Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Abstract

The community structure of colonised bacteria in the gastrointestinal tracts (GITs) of pre-weaned calves is affected by extrinsic factors, such as the genetics and diet of the calves; however, the dietary impact is not fully understood and warrants further research. Our study revealed that a total of 6, 5, 2 and 10 bacterial genera showed biologically significant differences in the GITs of pre-weaned calves fed four waste-milk diets: acidified waste milk, pasteurised waste milk, untreated bulk milk, and untreated waste milk, respectively. Specifically, generic biomarkers were observed in the rumen (e.g., Bifidobacterium, Parabacteroides, Fibrobacter, Clostridium, etc.), caecum (e.g., Faecalibacterium, Oxalobacter, Odoribacter, etc.) and colon (e.g., Megamonas, Comamonas, Stenotrophomonas, etc.) but not in the faeces. In addition, the predicted metabolic pathways showed that the expression of genes related to metabolic diseases was increased in the calves fed untreated waste milk, which indicated that untreated waste milk is not a suitable liquid diet for pre-weaned calves. This is the first study to demonstrate how different types of waste milk fed to pre-weaned calves affect the community structure of colonised bacteria, and the results may provide insights for the intentional adjustment of diets and gastrointestinal bacterial communities.

Figure 1. Diet-induced changes in bacterial composition based on UniFrac distances and LEfSe in the rumen.

(a) Average relative abundances of the predominant rumen mucosa- and digesta-associated bacteria; (b) comparison of the predominant genera in the rumen mucosa and digesta samples (relative abundance >1% in at least one dietary group); (c) UniFrac distance between the groups in the rumen; (d) histogram of the LDA scores calculated for differentially abundant features in the rumen at the genus level among dietary groups (only the genera LDA scores above 3 are shown); and (e) taxonomic cladograms reporting the different taxa abundances in the rumen among the dietary groups. LEfSe, linear discriminant analysis (LDA) effect size; UBM, calves fed untreated bulk milk (control group); AWM, calves fed acidified waste milk; PWM, calves fed pasteurised waste milk; UWM, calves fed untreated waste milk.

Figure 2. Diet-induced changes in bacterial composition based on UniFrac distances and LEfSe in the caecum.

(a) Average relative abundances of the predominant caecum mucosa- and digesta-associated bacteria; (b) comparison of the predominant genera in caecum mucosa and digesta samples (relative abundance >1% in at least one dietary group); (c) UniFrac distance between groups in the caecum; (d) histogram of the LDA scores calculated for differentially abundant features in the caecum at the genus level among the dietary groups (only the genera LDA scores above 3 are shown); and (e) taxonomic cladograms reporting the different taxa abundances in the caecum among the dietary groups. LEfSe, linear discriminant analysis (LDA) effect size; UBM, calves fed untreated bulk milk (control group); AWM, calves fed acidified waste milk; PWM, calves fed pasteurised waste milk; UWM, calves fed untreated waste milk.

Figure 3. Diet-induced changes in bacterial composition based on UniFrac distances and LEfSe in the colon.

(a) Average relative abundances of the predominant colon mucosa- and digesta-associated bacteria; (b) comparison of the predominant genera in colon mucosa and digesta samples (relative abundance >1% in at least one dietary group); (c) UniFrac distance between groups in the colon; (d) histogram of the LDA scores calculated for differentially abundant features in the colon at the genus level among the dietary groups (only the genera LDA scores above 3 are shown); and (e) taxonomic cladograms reporting the different taxa abundances in the colon among the dietary groups. LEfSe, linear discriminant analysis (LDA) effect size; UBM, calves fed untreated bulk milk (control group); AWM, calves fed acidified waste milk; PWM, calves fed pasteurised waste milk; UWM, calves fed untreated waste milk.

Figure 4. Diet-induced changes in bacterial composition based on UniFrac distances and LEfSe in the faeces.

(a) Average relative abundances of the predominant faeces mucosa- and digesta-associated bacteria; (b) comparison of the predominant genera in faeces mucosa and digesta samples (relative abundance >1% in at least one dietary group); and (c) UniFrac distance between groups in the faeces. UBM, calves fed untreated bulk milk (control group); AWM, calves fed acidified waste milk; PWM, calves fed pasteurised waste milk; UWM, calves fed untreated waste milk.

Figure 5. Comparison of KEGG pathways predicted by PICRUSt according to diet.

(a) Heatmap of 41 second-level classification KEGG pathways identified in the gut samples. Histogram of the LDA scores calculated for the differentially abundant features in the caecum (b), colon (c), and faeces (d) for second-level classification KEGG pathways among the dietary groups (only the LDA scores above 3 are shown). LDA, linear discriminant analysis; UBM, calves fed untreated bulk milk (control group); AWM, calves fed acidified waste milk; PWM, calves fed pasteurised waste milk; UWM, calves fed untreated waste milk.