We are improving efficiency of gastrointestinal microbes and their animal hosts in several ways.

Tackling poor efficiency of microbial growth
Microbes are inefficient and use as little as 1/3 of cellular energy (ATP) for growth. This is a problem because protein from growing cells nourishes the ruminant. We are tackling this problem by characterizing cellular mechanisms, such energy spilling and glycogen synthesis, which are at root of poor efficiency.

Unraveling how microbes ferment carbohydrates

Ruminants rely on microbes to ferment carbohydrates found in feed.  We thought we knew how microbes carried out fermentation—biochemical pathways for fermentation have been chiseled in the stone of textbooks for decades.  We have found that many microbes are missing textbook pathways, though, and we are unraveling what pathways they use instead.  This work is important to identifying targets (enzymes) for manipulating fermentation.

Uncovering the diversity of microbes and their metabolism

Microbes are the most diverse organisms on the planet.  Additionally, they can metabolize more chemical compounds than any other group of organisms.  We are developing new tools to uncover the full scope of this diversity.  First, we have developed a tool that can accurately measure diversity from nucleotide sequences.  Our tool outperforms several leading tools developed for this purpose.  Second, we are developing a tool to extract information on metabolism buried in scientific literature.  With this tool, we plan a build a database on microbial metabolism, helping investigators discover the capabilities of microbes in their samples.

Identifying what food compounds (substrates) uncultured bacteria eat
What foods an organism eats is one of its most basic characteristics, but determining what bacteria eat is a problem because >90% have not been cultured in the lab. We have used fluorescent analogues of carbohydrates to literally see which bacteria eat what. This work is helping identify what the uncultured majority are doing and their role in the ruminant.