**AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** SUSTAINABLE DAIRY AND BEEF PRODUCTION ARE A MAJOR GOAL OF US AGRICULTURAL RESEARCH. IN ORDER TO INCREASE PRODUCER PROFITS AND REDUCE ENVIRONMENTAL IMPACTS, WE MUST IDENTIFY INEFFICIENCIES IN THE SYSTEM AND PROVIDE DATA-DRIVEN RECOMMENDATIONS FOR ANIMAL HUSBANDRY. MUCH PROGRESS HAS BEEN MADE IN THE FIELDS OF CATTLE GENETICS AND ANIMAL NUTRITION TOWARDS SUSTAINABLE PRODUCTION; HOWEVER, A MAJOR COMPONENT OF BEEF AND DAIRY SYSTEMS REMAINS LARGELY UNCHARACTERIZED: THE RUMEN MICROBIOME. RESPONSIBLE FOR ALL OF THE DIGESTION OF FEED AND PLANT MATERIALS FOR THE HOST COW, THE MICROBES OF THE RUMEN REPRESENT A COMPOSITE OF THOUSANDS OF DIFFERENT SPECIES EACH WITH DIFFERENT IMPACT ON THE COW'S FEED EFFICIENCY. BACTERIA ARE TYPICALLY THE DIGESTERS OF FIBER IN THE RUMEN, WHEREAS ARCHAEA ARE THE PRIMARY METHANE PRODUCERS -- THE GREENHOUSE GAS THAT IS OVER 35 TIMES MORE POTENT THAN CARBON DIOXIDE. MIXED IN WITH BACTERIAL AND ARCHAEAL CELLS IN THE RUMEN MICROBIOME ARE CILIATED PROTOZOA CELLS THAT NAVIGATE RUMEN FLUID TO CONSUME BACTERIA, PLANT MATERIALS OR CHEMICALS.BEING APPROXIMATELY 100 TIMES LARGER THAN THE AVERAGE RUMEN BACTERIAL CELLS, THESE PROTOZOA ARE THE EQUIVALENT OF WHALES IN THE OCEAN OF THE RUMEN DIGESTA; HOWEVER, WE KNOW VERY LITTLE ABOUT THEIR BIOLOGY AND IMPACTS ON THE SYSTEM. THERE ARE MANY SIGNS THAT THE PROTOZOA ARE MORE DIVERSE IN FUNCTION AND GENETICS THAN WE HAVE PRESENTLY OBSERVED, BUT WE LACK SUFFICIENT TOOLS TO IDENTIFY DIFFERENCES IN EACH SPECIES ON A GENETIC LEVEL. UNLIKE THE BACTERIA, PROTOZOA ARE NOT ESSENTIAL TO CATTLE RUMEN FUNCTION SO THEY CAN BE REMOVED FROM THE SYSTEM WITHOUT MAJOR DETERIMENTAL EFFECTS TO THE COW.OBSERVATIONS HAVE BEEN MADE THAT PROTOZOA INCREASE THE AMOUNT OF METHANE EMITTED BY THE COW, BUT ONLY ANECDOTAL EVIDENCE EXISTS AS TO WHY THIS IS THE CASE. TO BEGIN TO UNRAVEL THE IMPACTS OF PROTOZOA ON CATTLE RUMEN FUNCTION, WE NEED TO DEVELOP GENETIC TOOLS TO IDENTIFY THEM IN THE COW AND HER ENVIRONMENT. USING THE LATEST IN DNA SEQUENCING TECHNOLOGIES, WE PLAN TO CREATE DETAILED GENETIC MAPS OF EACH PROTOZOA SPECIES SO THAT THEY CAN BE INVESTIGATED FOR THEIR UNIQUE CHEMICAL AND BIOLOGICAL IMPACTS ON THE SYSTEM. IF SUCCESSFUL, WE BELIEVE OUTCOMES FROM OUR WORK WILL HAVE IMPACTS ON DAIRY AND BEEF PRODUCTION EFFICIENCY BY REDUCING GREENHOUSE GAS EMISSIONS AND CONVERTING THEM INTO IMPROVED NUTRITION FOR THE COW HERSELF.