Also in the Article

• Experimental design and subject details

• Method details

• Quantification and statistical analysis

• Utilization of primer sets derived microbiome data in the statistical analysis

• Converting OBITools intermediate fasta files to QIIME ready format

• Clustering of microbial marker gene amplicon sequences and picking representative de novo species OTU

• Assigning taxonomy to OTU

• Creation of OTU tables and sample subsetting and subsampling

• Correlating microbial domain cell count

• Correlating microbial domain cell counts to experimental variables

• Correlating microbial domain richness to experimental variables

• Prediction of phenotypes and other experimental variables by core microbiome

• Prediction of phenotypes by core microbiome while correcting for diet

• Prediction of phenotypes by diet components

• Prediction of phenotypes and other experimental variables by core microbiome using RF

• Bovine genotype quality control

• Testing association of the global rumen prokaryotic core with host genetics

• Creation of genetic relationship matrix

• Heritability estimation

• Heritability confidence interval estimation

• Bovine genome SNPs—Microbe association effort

• Estimating kinship matrix

• Genomic prediction

• Associating microbes’ abundance with experimental variables

• Inference of microbial interaction network within domains

• Inference of interdomain microbial network

• Comparing phylogenetic relatedness of core prokaryotic microbes to random sampling

• Examining core and trait-related microbiome for taxonomic enrichment

• Comparing heritable microbes to other core miocrobes’ ability to explain experimental variables