Data_Sheet_1_Different microbial genera drive methane emissions in beef cattle fed with two extreme diets.PDF

The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.</p

Table_1_Different microbial genera drive methane emissions in beef cattle fed with two extreme diets.XLSX

The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.</p

Bulletin municipal officiel de la ville de Paris. Délibérations des assemblées de la Ville de Paris et du Département de la Seine. Conseil municipal de Paris

11 janvier 19621962/01/11 (A81,N17)

Additional file 3: Table S3. of The rumen microbial metagenome associated with high methane production in cattle

KEGG dataset in order of average gene abundance. (XLSX 1400 kb

Additional file 4: Table S4. of The rumen microbial metagenome associated with high methane production in cattle

KEGG dataset in order of the ratio of gene abundance, high:low emitters. (XLSX 443 kb

Additional file 1: Figure S1. of The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle

Relative abundance (%) of 20 groups of functional genes representing 204 selected genes (number of animals, n = 50 samples). The sum of the relative abundance (%) of genes grouping within the same function is shown in this figure. Figure S2A. Total abundance of 204 selected genes based on diet treatments (n = 50). *P value < 0.05. Figure S2B. Shannon index diversity of 204 selected genes based on diet treatments (n = 50). *P value < 0.05, °P value < 0.1. Figure S3. Canonical Variate analysis (CVA) on the structure of 204 genes selected based on breed, age, weight, Proteobacteria ratio, FCR and methane grouping (n = 50). Figure S4. Factors explaining the significant differences observed for Proteobacteria ratio (n = 50). Figure S5. Microbial community composition at the phylum level (n = 50). Table S1. Characteristics of the cattle used in the experiment. Table S2. Groups of AMR genes significantly correlated with abundance of the Proteobacteria phylum and Proteobacteria ratio. Table S3. The relative abundance of AMR genes. Table S4, Proteobacteria populations strongly correlated with the Proteobacteria ratio. Table S5. Functional genes significantly correlated with Proteobacteria ratio (PLS). Table S6. Cluster distribution of functional genes significantly different between diets. (DOCX 60 kb

Additional file 6: Figure S1. of The rumen microbial metagenome associated with high methane production in cattle

KEGG pathways associated with methane metabolism. Highlighted EC gene numbers are those genes that differed significantly between high and low emitting cattle. Red – genes that had higher abundance in high emitters; blue - genes that had lower abundance in high emitters. (DOC 22 kb

Additional file 5: Table S5. of The rumen microbial metagenome associated with high methane production in cattle

Gene abundance of genes of pyruvate metabolism in low and high methane steers. (DOCX 14 kb

Distribution of methane emissions and archaea:bacteria ratios within breed type and diet.

<p>The box plot shows the large variation and range of methane emissions (per day or per kg DMI = dry matter intake) and archaea:bacteria ratios within crossbred breed type (AA = Aberdeen Angus sired, LIM = Limousin sired) and diet (CON = concentrate based diet, FOR = forage based diet). The total number of animals in the 2 × 2 factorial design experiment was 68.</p

Host genetic effects on methane emissions and relative microbial abundance.

<p>Host genetic effects were estimated by least squares means (± standard errors, different letters above bars indicate significant different estimates) of sire progeny groups (AA = Aberdeen Angus sired, LIM = Limousin sired) adjusted for diet, respiration chamber and randomized block effects. Relative microbial abundance was calculated as archaea:bacteria ratio.</p