# Gut Microbial Factors in Farming Lifestyle and Allergic Sensitization

> **NIH NIH U19** · UNIVERSITY OF ROCHESTER · 2024 · $300,399

## Abstract

PROJECT SUMMARY/ABSTRACT – PROJECT 1
Atopic diseases, including atopic dermatitis (AD), food allergy (FA), allergic rhinitis, and asthma, are the most
common chronic medical conditions affecting children in the US, and prevention strategies remain largely
unsuccessful. While the risk of asthma is reduced in infants with a farming lifestyle, which includes exposure to
a diverse microbiome in early life, the microbial mechanisms of protection against AD and FA under this lifestyle
are still being investigated. Multiple bacterial metabolites have been also explored for their connection with atopic
disease: short-chain fatty acids (SCFA), which can induce the differentiation of anti-inflammatory colonic Tregs,
tryptophan metabolism, which modulates epithelial barrier permeability, or bile acids, which regulate T-cell
differentiation in the lamina propria. Our published and preliminary results demonstrate that, compared to infants
from urban/suburban Rochester (ROC), the traditional agrarian community of Old Order Mennonites (OOM) are
protected against atopic diseases and harbor a distinct gut bacterial community, including an enrichment in
Bifidobacteria and Clostridia species, suggesting that lifestyle and early life microbiome accelerate
immunocompetence and might play a protective role in atopic diseases. The goals of this proposal are to
determine how the gut microbiome and its byproducts develop in infants to modulate the risk of atopic diseases,
to identify microbial and metabolite biomarkers to screen high-risk infants, and to assess mechanisms associated
with protective innate and adaptive immune markers and skin barrier integrity and microbiome by integration of
data with Projects 2 and 3. Our central hypothesis is that the microbiome of infants who do not develop
AD and FA modulates the bacterial metabolite pool that confers protection or risk of atopic disease. We
hypothesize that the gut microbiome of non-atopic urban Rochester infants and OOM infants will be enriched in
species with anti-inflammatory properties and genes related to short-chain fatty acid production, lactic acid
metabolism, and tryptophan and bile acid metabolism, as well as an accelerated gut microbiome maturation
compared with atopic infants. In parallel, we will also assess the fecal metabolome of OOM and ROC infants,
and test its association with atopic outcomes: we hypothesize that tryptophan, short-chain fatty acids and bile
acids will be differential between atopic and non-atopic infants, and that correlations between microbiome and
metabolome will also be differential based on health outcomes. Finally, we will evaluate the longitudinal
development of the gut microbiome and metabolome to identify groups of infants with similar changes over time
that are associated with atopic disease, as well as with biomarkers from Projects 2 and 3. The rational design of
our strategy will identify novel bacterial and metabolite biomarkers that are associated with protection or ri...

## Key facts

- **NIH application ID:** 10823352
- **Project number:** 5U19AI175113-02
- **Recipient organization:** UNIVERSITY OF ROCHESTER
- **Principal Investigator:** Jose C Clemente
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $300,399
- **Award type:** 5
- **Project period:** 2023-04-07 → 2028-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10823352

## Citation

> US National Institutes of Health, RePORTER application 10823352, Gut Microbial Factors in Farming Lifestyle and Allergic Sensitization (5U19AI175113-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10823352. Licensed CC0.

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