. Metabolic pathway enrichment analysis based on significantly different metabolites (c) and shared metabolites (d) among the three age groups (p < 0.05).

Figure 5

Associations of the significantly different fecal genera and metabolites in juvenile sika deer with different age groups. (a) MCIA of fecal bacterial functions among the different age groups. (b) Differences in the co-occurrence association networks of juvenile sika deer among the different age groups. The association network was visualized in Cytoscape using the radial layout algorithm. The circles and rectangles represent microorganisms and metabolites, respectively. The colors in the notes indicate the bacterial genera or metabolites with the highest relative abundances or concentrations in D1, D42, and D70, respectively. The blue and red edge lines represent the negative and positive correlations, respectively.