Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo

Abstract

The microbiota of the gastrointestinal tract (GIT) are crucial for host health and production efficiency in ruminants. Its microbial composition can be influenced by several endogenous and exogenous factors. In the beef and dairy industry, the possibility to manipulate gut microbiota by diet and management can have important health and economic implications. The aims of this study were to characterize the different GIT site microbiota in water buffalo and evaluate the influence of diet on GIT microbiota in this animal species. We characterized and compared the microbiota of the rumen, large intestine and feces of water buffaloes fed two different diets with different non-structural carbohydrates/crude proteins (NSC/CP) ratios. Our results indicated that Bacteroidetes, Firmicutes and Proteobacteria were the most abundant phyla in all the GIT sites, with significant differences in microbiota composition between body sites both within and between groups. This result was particularly evident in the large intestine, where beta diversity analysis displayed clear clustering of samples depending on the diet. Moreover, we found a difference in diet digestibility linked to microbiota modification at the GIT level conditioned by NSC/CP levels. Diet strongly influences GIT microbiota and can therefore modulate specific GIT microorganisms able to affect the health status and performance efficiency of adult animals.

Keywords: diet; feces; fiber; food industry by-products; gastrointestinal microbiota; large intestine; rumen; tomato peel; water buffalo.

Figure 1

Taxonomy plots at Phylum level of the rumen, large intestine and feces from traditionally fed buffaloes. Relative abundance (mean relative frequency) of the bacterial Phyla identified in different GIT (rumen, large intestine and feces) from traditionally fed water buffaloes (n = 10). In the taxa list reported on the right of the figure, the letter d_ indicates Domain, p_ indicates Phylum.

Figure 2

Core microbiota at the Genus level of the rumen, large intestine and feces from differentially fed water buffaloes. Genera shared by at least 80% of samples included in each body site: (A) traditionally fed water buffaloes (n = 10); (B) alternatively fed water buffaloes (n = 10).

Figure 3

Alpha diversity analysis among the rumen, large intestine and feces from traditionally fed water buffaloes (n = 10). Differences in alpha diversity metrics among different body sites: (A) Observed ASVs; (B) Pielou evenness index.

Figure 4

Beta diversity box plots within and between body sites from traditionally fed water buffaloes (n = 10). Distances calculated with different matrices: (A) Bray–Curtis, (B) Unweighted UniFrac and (C) Weighted UniFrac. The letter F indicates feces, I indicates large intestine, R indicates rumen.

Figure 4

Beta diversity box plots within and between body sites from traditionally fed water buffaloes (n = 10). Distances calculated with different matrices: (A) Bray–Curtis, (B) Unweighted UniFrac and (C) Weighted UniFrac. The letter F indicates feces, I indicates large intestine, R indicates rumen.

Figure 5

Taxonomy bar plots at Phylum level of the rumen, large intestine and feces from traditionally fed water buffaloes (n = 10). Relative abundance (mean relative frequency) of the bacterial Phyla identified in different GIT sites (rumen, large intestine and feces) from traditionally (n = 10) and alternatively (n = 10) fed water buffaloes.

Figure 6

Beta diversity Principal Coordinates Analysis between traditionally (n = 10) and alternatively fed water buffaloes (n = 10). PCoA analysis based on Weighted UniFrac distance matrices between traditionally and alternatively fed water buffaloes in the rumen (p-value = 0.25) (A), large intestine (p-value = 0.002) (B) and feces (p-value = 0.009) (C).

Figure 7

ANCOM results between traditionally (n = 10) and alternatively (n = 10) fed water buffaloes. Dots represent features identified by ANCOM as differentially abundant between groups. Statistically significant differentially abundant taxa are represented by the dots in the upper corners of the graph.

Figure 7

ANCOM results between traditionally (n = 10) and alternatively (n = 10) fed water buffaloes. Dots represent features identified by ANCOM as differentially abundant between groups. Statistically significant differentially abundant taxa are represented by the dots in the upper corners of the graph.