# Spatially Organized Bacterial Interaction Networks in the Gut Microbiota

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA SANTA CRUZ · 2023 · $378,567

## Abstract

SUMMARY
Each adult human harbors hundreds of bacterial species in their intestine. However, the networks of microbe-
microbe interactions that underly the stable co-existence of resident species, and exclude additional species,
are not well defined. The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and dietary
plant cell wall fragments are distributed with high heterogeneity, and redistributed on the time scale of seconds.
We propose that bacteria selectively adhere to dietary particles in the gut lumen and that interactions with their
co-adherent microbial partners dictate whether they persist. We created multiplex libraries of artificial food
particles (consisting of glycan-coated magnetic beads) to measure gut bacterial adhesion in vivo, and
discovered that many members of the phylum Bacteroidetes adhere to dietary glycan particles in a strain-
specific and glycan-specific manner. We will first identify families of adhesion proteins required for these
binding phenotypes using transposon mutagenesis and insertion site sequencing. Next, we will identify
networks of interacting strains that co-adhere to dietary particles. Using orally administered libraries of
fluorescently labeled beads, we will map co-adhesion networks in gnotobiotic mice colonized with strains that
have evolved together in a single donor host. Finally, we will establish a mutational selection strategy that
permits the simultaneous generation of different binding specificities in genetically intractable gut microbes.
Analysis of these mutations will reveal the potential origins of adhesion-dependent interspecies relationships.
These studies will shed light on the poorly defined spatial structure of the gut microbiota. The technologies we
develop in this proposal hold promise as a means to intentionally position the members of microbial
communities in physical configurations that prevent or ameliorate metabolic, immunologic, and infectious
diseases.

## Key facts

- **NIH application ID:** 10715436
- **Project number:** 1R35GM150732-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA SANTA CRUZ
- **Principal Investigator:** Michael L Patnode
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $378,567
- **Award type:** 1
- **Project period:** 2023-07-20 → 2028-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10715436

## Citation

> US National Institutes of Health, RePORTER application 10715436, Spatially Organized Bacterial Interaction Networks in the Gut Microbiota (1R35GM150732-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10715436. Licensed CC0.

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