Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves

Abstract

This study investigated the effect of supplementing the diet of calves with two direct fed microbials (DFMs) (Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) and Lactobacillus acidophilus BT1386 (LA)), and an antibiotic growth promoter (ATB). Thirty-two dairy calves were fed a control diet (CTL) supplemented with SCB or LA or ATB for 96 days. On day 33 (pre-weaning, n = 16) and day 96 (post-weaning, n = 16), digesta from the rumen, ileum, and colon, and mucosa from the ileum and colon were collected. The bacterial diversity and composition of the gastrointestinal tract (GIT) of pre- and post-weaned calves were characterized by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The DFMs had significant impact on bacteria community structure with most changes associated with treatment occurring in the pre-weaning period and mostly in the ileum but less impact on bacteria diversity. Both SCB and LA significantly reduced the potential pathogenic bacteria genera, Streptococcus and Tyzzerella_4 (FDR ≤ 8.49E-06) and increased the beneficial bacteria, Fibrobacter (FDR ≤ 5.55E-04) compared to control. Other potential beneficial bacteria, including Rumminococcaceae UCG 005, Roseburia and Olsenella, were only increased (FDR ≤ 1.30E-02) by SCB treatment compared to control. Furthermore, the pathogenic bacterium, Peptoclostridium, was reduced (FDR = 1.58E-02) by SCB only while LA reduced (FDR = 1.74E-05) Ruminococcus_2. Functional prediction analysis suggested that both DFMs impacted (p < 0.05) pathways such as cell cycle, bile secretion, proteasome, cAMP signaling pathway, thyroid hormone synthesis pathway and dopaminergic synapse pathway. Compared to the DFMs, ATB had similar impact on bacterial diversity in all GIT sites but greater impact on the bacterial composition of the ileum. Overall, this study provides an insight on the bacteria genera impacted by DFMs and the potential mechanisms by which DFMs affect the GIT microbiota and may therefore facilitate development of DFMs as alternatives to ATB use in dairy calf management.

Figure 1

Distribution of 159 samples with complete 16S rRNA gene sequences of bacteria phylum and genera.

Figure 2

Principal coordinate analysis (PCoA) plots for treatment effect on each site at pre- and post-weaning periods. (a) Principal coordinate analysis (PCoA) plots for treatment effect on Rumen digesta at pre-weaning and post-weaning. (b) Principal coordinate analysis (PCoA) plots for treatment effect on ileum mucosa at pre-weaning and post-weaning. (c) Principal coordinate analysis (PCoA) plots for treatment effect on ileum digesta at pre-weaning and post-weaning. (d) Principal coordinate analysis (PCoA) plots for treatment effect on colon digesta at pre-weaning and post-weaning. (e) Principal coordinate analysis (PCoA) plots for treatment effect on colon mucosa at pre-weaning and post-weaning. Distances between the samples are based on similarity in OTU composition (OTU similarity 97%). A greater distance implies lower similarity, whereas similar OTUs will cluster together. The clustering pattern of the bacterial communities were tested using PERMANOVA and (P < 0.05) were considered significant.

Figure 3

Stack bar charts of phylum level bacterial composition for the treatment effect on each site at pre- and post-weaning periods. CoM = colon mucosa, CoD = colon digesta, IM = ileum mucosa, IlD = ileum digesta, RuD = rumen digesta.

Figure 4

Stack bar charts of genus level bacterial composition for the treatment effect on each site at pre- and post-weaning periods. CoM = colon mucosa, CoD = colon digesta, IlM = ileum mucosa, IlD = ileum digesta, RuD = rumen digesta.

Figure 5

The common and specific genera in the (a) pre-weaning and (b) post-weaning periods for the different treatments.