Spotlight on Our AVITI™ for All Grant Winner and Gut Microbiomes

Innovative genomics solutions require the creativity of scientists and the funding to move research forward at a competitive pace. The inaugural grant in the AVITI Accelerator Grant Program, the 2023 AVITI for All Grant, created the opportunity to advance any research from cancer genomics, plant science, animal science, or metagenomics to any other field of biology. Avidity base chemistry—the unique technology that powers AVITI sequencing—supports a broad spectrum of applications, in turn allowing us to make this opportunity available to virtually any area of research.

For the 2023 AVITI for All Grant, offered in partnership with AVITI service provider AUGenomics, Element Biosciences received many applications reflecting a brilliant diversity of research areas and ideas. From among all the excellent submissions, Element chose a winner who proposed deepening a microbiome study with isolate sequencing while giving undergraduates an opportunity to publish.

Patrick Degnan, PhD, Associate Professor, University of California, Riverside

Exploring complex microbial communities

The winning proposal explores how the gut microbiome mediates the metabolic impact of thiamine supplementation on consumption of a high-fat diet. At University of California, Riverside (UCR), Patrick Degnan seeks to understand how individual species contribute to the overall functioning of complex microbial communities through a combination of metagenomics, isolate cultivation, and molecular genetics. One area of interest is understanding how dietary deficiencies in vitamins such as thiamine (vitamin B1)—a deficiency that occurs even in developed countries—can confer a range of deleterious health effects.

In previous experiments, Degnan and his UCR colleagues have shown that thiamine supplementation has a protective effect for mice fed a soybean oil high fat diet (SO-HFD), reducing weight gain by ~40% over the course of 18 weeks. To explore how thiamine can drive such different metabolic outcomes, his lab is delving more deeply into the mouse fecal microbiomes. Students taking Degnan’s experimental microbiology course have isolated ≥ 1000 anaerobic gut bacterial strains from the fecal pellets of study mice, identifying numerous microbes that are unique to each treatment group.

Sequencing isolated strains

With additional library prep support from Quantabio, the 2023 AVITI for All Grant empowers Degnan and his team to start sequencing isolated strains, providing insights into the functional capacities of microbes that vary in abundance between mice on different diets. Students will conduct assembly analyses and the annotation of sequencing data. The students will also have the opportunity to publish their results as first author in Microbiology Resource Announcements (MRA), an American Society for Microbiology (ASM) journal.

We are excited to support Patrick’s work as both a researcher and an educator, and to find new avenues for continuing the work of making sequencing accessible to all. Helping drive innovation and supporting students is certainly a highlight.

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