Funded Pilot Projects 2019

The Microbiome Center is pleased to announce the 6 pilot projects we funded in Jul 2019 to promote cross-faculty research initiatives in all aspects of microbiome research.

The PIs aim to pioneer the oviparous little skate, Leucoraja erinacea, as a new model system for understanding the microbiomes of marine vertebrates by characterizing the establishment and maturation of the skate microbiome during embryonic development. We will address fundamental questions including: Do skate embryos inherit a maternal microbiome, and is this microbiome conserved in embryos from different locations? and To what extent are a subset of environmental microbes culled to form the skate microbiome and are these conserved across different locations?  Results from this pilot project will link marine vertebrate microbiome populations with water systems, host genetics, and effect on vertebrate development.


Nitrogen fixation genes in bacteria contain those that have been known for many years and some that are newly discovered. The PIs will test for nitrogen fixation genes in bacteria in coastal environments on both coasts where nitrogen fixation has been little studied. Our investigations will focus especially on coastal vegetation where nitrogen fixing bacteria may enhance primary production.

This collaboration will use microfluidics to explore single cell bacteria and phage interactions in cyanobacteria. Our goal is to develop methods to understand phage prevalence and the effects of phage on bacterial hosts in aquatic environments, while method development will have application to multiple systems.

The PIs are testing the hypothesis that a key event in chronic inflammatory diseases is the bacterial dependent upregulation of β-catenin/TCF-1 activity and expansion of Tregs with pro-inflammatory properties. These pilot data may lead to further bone marrow reconstitution studies in germ free mice and additional mechanistic studies on the role of the microbiome in modulating immune responses.

We will implant human sinus microbiota in the upper airway of mice and assay related immune responses. Our research will set the stage for detailed mechanistic experiments linking microbes with chronic mucosal inflammation in the sinuses and ultimately inform therapeutic development.


Most studies of regeneration focus on the role of gene regulation, cell migration, and genomics in the organism to delineate the mechanisms of regeneration. However, the role of the microbiome in regeneration has not been widely studied and represents a significant gap in knowledge. We bring together a strong inter-disciplinary team to investigate this exciting new area of research in segmented worms.