Table 1.
Overview of rumen samples analyzed in this study.
Table 2.
Oligonucleotide primers used to amplify bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal ITS1 genes.
Figure 1.
Distribution of barcode mappable and quality-filtered sequencing reads across domains for each mixing ratio tested.
The mixing ratios represent bacteria:archaea:ciliate protozoa (1∶1∶1), and bacteria:archaea:ciliate protozoa:fungi (5∶1∶1∶1 and 5∶1∶1∶0.2).
Figure 2.
Relative composition of microbial communities in the 12 pyrosequencing libraries.
Community composition of (A) bacteria, (B) archaea, (C) ciliate protozoa, and (D) anaerobic fungi in 12 DNA samples obtained from three different ruminant species feeding on a variety of natural diets.
Figure 3.
Correlations between selected groups of microorganisms.
Correlation between relative abundances of (A) Bacteroidales- and Clostridiales-related sequencing reads, and (B) methanogens of the Methanobrevibacter ruminantium and M. gottschalkii clades in pyrosequencing libraries of the 12 analyzed DNA samples.
Figure 4.
Spearman's rank correlation matrix of the dominant microbial populations across domains in analyzed rumen samples.
Microbial populations listed represent at least 1% of the bacterial, archaeal, ciliate, or fungal communities in at least one sample and were detected in at least 50% of the rumen samples analyzed. Strong correlations are indicated by large squares, whereas weak correlations are indicated by small squares. The colours of the scale bar denote the nature of the correlation with 1 indicating perfect positive correlation (dark blue) and -1 indicating perfect negative correlation (dark red) between two microbial populations. Correlations marked with circles are discussed in the text.