Additional file 1 of Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle

Additional file 1: Figure S1. Schematic representation of the four in vivo trials used in the comparative analysis, including short-term and long-term 3-NOP supplementation studies in beef and dairy cattle (Beef1: Romero-Perez et al., 2014 [9]; Beef2: Romero-Perez et al., 2015 [10]; Dairy1: Haisan et al., 2014 [15]; Dairy2: Haisan et al., 2017 [16]). Figure S2. Effect of short-term 3-nitrooxypropanol (3-NOP) supplementation on the abundance of A bacterial, B archaeal, and C protozoal taxa in beef cattle. *3-NOP dose level information: con: 0, low: 53, med: 161, high: 345 mg/kg of DM. Others indicates taxa with less than 5% abundance; UCF: uncultured family-level; UCG: uncultured genus-level; UG: unclassified genus-level. Figure S3. Effect of long-term 3-nitrooxypropanol (3-NOP) supplementation on the abundance of A bacterial, B archaeal, and C protozoal taxa in beef cattle. *3-NOP dose level information: con: 0, high: 280 mg/kg of DM. Others indicates taxa with less than 5% abundance; UCG: uncultured genus-level; UG: unclassified genus-level; recov: recovery period. Figure S4. Effect of 3-nitrooxypropanol (3-NOP) supplementation on the abundance of A bacterial, B archaeal, and C protozoal taxa in dairy cattle. *3-NOP dose level information: con: 0, high: 130 mg/kg of DM. Others indicates taxa with less than 5% abundance; UCG: uncultured genus-level; UG: unclassified genus-level. Figure S5. Dose response effect of 3-nitrooxypropanol (3-NOP) supplementation on the abundance of A bacterial, B archaeal, and C protozoal taxa in dairy cattle. *3-NOP dose level information: con: 0, low: 68, high: 132 mg/kg of DM. Others indicates taxa with less than 5% abundance; UCG: uncultured genus-level; UG: unclassified genus-level. Figure S6. Alpha diversity and beta diversity analysis of rumen microbiota before and after batch correction. Alpha diversity was measured by Shannon index in A bacteria, B archaea, and C protozoa of control and 3-NOP treated groups. P values were calculated using Wilcoxon rank sum test, with significance set at P 1 are shown. Data with error bars are indicated as mean ± standard error. Asterisks indicate significance: *P 1 are shown. Data with error bars are indicated as mean ± standard error. Asterisks indicate significance: *P 1 are shown. Data with error bars are indicated as mean ± standard error. Asterisks indicate significance: *P 1 are shown. Data with error bars are indicated as mean ± standard error. Asterisks indicate significance: *P < 0.1, **P < 0.05. Figure S13. Effect of 3-nitrooxypropanol (3-NOP) supplementation on the distributions of hydrogenases, associated terminal reductases, and electron transferases in beef cattle. A results were obtained from a comparative analysis using MMUPHin and further validated by MaAsLin2 analysis. The gray, yellow, and skyblue strips represent hydrogenases, associated terminal reductases, and electron transferases, respectively. The comparative analysis was conducted with a threshold of Q < 0.05 and cross-verified by MaAsLin2 with Q < 0.05. CPM: count per million; DM: dry matter. Figure S14. Effect of 3-nitrooxypropanol (3-NOP) supplementation on the distributions of hydrogenases and associated terminal reductases in dairy cattle. A results were obtained from a comparative analysis using MMUPHin and further validated by MaAsLin2 analysis. The gray and skyblue strips represent hydrogenases and associated terminal reductases, respectively. The comparative analysis was conducted with a threshold of Q < 0.05 and cross-verified by MaAsLin2 with Q < 0.05. CPM: count per million; DM: dry matter.