Reducing enteric methane emission in dairy goats: impact of dietary inclusions of quebracho tannin extract on ruminal microbiota

Abstract

Introduction: Condensed tannins (CT) influence ruminal microbiota, feed digestibility, and methane emissions, yet their effects in goats are poorly understood.

Methods: This study evaluated the impact of dietary quebracho CT extract at 0%, 2%, 4%, or 6% of dry matter on the composition of the dairy goat ruminal microbiota with a two-times repeated 4 × 4 Latin square design. Bacterial, archaeal, fungal, and protozoan communities were analyzed at the end of each feeding period for relative abundance changes, and their relationship to methane production, nutrient digestibility and feed efficiency were also assessed.

Results: Increasing CT levels reduced alpha- and beta-diversity, with the 6% CT diet showing the most pronounced decline. CT inclusion induced phylum-level shifts in fiber-degrading microbes, including inversion of the Firmicutes to Bacteroidota ratio. Prevotellaceae and Succiniclasticum, tolerant to CT, increased significantly (P < 0.05), in line with higher propionate and lower methane production. The proteolytic bacteria Anaerolineaceae and Synergistaceae decreased (P < 0.05), consistently with the reduced isobutyrate and isovalerate ruminal concentration and with the reduced urinary nitrogen excretion. Methanobrevibacter, a key methane producer, was reduced by dietary CT (P < 0.05). The overall fungal biodiversity was also significantly changed (P < 0.05); the fiber-degrading Liebetanzomyces decreased, while the tannin-degrading Aspergillus increased (P < 0.05). Concerning protozoa, Diplodinium was reduced (P < 0.05) and Polyplastron and Isotrichia were increased (P < 0.05) by dietary CT.

Discussion: These and other microbial abundance changes correlated with reduced methane emission, altered fiber and protein digestibility, and modified volatile fatty acid (VFA) profiles. This study shows that decreased nutrient degradability in the rumen due to higher dietary CT alters the goat rumen microbiota and clarifies microbial taxa changes in relation to the zootechnical outcomes, including reduced methane production.

Keywords: condensed tannins; environmental sustainability; methanogenesis; microbiota modulation; rumen fermentation.

Figure 1

Piecharts illustrating the relative abundance over all the rumen microbiota samples at the lowest resolved taxonomic level. (A): prokaryotic microbiota. (B): fungal microbiota. (C): protozoan microbiota. Taxa with a relative abundance <2% on average for Prokaryotes and Fungi or <1% on average for Protozoa are grouped in the “Other” category.

Figure 2

(A) Rarefaction curves of the ruminal prokaryotic microbiota according to the PD whole tree metrics based on the zero-radius operational taxonomic units (zOTU) tree for all the experimental diets assessed in this study. The line represents the average over the samples collected from goats subjected to the same diet; error bars representing the intra-diet standard deviation are also represented. (B) principal coordinate analysis (PCoA) based on the unweighted UniFrac distance between samples illustrating the clustering of rumen microbiota samples according to goat diet. Each point represents a sample, colored according to the diet group, centroids are the average of the coordinates and ellipses represent the SEM-based confidence interval. The first and third principal coordinates are represented. (C) Boxplots representing the distribution of the unweighted UniFrac distances among samples from the same diet group. Stars above boxplots indicate a statistically significant difference (P < 0.05) between groups. (D) Boxplots representing the distribution of the unweighted UniFrac distances among samples from the three diet groups (i.e., Q2, Q4, and Q6) and C diet. Stars above boxplots indicate a statistically significant difference (P < 0.05) between groups. (E) Boxplots representing the distribution of the unweighted UniFrac distances among samples for increasing tannin concentrations. Stars above boxplots indicate a statistically significant difference (P < 0.05) between groups. C: control diet. Q2, Q4, Q6: diets integrated with 2, 4, 6% on DM of quebracho tannin extract, respectively.

Figure 3

Boxplot representing the relative abundance of some selected taxa (average rel. ab >1% in at least one treatment). In each boxplot, individual samples are represented as black dots; average abundance is represented as a white line, whereas median abundance is depicted as a black line. C: control diet. Q2, Q4, Q6: diets integrated with 2, 4, 6% on DM of quebracho tannin extract, respectively.

Figure 4

Spearman's rank correlation between zootechnical parameters and the main prokaryotic and eukaryotic taxa. For prokaryota (A), we considered the classification at the family level and only families with mean relative abundance >0.5%; for fungi (B) and protozoa (C), we considered genera with a mean relative abundance of 0.2% or more. White stars indicate a significant (hypothesis of no correlation against the alternative hypothesis of a non-zero correlation, P < 0.05) taxon-parameter combination. Heatmaps were clustered over taxa according to Euclidean distance and complete linkage to highlight common patterns of correlation for multiple taxa.