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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Research Project #439748

Research Project: Assembly and Annotation of Rumen Protist Genomes to Determine their Metabolic Contribution and Environmental Presence

Location: Cell Wall Biology and Utilization Research

Project Number: 5090-31000-028-047-A
Project Type: Cooperative Agreement

Start Date: Feb 1, 2021
End Date: Jan 31, 2025

We propose to generate reference quality assemblies for the rumen protist populations to aid further research into their ecological significance in cattle rumen and methane emissions/feed efficiency.

To reduce the difficulty in separating protist genomes from bacterial and archaeal genomes in silico, we have developed a method of low-g centrifugation that greatly enriches the protist composition of a rumen sample. We will then sequence existing protist enrichment samples to generate high fidelity (HiFi) reads with lower error rates. We will then assemble HiFi reads into contigs and annotate those contigs with gene loci. We will then use high-throughput sequencing read data to bin protist contigs and to identify potential associations with bacteria that would suggest a predator-prey relationship. This data will be further explored to identify the metabolic impact of rumen protist presence in the rumen, by identifying the metabolic contribution of prey bacteria to the rumen ecosystem. Finally, we will develop markers that distinguish between rumen protist species and use them in amplicon sequencing experiments on eight cannulated holstein cows. After validating these markers, we will then test environmental samples in the vicinity of these cows to identify potential surfaces that could spread protists to other animals.