Fecal Microbial Changes in Response to Finishing Pigs Directly Fed With Fermented Feed

Abstract

The present study investigated the effects of fermented complete feed (FCF) on fecal microbial composition during the grower-finisher period. A total of 20 pigs (Duroc × Landrace × Yorkshire, 48.74± 1.49 kg) were divided randomly into two groups: the CN group (pigs fed with a basal diet) and the FCF group (pigs fed with FCF). After a 60-day trial period, 3 pigs with middle-weight from each treatment were selected for fecal sampling and fecal microbiota analysis. The results showed that the FCF significantly increased operational taxonomic units (OUT) numbers, alpha diversity (Simpson index and Shannon index), and beta diversity, which means that FCF increased the fecal microbiota diversity. At the phylum level, the abundance of Tenericutes, Spirochaetae, Verrucomicrobia, and Cyanobacteria were changed in pigs fed with FCF; and at the genus level, the abundance of Christensenellaceae_R-7_group, Treponema_2, Ruminococcaceae_UCG-005, Prevotellaceae_UCG-003, Phascolarctobacterium, Roseburia, and Prevotella_9 were changed in pigs fed with FCF. The linear discriminant analysis effect size (LEfSe) analysis showed that Roseburia and Prevotella_9 genera were increased, while Tenericutes phyla and Streptococcus, Christensenellaceae_R-7_group, and Lactobacillus genera were decreased in the FCF group compared to the CN group. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) results predicted that the relative abundance of infectious diseases: parasitic associated genes, xenobiotics biodegradation, and metabolism-associated genes were significantly reduced in the FCF group when compared with the CN group, and the relative abundance of signal transduction associated genes, amino acid metabolism-related genes, and replication and repair associated genes were significantly higher in the FCF group when compared with the CN group. In addition, the relative abundance of transport and catabolism-associated genes, membrane transport-associated genes, and biosynthesis of other secondary metabolite-associated genes tended to be higher in the FCF group when compared with the CN group; and the relative abundance of immune diseases associated genes tended to be lower in the FCF group when compared with the CN group. In conclusion, the FCF influenced the alpha and beta diversity of the fecal microbiota of pigs.

Keywords: fecal microbiome; fermented complete feed; genome prediction; microbial diversity; pigs.

Figure 1

Effects of fermented complete feed on an operational taxonomic unit (OTUs) in fecal samples. Values are expressed as mean ± SEM, n = 3. (A) The number of observed OTUs between CN and FCF groups; (B) Venn diagram of OTUs; Control group; FCF, fermented complete feed group. A p < 0.05 was taken to indicate statistical significance.

Figure 2

The alpha diversity of the fecal microbial community in pigs fed with a basal diet (CN) or fermented complete feed (FCF). Values are expressed as mean ± SEM, n = 3. (A) ACE index; (B) Chao1 index; (C) Simpson index; (D) Shannon index. A p < 0.05 was taken to indicate statistical significance.

Figure 3

The relative abundance of major phylum in response to pigs fed with a basal diet (CN) or fermented complete feed (FCF). Values are expressed as mean ± SEM, n = 3. (A) Relative abundance of bacterial communities at the phylum level; (B) Unpaired t-test analysis of the difference between CN and FCF group. A p < 0.05 was taken to indicate statistical significance.

Figure 4

The beta diversity of the fecal microbial community in pigs fed with a basal diet (CN) or fermented complete feed (FCF) (n = 3). (A) Cluster analysis by principal component analysis (PCA); (B) Cluster analysis by a heatmap, the color gradient from blue to red indicates the distance from near to far between samples.

Figure 5

LEfSe analysis filtered out the biomarkers of the microbial community after pigs received basal diet (CN) or fermented complete feed (FCF) (n = 3). Red bars (negative LDA scores) represent bacteria that are more abundant in CN fecal samples than in FCF. Green bars (positive LDA scores) represent bacteria that are more abundant in FCF fecal samples than in CN fecal samples.

Figure 6

Predictive functional profiling of microbial communities by PICRUSt. Values are expressed as mean ± SEM, n = 3. (A) Human diseases; (B) Cellular processes; (C) Environmental information processing; (D) Metabolism; (E) Organismal systems; (F) Genetic information processing. CN, Control group; FCF, fermented complete feed group. A p < 0.05 was taken to indicate statistical significance.