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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.

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