Fig 1.
qPCR of bacterial 16S rRNA, archaeal mcrA, protozoal 18S rRNA genes and fungal region between 18S rRNA and ITS1 of rumen digesta samples.
Samples collected from lactating cows fed four diets: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). Results are expressed as copy number per ng of extracted DNA. Error bars represent standard deviations (SD), n = 4 per diet.
Fig 2.
Relative abundance of bacteria, archaea, ciliate protozoa and fungi among diets.
Bubble-charts represent taxonomy at the phylum level for bacteria and genus level for the rest. Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively).
Fig 3.
Bacterial, archaeal, protozoal and fungal diversity (Simpson’s index) as measured from amplicon sequence data in four diets.
Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively).
Fig 4.
NMDS plots of bacteria, archaea, ciliate protozoa and fungi, based on amplicon sequence data.
Individual animals are represented by dots, colored based on the diet: high (H—black) or low (L—green) proportion of concentrates without oil, or supplemented with SO (HSO–red, and LSO—blue).
Table 1.
Changes in rumen microbial community abundances from amplicon sequence data in four diets, represented as average abundance per diet ± standard deviation (SD).
Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). Only taxa significantly affected by diet are presented. The small letter at the beginning of each bacterial taxon name identifies the deepest classification level to which the OTUs were assigned. Diet effect represents significant (P < 0.05) microbial abundance changes due to FC, SO or FC × SO interaction.
Fig 5.
Graphical networks representing the interactions between rumen microorganisms within three diet comparisons.
a) L-H, b) L-LSO, and c) H-HSO diet comparisons. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.25, respectively. Microbial taxa are colored by taxonomy: archaea—light gray, ciliate protozoa—white, fungi—dark grey, bacteria: Bacteroidetes—green, Firmicutes—moss green, Proteobacteria—brown, others—blue.