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The Ozcam Lab shotgun metagenome pipeline is live
Developed in collaboration with the Institute for Genome Sciences (IGS) and IFX, this platform was built to streamline large scale microbiome analyses while maintaining consistency across cohorts and studies. It integrates state of the art functional annotation with HUMAnN 4, alongside taxonomic profiling using Kraken and Sourmash. Designed for scale, the pipeline can process thousands of samples, which is essential for our longitudinal studies where individuals are sampled repeatedly from birth through allergic disease development. This enables us to capture both microbial composition and functional capacity over time and identify features associated with allergic disease risk. Beyond supporting our own studies, the pipeline allows us to deliver high quality, harmonized shotgun metagenome data for collaborators. These efforts feed directly into our broader goal of testing mechanistic hypotheses in vitro, in vivo, and organoid models, with the aim of developing microbiome targeted prevention strategies such as diet based interventions and live biotherapeutics to reduce allergic disease risk in high risk children.
Image description. Infographic showing a longitudinal study design for infants at high risk for FA. The top panel illustrates 8 time points from birth through early childhood, with repeated sample collection. Outcomes include either food allergy diagnosis or healthy status. The middle panel shows microbiome analysis using a shotgun metagenome pipeline from the Ozcam Lab, including functional and taxonomic profiling and large scale harmonized data processing with network, strain, machine learning, and multi-omics analyses. The lower panel depicts preclinical testing in in vitro, in vivo, and organoid models, followed by intervention strategies such as dietary modification and live biotherapeutics. A circular flow connects these steps to data integration across transcriptomics, metabolomics, proteomics, and patient metadata, ultimately supporting prevention and improved health outcomes in high risk children.
Jakobi and Lina present at the M3 Microbiome Symposium
Jakobi and Lina present at the M3 Microbiome Symposium
Jakobi, a previous rotation student from the MMI program, and Lina, our undergraduate researcher and lab manager, presented their work at the M3 Meetup: Symposium in Engineering and Analytics in Microbiome Research at the University of Maryland. M3 is a regional meeting that brings together microbiome scientists to share advances in engineering, computational analytics, and experimental approaches to studying complex microbial communities. Their work focused on identifying gut microbiome-derived metabolites associated with epinephrine use and adverse reactions during peanut oral immunotherapy.
NIAID-DP2 NIH Director’s New Innovator Award
NIAID-DP2 NIH Director’s New Innovator Award
Our laboratory has received support through a NIAID-DP2 NIH Director’s New Innovator Award, part of the NIH High-Risk, High-Reward Research Program. This award will support research investigating how the early-life gut microbiome influences food allergy development and resolution, with an emphasis on translational applications.
We acknowledge the support of NIH and NIAID, as well as collaborators who contributed to this work. In addition, we thank the Immune Tolerance Network for providing clinical samples central to this study. This funding will support efforts to address knowledge gaps in microbiome and food allergy research while contributing to the training of researchers in this area.
Podcast Episode with ReachMD
Emerging research is redefining the role of the gut microbiome in food allergy and immune tolerance. In the Translational Microbiome and Immune Tolerance Laboratory, we investigate how gut microbes metabolize allergenic proteins, shape immune development, and may serve as biomarkers to predict the success of oral immunotherapy in patients with food allergy.
We recently discussed these findings at the 2026 Annual Meeting of the American Academy of Allergy, Asthma & Immunology. Our work focuses on understanding how microbial functions in the gut influence allergic disease and how these insights can be translated into new strategies for predicting treatment responses and improving therapies.
Breaking Down Biology for Oral Immunothereapy and Microbiome
Breaking Down Biology for Oral Immunothereapy and Microbiome
Mustafa recently joined the Breaking Down Biology blog and podcast to discuss research exploring how the gut microbiome may influence outcomes of peanut oral immunotherapy (POIT).
The interview highlights findings from the Immune Tolerance Network IMPACT clinical trial, which identified links between gut microbial metabolism, bile acid profiles, and treatment response. This feature provides an accessible overview of the study design, key findings, and clinical implications for microbiome-informed strategies to improve food allergy therapies.
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New Paper
New Paper
We are excited to share our recent publication in Nature Communications titled Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure. Using integrated multi-omics analyses of samples from the IMPACT clinical trial, this study demonstrates that gut microbiome metabolic activity prior to treatment can predict peanut oral immunotherapy outcomes and reveals microbial protein and bile acid metabolism as potential mechanisms underlying treatment failure. These findings highlight the importance of microbiome-derived metabolic functions as biomarkers and therapeutic targets to improve food allergy immunotherapy efficacy.
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