Explanipedia

From stool to sequence: decoding the human diet with FoodSeq Open

Dorothy K. Superdock, Brianna L. Petrone, Michelle C. Kirtley, Lawrence A. David · 2025

Diet plays a pivotal role in human health and disease. Yet, nutrition studies have long relied on self-report methods for collecting dietary intake data despite known limitations. Although new technologies for dietary intake assessment and…

Stool Genomics for Enhanced Monitoring of Nutrition Interventions in Childhood Malnutrition Open

Ammara Aqeel, Najeeha Talat Iqbal, Sanam Iram Soomro, Sheraz Ahmed, Torin McDonald , et al. · 2025

Ready-to-use therapeutic and supplementary foods (RUTF/RUSF) are a primary treatment for childhood malnutrition, but measuring intervention compliance is labor intensive. We applied FoodSeq, a fecal genomic dietary assessment biomarker, in…

Small intestinal microbial fiber metabolism dysfunction in celiac disease Open

Elena F. Verdú, Mark Wulczynski, Marco Constante, Heather J. Galipeau, Jedid-Jah Blom , et al. · 2025

Personalized Genomic Dietary Data Return to Incentivize Research Participation and Develop Nutrition Education: Study Protocol Open

Kylie Reed, Caroline Rivera, Ammara Aqeel, Matthew J. Gedye, Lawrence A. David · 2025

DNA Metabarcoding as a Tool for Dietary Intake Analysis in Inflammatory Bowel Disease Open

Dorothy K. Superdock, Nolan Ives, Anna C. Salvador, Shehzad Sheikh, Lawrence A. David · 2025

Dietary plant diversity predicts early life microbiome maturation Open

Torin McDonald, Ammara Aqeel, Ben Neubert, A. Bauer, Sharon Jiang , et al. · 2025

Summary Despite established links between the infant gut microbiome and health, how complementary feeding shapes colonization remains unclear. Using FoodSeq, a DNA-based dietary assessment technique, we surveyed food intake across 729 chil…

Branched chain amino acid metabolism and microbiome in adolescents with obesity during weight loss therapy Open

Jessica R. McCann, Chengxin Yang, Nathan A. Bihlmeyer, Runshi Tang, Tracy Truong , et al. · 2025

BACKGROUND Obesity and weight loss in adults have been associated with distinct metabolome and gut microbiome features, but the extent to which those associations apply to adolescent stages remain unclear. METHODS The Pediatric Obesity Mic…

Dietary Plant Diversity Predicts Early Life Microbiome Maturation Open

Torin McDonald, Ammara Aqeel, Ben Neubert, A. Bauer, Sharon Jiang , et al. · 2025

A pilot study of metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans Open

Brianna L. Petrone, Alexandria Bartlett, Sharon Jiang, Abigail Korenek, Simina Vintila , et al. · 2024

In a pilot study of five individuals, we evaluated the concordance between conventional diet records and DNA- and protein-based biomarkers of food intake in their stool.

Weight, habitual fibre intake, and microbiome composition predict tolerance to fructan supplementation Open

Jeffrey Letourneau, Benjamin C. Neubert, Diana Dayal, Verónica M Carrion, Heather K. Durand , et al. · 2024

Fructans are commonly used as dietary fibre supplements for their ability to promote the growth of beneficial gut microbes. However, fructan consumption has been associated with various dosage-dependent side effects. We characterised side …

Interplay between particle size and microbial ecology in the gut microbiome Open

Jeffrey Letourneau, Verónica M Carrion, Sharon Jiang, Olivia Osborne, Zachary C. Holmes , et al. · 2024

Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. H…

Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans Open

Brianna L. Petrone, Alexandria Bartlett, Sharon Jiang, Abigail Korenek, Simina Vintila , et al. · 2024

Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin or hair, but detection of consumed foods in stool has also been…

The Binding Properties of Antibodies to Z-DNA in the Sera of Normal Healthy Subjects Open

David S. Pisetsky, Matthew J. Gedye, Lawrence A. David, Diane M Spencer · 2024

Antibodies to DNA are a diverse set of antibodies that bind sites on DNA, a polymeric macromolecule that displays various conformations. In a previous study, we showed that sera of normal healthy subjects (NHS) contain IgG antibodies to Z-…

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome Open

Jeffrey Letourneau, LaShawndra Walker, Se Hyang Han, Lawrence A. David, Noelle Younge · 2024

The infant gut microbiome is a crucial factor in health and development. In preterm infants, altered gut microbiome composition and function have been linked to serious neonatal complications such as necrotizing enterocolitis and sepsis, w…

Ultra-processed food intake, gut microbiome, and glucose homeostasis in mid-life adults: Background, design, and methods of a controlled feeding trial Open

Bailey T. Capra, Summer Hudson, Mckenna Helder, Eleni Laskaridou, Aubrey L. Johnson , et al. · 2024

Interplay between particle size and microbial ecology in the gut microbiome Open

Jeffrey Letourneau, Verónica M Carrion, Jun‐Jie Zeng, Sharon Jiang, Olivia Osborne , et al. · 2024

Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. H…

Fecal pH and redox as functional markers in the premature infant gut microbiome Open

Jeffrey Letourneau, LaShawndra Walker, Se Hyang Han, Lawrence A. David, Noelle Younge · 2023

The infant gut microbiome is a crucial factor in health and development. In preterm infants, altered gut microbiome composition and function have been linked to serious neonatal complications such as necrotizing enterocolitis and sepsis, w…

PTFS09-05-23 Impact of an Online Grocery Shopping Intervention in Children With Obesity Assessed Through a Novel Dietary DNA Biomarker Method Open

Ammara Aqeel, Chengxin Yang, Tracy Truong, Jun Zeng, Brianna L. Petrone , et al. · 2023

P14-066-23 Dietary Patterns Identified Through DNA Metabarcoding and Their Association With Geographic Location and Health Indicators Open

Benjamin C. Neubert, Brianna L. Petrone, Sharon Jiang, Lara R. Dugas, Candice Choo-Kang , et al. · 2023

Diversity of plant DNA in stool is linked to dietary quality, age, and household income Open

Brianna L. Petrone, Ammara Aqeel, Sharon Jiang, Heather K. Durand, Eric P. Dallow , et al. · 2023

Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL -P6 marker to 1,029 fecal samples from 324 parti…

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression Open

Lauren Davey, Per Malkus, Max M. Villa, Lee Dolat, Zachary C. Holmes , et al. · 2023

Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity Open

Firas S. Midani, Lawrence A. David · 2023

Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cros…

Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana Open

Sweta Patel, John Farirai, Mohamed Z. Patel, Sefelani Boiditswe, Leabaneng Tawe , et al. · 2022

Children living with HIV (CLWH) are at high risk of colonization and infection by bacterial respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on develo…

Horizontal gene transfer enables programmable gene stability in synthetic microbiota Open

Teng Wang, Andrea Weiss, Ammara Aqeel, Feilun Wu, Allison J. Lopatkin , et al. · 2022

Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease Open

Zachary C. Holmes, Helen Tang, Congxiao Liu, Amy Bush, Benjamin C. Neubert , et al. · 2022

Previous studies suggest that gut microbiome disruption induced by chemotherapy, dietary deficiencies, and/or antibiotics are associated with increased incidence of acute graft-versus-host disease (aGVHD) following hematopoietic stem cell …

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake Open

Zachary C. Holmes, Max M. Villa, Heather K. Durand, Sharon Jiang, Eric P. Dallow , et al. · 2022

Ecological memory of prior nutrient exposure in the human gut microbiome Open

Jeffrey Letourneau, Zachary C. Holmes, Eric P. Dallow, Heather K. Durand, Sharon Jiang , et al. · 2022

Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structur…

DNA metabarcoding captures dietary plant diversity in individuals and cohorts Open

Brianna L. Petrone, Ammara Aqeel, Sharon Jiang, Heather K. Durand, Eric P. Dallow , et al. · 2022

Eating a varied diet is a central tenet of good nutrition. Here, we develop the first molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL -P6 marker to 1,001 fecal samples from 3…

Multicolor flow cytometry of monocultures and co-cultures of Bacteroides species Open

Firas S. Midani, Lawrence A. David · 2022

Dataset of FCS (Flow Cytometry Standard) files, along with meta-data, related to a flow cytometry analysis of monocultures and co-cultures of Bacteroides species under several different conditions. Data Collection. This dataset accompanies…

Mucin foraging enables Akkermansia muciniphila to compete against other microbes in the gut and to modulate host sterol biosynthesis Open

Lauren Davey, Per Malkus, Max M. Villa, Lee Dolat, Zachary Holmes , et al. · 2022

Akkermansia muciniphila, a prominent member of the gastrointestinal tract (GI) microbiota, uses mucins as a sole source of carbon and nitrogen. A. muciniphila is considered a next-generation probiotic because its abundance in humans positi…

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