Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics

Abstract

Gut microbiota plays an important role in host health and nutrient digestion of animals. Probiotics have become one of effective alternatives to antibiotics enhancing animal health and performance through modulating gut microbiota. Previously, our research demonstrated that dietary Enterococcus Faecalis UC-100 substituting antibiotics enhanced growth and health of weaned pigs. To investigate the alterations of microbiota in the distal gut of pigs fed E. faecalis UC-100 substituting antibiotics, this study assessed fecal microbiota in pigs from different dietary treatments: the basal diet group, the E. faecalis group, and the antibiotic group on d 0, 14, and 28 of feeding through 16 S rRNA sequencing. Twenty-one phyla and 137 genera were shared by all pigs, whereas 12 genera were uniquely identified in the E. faecalis group on d 14 and 28. Bacterial abundance and diversity in the E. faecalis group, bacterial diversity in the antibiotic group, especially abundances of Fibrobacteres phylum and 12 genera in the E. faecalis group and antibiotics group were lower than that in the basal diet group on d 28. These results showed that microbial shifts in the porcine gut in response to diets containing E. faecalis were similar to the response to which containing antibiotics.

Figure 1. Comparison of the Ace index and OTUs in the nine groups.

The number of observed OTUs sharing ≥ 97% nucleotide sequence identity. Bacterial abundance was reflected with Ace index and bacterial diversity was reflected with OTUs number. (A) Ace index was compared among the basal diet group, the Enterococcus faecalis group and the antibiotic group at 3 different phases (d 0, 14, and 28 of feeding), respectively. (B) Ace index was compared among 3 different phases in the basal diet group, the Enterococcus faecalis group and the antibiotic group, respectively. (C) OTUs number was compared among the basal diet group, the Enterococcus faecalis group and the antibiotic group at 3 different phases, respectively. (D) OTUs number was compared among 3 different phases in the basal diet group, the Enterococcus faecalis group and the antibiotic group, respectively. (*p < 0.05, **p < 0.01).

Figure 2

PCoA of the weighted UniFrac distances for three groups on d 14 (A,B and C) and d 28(D,E and F) of feeding. The percent variation explained by each principal coordinate (A,B,C,D,E and F) is indicated on the axes.

Figure 3. The bacterial abundances of Fibrobacteres significantly differ among different groups.

(A) The abundances of Fibrobacteres was compared among 3 different treatments on d 0, 14, and 28 of feeding, respectively. (B) The abundances of Fibrobacteres was compared among 3 different phases of experiment in the basal diet group, the Enterococcus faecalis group and the antibiotic group, respectively.