## 3 Results and Discussion
### Microbial Profiles in the Faeces of Calves  
In total, 39,676 and 41,469 bacterial reads were obtained from the CON and MP groups, respectively, before the experiment began. The bacterial composition was similar in both \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Microorganisms** & **Day** & **CON** & **MP** & \(p\)**Day \(\times\)**Treat. Int.** \\ \hline \multirow{2}{*}{LAB} & Baseline & 5.29 \(\pm\) 1.89 A\({}^{\text{;a}}\) & 6.14 \(\pm\) 1.46 A\({}^{\text{;a}}\) & \multirow{2}{*}{0.004} \\  & 14 & 6.14 \(\pm\) 1.46 A\({}^{\text{;a}}\) & 7.40 \(\pm\) 0.43 B\({}^{\text{;b}}\) & \\ \hline \multirow{2}{*}{TCE} & Baseline & 6.15 \(\pm\) 0.04 A\({}^{\text{;a}}\) & 7.23 \(\pm\) 1.35 B\({}^{\text{;a}}\) & \multirow{2}{*}{0.200} \\  & 14 & 7.71 \(\pm\) 0.55 A\({}^{\text{;b}}\) & 6.91 \(\pm\) 0.64 A\({}^{\text{;a}}\) & \\ \hline \multirow{2}{*}{TCM} & Baseline & 6.89 \(\pm\) 1.54 A\({}^{\text{;a}}\) & 7.55 \(\pm\) 1.25 A\({}^{\text{;a}}\) & \multirow{2}{*}{0.076} \\  & 14 & 8.26 \(\pm\) 0.93 B\({}^{\text{;a}}\) & 7.71 \(\pm\) 0.63 A\({}^{\text{;a}}\) & \\ \hline \multirow{2}{*}{_Enterococcus faecalis_} & Baseline & 5.86 \(\pm\) 1.12 A\({}^{\text{;a}}\) & 6.20 \(\pm\) 0.97 A\({}^{\text{;a}}\) & \multirow{2}{*}{0.053} \\  & 14 & 5.04 \(\pm\) 0.93 A\({}^{\text{;a}}\) & 5.41 \(\pm\) 0.78 B\({}^{\text{;a}}\) & \\ \hline \multirow{2}{*}{Y/F} & Baseline & 4.77 \(\pm\) 1.08 A\({}^{\text{;a}}\) & 5.40 \(\pm\) 0.92 A\({}^{\text{;a}}\) & \multirow{2}{*}{0.764} \\  & 14 & 5.06 \(\pm\) 0.80 A\({}^{\text{;a}}\) & 5.35 \(\pm\) 1.20 A\({}^{\text{;a}}\) & \\ \hline \hline \end{tabular}  
* The data are presented as the mean \(\pm\) standard error (\(n=10\)/group). Baseline measurements were done on day 2 before the start of the feeding experiment. CFU, colony-forming units; LAB, lactic acid bacteria count; TCE, total count of enterobacteria; TCM, total count of aerobic and facultative anaerobic microorganisms; Treat. Int., treatment interaction; Y/F, yeast/fungi. A\({}^{\text{;b}}\) different capitals indicate significant time-related differences (\(p<0.05\)). \({}^{\text{;b}}\) different letters indicate differences among treatments (\(p<0.05\)).  
\end{table} 
Table 2: Faecal microbiological parameters of calves fed with milk replacer only (CON group) or supplemented with fermented milk permeate (MP group). groups of newborn calves (Figure 1). Six genera (_Escherichia_, _Streptococcus_, _Clostridium_, _Enterococcus_, _Klebsiella_, and _Terrisporobacter_) represented >93% of the total bacterial reads. At the end of the experiment, 28,265 and 26,968 bacterial reads were obtained from the faeces of the MP and CON groups, respectively. The microbial profiles differed significantly between the groups (Figure 2). Figure 1: Bacterial genera percentage prevalence in the faeces of calves before the experiment. The genera are included in the list only if the prevalence was at least 1% of the total bacterial reads in the faeces of both groups combined. CON, calves fed with milk replacer only; MP, calves fed with milk replacer and supplemented with fermented milk permeate. Figure 2: Bacterial genera percentage prevalence in the faeces of calves after the experiment. The genera are included in the list only if the prevalence was at least 1% of the total bacterial reads in the faeces of both groups. CON, calves fed with milk replacer only; MP, calves fed with milk replacer and supplemented with fermented milk permeate. * Significant differences between the groups. The most prevalent bacterial genera in the MP group were _Lactobacillus_ and _Bifthobacteria_, whereas in the CON group the most prevalent were _Blautia_ and _Tyzzerella_ (Figure 2). Bacteria of these genera accounted for 45.2% and 53.5% of all bacterial counts in the MP and CON groups, respectively. The other most prevalent genera included _Bacteroides_, _Erysipelatoclostridium_, _Escherichia_, _Butyricicoccus_, _Ruminococcus_, and _Faecalibacterium_ (Figure 1, Tables S4 and S5).