The rumen microbial metagenome associated with high methane production in cattle

BMC Genomics

Table 3 Partial least squares estimates of KEGG genes and diet effects and the variation in methane emissions. Partial least squares estimates of KEGG genes and diet effects in an analysis where the partial least squares factors^a explaining 87.6 % of the variation of model effects and 87.9 % of the variation in methane emissions

KEGG ID/Diet	Description	^bEstimate	^cVIP
K06001	Tryptophan synthase beta chain [EC:4.2.1.20]	0.13310	1.233
Diet conc	Concentrate based diet	−0.14695	1.204
Diet mixed	Mixed forage-concentrate diet	0.14695	1.204
K02118	V/A-type H ⁺ -transporting ATPase subunit B [EC:3.6.3.14]	0.07984	1.151
K02117	V/A-type H ⁺ -transporting ATPase subunit A [EC:3.6.3.14]	0.08564	1.133
K00638	Chloramphenicol O-acetyltransferase [EC:2.3.1.28]	0.06182	1.082
K00200	Formylmethanofuran dehydrogenase subunit A [EC:1.2.99.5]	0.06042	1.070
K03531	Fell division protein FtsZ	0.07526	1.065
K00201	Formylmethanofuran dehydrogenase subunit B [EC:1.2.99.5]	0.04859	1.049
K00399	Methyl-coenzyme M reductase alpha subunit [EC:2.8.4.1]	0.03843	1.021
K00123	Formate dehydrogenase, alpha subunit [EC:1.2.1.2]	0.03417	1.013
K03388	Heterodisulfide reductase subunit A [EC:1.8.98.1]	0.02734	0.997
K14126	F ₄₂₀ -non-reducing hydrogenase subunit A [EC:1.12.99.-]	0.00384	0.933
K01079	Phosphoserine phosphatase [EC:3.1.3.3]	0.03424	0.932
K00401	Methyl-coenzyme M reductase beta subunit [EC:2.8.4.1]	0.00484	0.909
K00527	Ribonucleoside-triphosphate reductase [EC:1.17.4.2]	0.03449	0.898
K02337	DNA polymerase III subunit alpha [EC:2.7.7.7]	−0.05338	0.886
K02837	Peptide chain release factor RF-3	0.00883	0.852
K01893	Asparaginyl-tRNA synthetase [EC:6.1.1.22]	−0.06673	0.812
K00925	Acetate kinase [EC:2.7.2.1]	−0.00903	0.812
K00656	Formate C-acetyltransferase [EC:2.3.1.54]	−0.00834	0.787
K02948	Small subunit ribosomal protein S11	−0.00400	0.734

Genes in bold type are archaeal genes associated with methane production
^aTwo factors were significant in the partial least squares analysis
^bEstimates based on predictors and responses to be centred and scaled to have mean 0 and standard deviation 1
^cVariable Importance for Projection (VIP) statistic of Wold [67], which summarizes the contribution of a variable marker to the model

ISSN: 1471-2164