Author

L. A. David

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 7 Ecology· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 8 Approach:experimental assay· 7 Assay:metagenomics· 7 Research Focus:cell type annotation· 4 Assay:bulk RNA-seq· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Research Focus:ecology & biodiversity· 2

Frequent Co-Authors

J. D. Silverman· 5 shared Z. C. Holmes· 5 shared S. Jiang· 4 shared E. P. Dallow· 3 shared H. K. Durand· 3 shared J. Letourneau· 3 shared J. F. Rawls· 2 shared A. A. Weil· 1 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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5 shared papersMicrobiology

J. D. Silverman

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

Interplay between particle size and microbial ecology in the gut microbiome

J. Letourneau, V. M. Carrion, S. Jiang, O. W. Osborne, Z. C. Holmes, A. Fox, P. Epstein, C. Y. Tan, M. Kirtley, N. K. Surana, L. A. David

This study investigates the factors influencing fecal particle size in humans and finds that gut microbiota, rather than diet or behavior, primarily shape particle size.

bioRxiv · Apr 26, 2024Microbiology

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

J. Letourneau, L. Walker, S. H. Han, L. A. David, N. Younge

This study identifies fecal pH and redox as potential biomarkers for metabolic state in preterm infants by linking them to microbiome composition and clinical outcomes.

bioRxiv · Aug 14, 2023 · PreprintMicrobiology

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

Z. C. Holmes, M. M. Villa, H. K. Durand, S. Jiang, E. P. Dallow, B. L. Petrone, J. D. Silverman, P.-H. Lin, L. A. David

The paper investigates how gut microbiota respond to different prebiotics within individuals and links these responses to habitual fiber intake.

bioRxiv · Jun 26, 2021Microbiology

Ecological memory of prior nutrient exposure in the human gut microbiome

J. Letourneau, Z. C. Holmes, E. P. Dallow, H. K. Durand, S. Jiang, S. K. Gupta, A. C. Mincey, M. J. Muehlbauer, J. R. Bain, L. A. David

The paper shows the human gut microbiome retains a memory of past carbohydrate exposures, enhancing future metabolic responses through rapid transcriptional changes.

bioRxiv · Jun 21, 2021Ecology

Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice

Z. C. Holmes, J. D. Silverman, H. K. Dressman, Z. Wei, E. P. Dallow, S. C. Armstrong, P. C. Seed, J. F. Rawls, L. A. David

This study examines SCFA production by gut microbiota from children with obesity in response to different prebiotics, finding significant inter-donor variation and donor-dependent effectiveness.

mBio · Aug 25, 2020Peer-reviewedMicrobiology

Conserved anti-inflammatory effects and sensing of butyrate in zebrafish

P. M. Cholan, A. Han, B. R. Woodie, A. R. Kurz, W. J. Britton, L. Ye, Z. C. Holmes, J. R. McCann, L. A. David, J. F. Rawls, S. H. Oehlers

The paper shows that butyrate, a short-chain fatty acid, has anti-inflammatory effects in zebrafish by reducing neutrophil and M1 macrophage recruitment to wounds, and identifies a conserved receptor for butyrate sensing in fish.

bioRxiv · May 13, 2020Immunology

Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study

I. Levade, M. M. Saber, F. S. Midani, F. Chowdhury, A. I. Khan, Y. Begum, E. T. Ryan, L. A. David, S. B. Calderwood, J. B. Harris, R. C. LaRocque, F. Qadri, B. J. Shapiro, A. A. Weil

This study uses metagenomic sequencing to predict cholera infection and disease severity in a cohort, identifying protective bacterial species and genes.

bioRxiv · Feb 25, 2020Microbiology

High-throughput isolation and culture of human gut bacteria with droplet microfluidics

M. Villa, R. J. Bloom, J. D. Silverman, H. K. Durand, S. Jiang, A. Wu, S. Huang, L. You, L. A. David

The paper develops a droplet microfluidics platform to isolate and culture human gut bacteria, demonstrating its use in studying metabolic variation and growth kinetics.

bioRxiv · May 7, 2019 · PreprintMicrobiology

Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies

J. D. Silverman, L. Shenhav, E. A. Halperin, S. A. Mukherjee, L. A. David

This paper reviews statistical challenges in longitudinal microbiome studies and provides guidelines for design and analysis.

bioRxiv · Oct 20, 2018 · PreprintMicrobiology

Phylofactorization - a graph partitioning algorithm to identify phylogenetic scales of ecological data

A. D. Washburne, J. D. Silverman, J. T. Morton, D. Becker, D. Crowley, S. Mukherjee, L. A. David, R. K. Plowright

This paper introduces Phylofactorization, a graph-partitioning algorithm to identify phylogenetic scales in ecological data, and demonstrates its application to mammalian body mass and gut microbiome studies.

bioRxiv · Jan 3, 2018Ecology