Fig. 4

Potential metabolic changes A in Holstein dairy cows that have shifted from summer to winter diets and B in calves before and after introduction of solid feed (B). The barplots show the number of unique (common are excluded) predicted enzymes (KOs) identified as DifRep for each KEGG pathway (top). Pathways that we refer to as “housekeeping” are grayed out. The asterisks highlight the metabolic pathways presented under each bar plot (see Table S9 & Suppl. Res. 2). At the bottom, C an overview of the predicted SCFA end products of the microbial metabolism. The MAGs that carry all the required KOs (manually verified) to produce the focal SCFAs are grouped by class. Arrowheads represent the number of predicted KOs required to produce each SCFA and are color coded to show the corresponding group of samples (summer or winter samples in our study; samples from calves before and after introduction of solid feed; [31]). Chemical compound illustrations (shown in hexagons) were obtained from PubChem (https://pubchem.ncbi.nlm.nih.gov/)