Project : USDA ARS

ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Research Project #433503

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

2022 Annual Report

Accomplishments
1. Developed new methods for microbiome screening leading to record number of genomes assembled. The microbiome is the combined genetic material of all microorganisms (bacteria, fungi, protozoa, and viruses) that live in a particular environment. Because those microorganisms exist in large communities that are difficult to assess using old DNA sequencing technologies, ARS researchers in Madison, Wisconsin, led a project conducted by an international and interdisciplinary team of researchers from four countries and two private U.S. companies in developing new methods for microbiome screening. ARS researchers worked with bioinformaticians in the private sector to develop the open-source software tool, MAGPhase, which automates the process of single nucleotide polymorphisms (SNP) discovery and validation in the microbiome. The improved accuracy of newer sequencing technologies allows the MAGPhase algorithm to identify genetic variants that are representative of divergent strains of microbes that may harbor antibiotic resistance or pathogenesis genes. Using MAGPhase and improved genome assembly algorithms, 428 complete microbial genomes were assembled from that single sample, which was a record for a field that celebrated the assembly of 10 genomes from one individual. This accomplishment was of such importance that it was published in the journal, Nature Biotechnology (https://doi.org/10.1038/s41587-021-01130-z), with an accompanying opinion article highlighting its importance in Nature Microbiology (https://doi.org/10.1038/s41564-021-01027-2). These innovations have created a new benchmark for the field and are likely to serve as the foundation for new surveys in human clinical and agricultural microbial systems.

2. Identified means to measure susceptibility or resistance of dairy cattle to lipid related metabolic disorders. Energy and nutrient demands of early lactation can result in the development of lipid related metabolic disorders (LRMD) in dairy cows, such as ketosis and fatty liver resulting in reduced productivity and profitability of the dairy farm. Determining cow susceptibility to LRMD and identification of biomarkers associated with LRMD would provide an important advancement in managing cows in early lactation. To evaluate cow susceptibility and adaptability to LRDM, ARS researchers in Madison, Wisconsin, in collaboration with scientists at the University of Wisconsin-Madison, conducted an experiment to discover differences in liver gene expression that are associated with a cow’s susceptibility or resistance to metabolic disorders. Cows were retrospectively categorized into LRMD susceptibility and resistance groups. Cow grouping as susceptible or resistant to LRMD was closely associated to changes related to oxidative stress. These results suggest that responses to oxidative stress in cows in early lactation may determine susceptibility and resistance to LRMD. These results provide novel insight into the role of oxidative stress in LRMD and suggests the potential for unique control points for LRMD progression and severity for dairy cows in early lactation. This may allow researchers to evaluate early treatment options and producers to group cows to more precisely manage them according to susceptibility to LRMD.

3. Identified plasma essential amino acid concentration profiles that are associated with dairy cow performance. Dairy cows typically utilize dietary protein with low efficiency for milk protein production resulting in high feed costs and excess nitrogen excretion into the environment. Feeding cows more precisely to meet their essential amino acid (EAA) requirements would result in improved cost and nitrogen use efficiency, but knowledge of the amount and proportion of EAA required for optimizing milk protein production and nutrient use efficiency is incomplete. Whereas most studies evaluate each EAA individually, dairy cows require an adequate amount and proportion of all EAA. To better understand the association of plasma EAA concentration with dairy cow productivity, ARS researchers in Madison, Wisconsin, in collaboration with scientists from the University of Wisconsin-Madison, performed a study that allowed for an evaluation of the whole plasma EAA profile and to determine if there is a profile of EAA that is most closely associated with dairy cow production responses. Dairy cow plasma EAA concentrations were grouped into two distinct clusters that were highly associated with productivity. This information will be important for researchers and dairy cow nutritionists when evaluating the EAA feeding strategy for optimizing productivity and nitrogen use efficiency.

4. New fiber digestion kinetics evaluations support simpler, more efficient options to evaluate diets and feeds to support nutritional needs of dairy cows. Fiber digestion kinetics describe factors important to determining the value of fiber in a cow’s diet for supporting her nutritional requirements, health, and performance. Among the kinetics values, estimating the proportions of indigestible and potentially digestible pools of fiber and the rate of fermentation of the latter are among the most important. In collaborative work with a mathematical modeler, ARS researchers from Madison, Wisconsin, found that using just 2-pools of ruminal fiber fit more of the forages tested and gave more reliable and less variable values as opposed to using a more complex approach which split the digestible pool into fast and slowly fermented fiber fractions each with its own fermentation rate. When used to predict the amount of fiber that would be fermented to release nutrients to the cow, the difference between the 2-pool and 3-pool models was minimal. The work affirmed that the simpler 2-pool model was appropriate to use for estimation of kinetics values. Kinetics values are determined using in vitro fermentation time courses measuring fiber use by rumen microbes; some recommended fermentations extend as long as 10 days. By comparing 2-pool kinetics values calculated from the full 11 time point data sets to those from data sets with hour sampling points removed, we found that the fermentation time could be reduced to 72 hours – a time reduction of seven days – and that it was important to retain time points early in the fermentation. Researchers and analytical laboratories can use these more robust and simplified kinetics calculations and use of much shorter fermentation time courses to make more efficient use of laboratory resources and provide fiber digestibility information more quickly for use in designing diets to support the nutritional needs of cows.

U.S. DEPARTMENT OF AGRICULTURE

Cell Wall Biology and Utilization Research: Madison, WI