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Additional file 1: Supplementary Information Text. Figure S1: Alpha diversity based on 16S rRNA amplicon archaeal sequencing data in cows supplemented with 3-nitrooxypropanol (3-NOP) at weeks 4, 8, and 12. (A) observed species in DNA liquid; (B) Shannon diversity in DNA liquid; (C) observed species in RNA liquid; (D) Shannon diversity in RNA liquid. NS = not significant. Figure S2: Schematic diagram of possible methanogenesis pathways. Table S1: Sequencing information for metagenomics. Trt: treatment group; W: week; 3-NOP: 3-nitrooxypropanol. Table S2: Sequencing information for metatranscriptomics. Trt: treatment group; W: week 3-NOP: 3-nitrooxypropanol. Table S3: Relative abundance (%) of archaeal taxonomy in metagenomics. SEM: Standard error of mean; Trt: treatment group; W: week; 3-NOP: 3-nitrooxypropanol. Table S4: Relative abundance (%) of archaeal taxonomy in metatranscriptomics, SEM: Standard error of mean; Trt: treatment group; W: week; 3-NOP: 3-nitrooxypropanol. Table S5: The 6 most abundant archaea (cpm; copies per million) contributing to steps 1-5 in the carbon dioxide (CO2)-hydrogen (H2) methanogenic pathway in the rumen of dairy cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. Table S6: The most abundant archaea (cpm; copies per million) utilizing methanol as a substrate for methanogenesis in the rumen of dairy cows supplemented with 3-NOP compared to control at weeks 4, 8, and 12. Table S7: The most abundant archaea (cpm; copies per million) utilizing methylamines as a substrate for methanogenesis in the rumen of dairy cows supplemented with 3-NOP compared to control at weeks 4, 8, and 12. Table S8: Transcripts (cpm; copies per million) coding for EC: 1.8.7.3 (HdrA, HdrB and HdrC) in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. ND = not detected. Table S9: Effect of 3-nitrooxypropanol (3-NOP) on bacterial taxonomical composition (relative abundance %) in DNA-based 16S rRNA sequencing. SEM: Standard error of mean; Trt: treatment group; W: week; 3-NOP: 3-nitrooxypropanol. Table S10: Effect of 3-nitrooxypropanol (3-NOP) on bacterial taxonomical composition (relative abundance %) in RNA-based 16S rRNA sequencing. SEM: Standard error of mean; Trt: treatment group; W: week. Table S11: Effect of 3-nitrooxypropanol (3-NOP) on bacterial taxonomical composition (relative abundance %) in metagenomics. SEM: Standard error of mean; Trt: treatment group; W: week. Table S12: Effect of 3-nitrooxypropanol (3-NOP) on bacterial taxonomical composition (relative abundance %) in metatranscriptomics. SEM: Standard error of mean; Trt: treatment group; W: week. Table S13: Average methane (CH4) and hydrogen (H2) gas data in control and 3-nitrooxypropanol (3-NOP) treated cows at weeks 2, 6, 9, and 15. Table S14: Effect of 3-nitrooxpropanol (3-NOP) on hydrogenase subgroups (cpm; copies per million) including [FeFe], [Fe], and [NiFe] hydrogenases in metagenomics. Table S15: Effect of 3-nitrooxpropanol (3-NOP) on hydrogenase subgroups (cpm; copies per million) including [FeFe], [Fe], and [NiFe] hydrogenases in metatranscriptomics. Table S16: Effect of 3-NOP on hydrogenases (cpm; copies per million) classified into H2 production and H2 consumption in metagenomics. Table S17: Effect of 3-NOP on hydrogenases (cpm; copies per million) classified into H2 production and H2 consumption in metatranscriptomics. Table S18: Effect of 3-nitrooxypropanol (3-NOP) on rumen fermentation variables in early-lactation dairy cows at weeks 4, 8, and 12. Table S19: Taxonomy (cpm; copies per million) associated with the butyrate pathway in metagenomics in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. Table S20: Taxonomy (cpm; copies per million) associated with the butyrate pathway in metatranscriptomics in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. Table S21: Taxonomy (cpm; copies per million) associated with the propionate pathway in metagenomics in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. Table S22: Taxonomy (cpm; copies per million) associated with the propionate pathway in metatranscriptomics in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. Table S23: List of metagenomes assembled genomes (MAGs) identified in early-lactation dairy cows. Table S24: Transcripts (cpm; copies per million) coding for EC: 1.8.98.1 in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. ND = not detected. Table S25: Transcripts (cpm; copies per million) coding for EC: 1.8.98.5 in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. ND = not detected. Table S26: Transcripts (cpm; copies per million) coding for EC: 1.8.98.6 in cows supplemented with 3-nitrooxypropanol (3-NOP) compared to control cows at weeks 4, 8, and 12. ND = not detected. |
