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.
Highlights
Tremendous gains have been made in dairy cattle efficiency and productivity through efforts in breeding and management over the last several decades (Miglior et al, 2017)
Three pairs of healthy, lactating, ruminally cannulated 3rd-lactation Holstein dairy cows were selected on the basis of disparate dry matter intake (DMI) with similar energy corrected milk (ECM) over their first two lactation cycles, designated as either high or low milk production efficiency within each pair (HE and LE, respectively)
Manipulation of the rumen microbial community is a promising approach for improving milk production efficiency (MPE) (Jami et al, 2014; Bickhart and Weimer, 2017; Weimer et al, 2017)
Summary
Tremendous gains have been made in dairy cattle efficiency and productivity through efforts in breeding and management over the last several decades (Miglior et al, 2017). Breeding for high production has resulted in consequent decreases in animal health and longevity (Knaus, 2009). This has led to an interest in breeding-independent strategies for improving milk production efficiency (MPE) to ensure a sustainable and economically viable future for the dairy industry. Inter-animal variability in rumen microbial metabolism can result in differences in both milk volume and components by altering the pool of precursors available to the host. The rumen microbial community has been repeatedly implicated in milk efficiency variability and production metrics in dairy cattle (Jami et al, 2014; Jewell et al, 2015; Shabat et al, 2016; Wallace et al, 2019)
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