Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows

Abstract

A major goal for the dairy industry is to improve overall milk production efficiency (MPE). With the advent of next-generation sequencing and advanced methods for characterizing microbial communities, efforts are underway to improve MPE by manipulating the rumen microbiome. Our previous work demonstrated that a near-total exchange of whole rumen contents between pairs of lactating Holstein dairy cows of disparate MPE resulted in a reversal of MPE status for ∼10 days: historically high-efficiency cows decreased in MPE, and historically low-efficiency cows increased in MPE. Importantly, this switch in MPE status was concomitant with a reversal in the ruminal bacterial microbiota, with the newly exchanged bacterial communities reverting to their pre-exchange state. However, this work did not include an in-depth analysis of the microbial community response or an interrogation of specific taxa correlating to production metrics. Here, we sought to better understand the response of rumen communities to this exchange protocol, including consideration of the rumen fungi. Rumen samples were collected from 8 days prior to, and 56 days following the exchange and were subjected to 16S rRNA and ITS amplicon sequencing to assess bacterial and fungal community composition, respectively. Our results show that the ruminal fungal community did not differ significantly between hosts of disparate efficiency prior to the exchange, and no change in community structure was observed over the time course. Correlation of microbial taxa to production metrics identified one fungal operational taxonomic unit (OTU) in the genus Neocallimastix that correlated positively to MPE, and several bacterial OTUs classified to the genus Prevotella. Within the Prevotella, Prevotella_1 was found to be more abundant in high-efficiency cows whereas Prevotella_7 was more abundant in low-efficiency cows. Overall, our results suggest that the rumen bacterial community is a primary microbial driver of host efficiency, that the ruminal fungi may not have as significant a role in MPE as previously thought, and that more work is needed to better understand the functional roles of specific ruminal microbial community members in modulating MPE.

Keywords: dairy cattle; milk production efficiency; rumen; ruminal contents exchange; ruminal microbiota.

FIGURE 1

Non-metric multidimensional scaling plot depicting Bray-Curtis dissimilarity of bacterial and fungal communities by pair of host animals. Standard error ellipses are color coded by initial MPE of host and time within study.

FIGURE 2

Beanplots expressing average degree-centrality of nodes by domain and over time for HE and LE-derived rumen liquids and solids. Shared letters indicate no difference in degree between timepoints (P > 0.05).

FIGURE 3

Beanplots expressing abundance of normalized bacterial reads classifying to genera Prevotella_1 and Prevotella_7 in liquid-derived rumen samples by time within the study and initial host efficiency. Shared letters indicate no difference in read abundance (p > 0.05).

FIGURE 4

Heatmaps summarizing correlations between SIMPER-implicated OTUs and phenotypic variables of interest within amplicon and sample type. Variables are energy corrected milk (ECM), gross feed efficiency (GFE), and molar fraction acetate (MF ACE), propionate (MF PRO) and butyrate (MF BUT). Genera displayed beneath OTU names. Color scale reflects strength and direction of correlation (Spearman’s ρ statistic), and asterisks within the heatmap indicate statistical significance (*P < 0.05, **P < 0.01, ***P < 0.001).

FIGURE 5

Scatterplots of LEfSe-implicated OTUs with significant correlations to production metrics. FDR-corrected p-values and the R² values for the linear mode (black) are expressed on each plot. Points are color coded by initial efficiency of host and time within trial. Genus-level classification of the OTUs are as follows: B_OTU 43: Prevotellaceae_UCG-003; B_OTU 93: Prevotella_1; B_OTU 34: Prevotella_1; B_OTU 108: Lachnobacterium; B_OTU 150: Ruminobacter; B_OTU 142: Selenomonas_1; F_OTU 6: Neocallimastix.