Fig 1.
Graphical schematic of the experimental methodologies.
Experimental design. Controls contained 1) Feed but no cecal content (“Feed only control”); 2) Cecal content but no feed (“Cecal only control”); 3) no prebiotic but cecal content and feed (“Feed + cecal control”). Experimental units contained feed, cecal content, and different prebiotics as indicated in the Materials and Methods section. Figure created with Biorender.com.
Fig 2.
S. Enteritidis enumeration at 0h, 24h, and 48h.
Survival of Salmonella Enteritidis strain SE 13A in in vitro mixed anaerobic cultures with and without prebiotics. The treatments included a commercial-type, wheat-based laying hen ration fed to the roosters housed at the Poultry Research Centre, rooster cecal contents only, feed and cecal contents only, the control diet with Citristim at 1.0 kg/tonne, the control diet with Immunowall at 0.5 kg/tonne, the control diet with Maxi-Gen at 1.0 kg/tonne, the control diet with Hilyses at 2.5 kg/tonne, and the control diet with XPC at 2.5 kg/tonne. Data points and brackets represent three biological replicates’ mean and standard error. At 48 hours, Hilyses and Immunowall had one and two ceca, respectively, with no detectable Salmonella by direct plating and TT enrichment but were recorded as “1 CFU/ml” because zero could not be graphed on a logarithmic scale. In some cases, lower error bars appear longer than upper error bars due to plotting on a log scale. Asterisks are included that show significance between the treatments and the feed and cecal contents only control.
Fig 3.
Alpha diversity of the in vitro cecal cultures.
A comparison of alpha diversity between treatment groups. Shannon’s entropy (a), observed features (b), Faith’s phylogenetic diversity (c), and Pielou’s evenness (d) shown using ANCOM analysis with significance at (P < 0.05). Treatments include feed alone; cecal contents alone; feed and cecal contents without treatment, and feed and cecal contents with various treatments: Citristim, Immunowall, Maxigen, Hilyses, and XPC. There was no alpha diversity significance between the feed and cecal contents treatment and any of the treatments.
Fig 4.
The main effect of beta diversity on Jaccard distance, Bray-Curtis dissimilarity, unweighted unifrac, and weighted unifrac.
A comparison of beta diversity metrics using ANOSIM between treatment groups. Jaccard (a), Bray-Curtis (b), unweighted unifrac (c), and weighted unifrac (d) were all measured, and significance was determined at (P < 0.05). Different colors were used to represent the treatment groups: red represents feed, orange represents ceca, yellow represents feed+ceca, green represents with feed+ceca+Citristim, teal represents feed+ceca+ Hilyses, light blue represents feed+ceca+Immunowall, dark blue represents with feed+ceca+Maxigen, purple corresponds with feed+ceca+XPC, and gray represents the negative control. There was no beta diversity signficance.
Fig 5.
Taxonomic relative abundance of the genera of the treatment groups.
The ANCOM analysis on the genera level representing the median relative abundance within the different treatment groups. Treatments include feed only, cecal contents only, feed and cecal contents only, and several treatments with feed and cecal contents: Citristim, Immunowall, Maxigen, Hilyses, and XPC.
Fig 6.
Comparison of shared core microbiome members.
Venn diagrams demonstrating the core microbiome commonalities between treatment groups and controls: a) Citristim compared to the controls, b) Immunowall, c) Maxigen, d) Hilyses, e) XPC, and f) the four prebiotic treatments, Citristim, Immunowall, Maxigen, and Hilyses. Parameters were set at a detection rate of 1% with prevalence in at least 50% of all samples in a treatment.
Table 1.
Core microbiome of both control and treated ceca present in 50% of samples in a treatment as shown as amplicon sequence variants (ASVs)1.
Fig 7.
Distribution of the core microbiome members within the treatments.
Distribution of the core microbiome within the five treatment groups, positive controls, and negative control for both the (a) phyla and (b) genera. Treatments include cecal contents alone, feed with no ceca or treatments, and cecal contents with feed and each respective treatment: Citristim, Hilyses, Immunowall, Maxigen, and XPC. Each treatment is represented by three samples.