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Houston's Rice University data scientists learn about microbial networks from Yellowstone's Park microbial mat

Jessica Yang

HOUSTON, TX — Rice’s University Brown School of Engineering scientists are conducting a new study led by Todd Treangen on microbial networks, supported by the National Science Foundation in the form of a five-year, $2.8 million grant.

They sought to define the social order of microbiomes through developing novel computational approaches to track environmental microbiome dynamics over time, across species and after perturbations.

https://twitter.com/RiceEngineering/status/1423292470897438720?s=20

They start with observing how the microbes form their own genome exchange networks through biofilm-based “species abundance networks” on scaffolds.

The team consists of Rice co-principal investigators, computer scientist Luay Nakhleh and electrical and computer engineer Santiago Segarra, and Devaki Bhaya, a molecular biologist at the Carnegie Institution for Science.

Treangen said they would leverage microbial mats, which are multilayered sheets of microbes that exist in hot springs, in the study.

The sample analyzed for this study is a slice of microbial mat from Yellowstone Park’s Octopus Spring that will help to reveal how microbiomes interact.

The microbial mats can be sampled at varying temperatures and light gradients, Treangen said, which will allow “for robust exploratory analyses and hypothesis testing specific to any observations” they make throughout the study.

For more than five years, they hope the data can help them define the rules and rates of horizontal gene transfer in microbial networks. They can now use these rules to identify the functional redundancies and key players in every host-associated microbiome environment.

Treangen explained how they would develop ‘graph grammar’ frameworks to build similar social networks by using an analogy of Facebook interaction, such as plotting out who interacts with whom on Facebook,

“However, instead of liking a photo or commenting on a post, we will use the exchange of DNA between bacteria as a proxy for interactions,” he said.

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