Lawrence Anthony David

Education

• Ph.D. Massachusetts Institute of Technology, 2010

Positions

• Associate Professor of Molecular Genetics and Microbiology
• Associate Professor of Biomedical Engineering
• Associate of the Duke Initiative for Science & Society
• Core Faculty in Innovation & Entrepreneurship

Awards, Honors, and Distinctions

• Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2014
• Harvard Society Junior Fellows. Harvard Society of Fellows. 2010

Courses Taught

• UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V
• MGM 593: Research Independent Study
• MGM 293: Research Independent Study I

Publications

• Petrone BL, Bartlett A, Jiang S, Korenek A, Vintila S, Tenekjian C, et al. A pilot study of metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans. Food Funct. 2024 Dec 12;
• Letourneau J, Neubert BC, Dayal D, Carrion VM, Durand HK, Dallow EP, et al. Weight, habitual fibre intake, and microbiome composition predict tolerance to fructan supplementation. Int J Food Sci Nutr. 2024 Sep;75(6):571–81.
• Letourneau J, Carrion VM, Jiang S, Osborne OW, Holmes ZC, Fox A, et al. Interplay between particle size and microbial ecology in the gut microbiome. bioRxiv. 2024 Apr 27;
• Petrone BL, Bartlett A, Jiang S, Korenek A, Vintila S, Tenekjian C, et al. Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans. 2024.
• Pisetsky DS, Gedye MJ, David LA, Spencer DM. The Binding Properties of Antibodies to Z-DNA in the Sera of Normal Healthy Subjects. Int J Mol Sci. 2024 Feb 22;25(5).
• Capra BT, Hudson S, Helder M, Laskaridou E, Johnson AL, Gilmore C, et al. Ultra-processed food intake, gut microbiome, and glucose homeostasis in mid-life adults: Background, design, and methods of a controlled feeding trial. Contemp Clin Trials. 2024 Feb;137:107427.
• Letourneau J, Carrion VM, Zeng J, Jiang S, Osborne OW, Holmes ZC, et al. Interplay between particle size and microbial ecology in the gut microbiome. ISME J. 2024 Jan 8;18(1).
• Letourneau J, Walker L, Han SH, David LA, Younge N. A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome. PLoS One. 2024;19(1):e0290598.
• Letourneau J, Walker L, Han SH, David LA, Younge N. Fecal pH and redox as functional markers in the premature infant gut microbiome. 2023.
• Davey LE, Malkus PN, Villa M, Dolat L, Holmes ZC, Letourneau J, et al. A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression. Nat Microbiol. 2023 Aug;8(8):1450–67.
• Petrone BL, Aqeel A, Jiang S, Durand HK, Dallow EP, McCann JR, et al. Diversity of plant DNA in stool is linked to dietary quality, age, and household income. Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2304441120.
• Holmes ZC, Tang H, Liu C, Bush A, Neubert BC, Jiao Y, et al. Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease. Blood. 2022 Nov 24;140(21):2300–4.
• Letourneau J, Holmes ZC, Dallow EP, Durand HK, Jiang S, Carrion VM, et al. Ecological memory of prior nutrient exposure in the human gut microbiome. ISME J. 2022 Nov;16(11):2479–90.
• Wang T, Weiss A, Aqeel A, Wu F, Lopatkin AJ, David LA, et al. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat Chem Biol. 2022 Nov;18(11):1245–52.
• Holmes ZC, Villa MM, Durand HK, Jiang S, Dallow EP, Petrone BL, et al. Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. Microbiome. 2022 Jul 29;10(1):114.
• Wu F, Ha Y, Weiss A, Wang M, Letourneau J, Wang S, et al. Modulation of microbial community dynamics by spatial partitioning. Nat Chem Biol. 2022 Apr;18(4):394–402.
• Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, et al. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. mSystems. 2022 Feb 22;7(1):e0137421.
• Midani FS, David LA. Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity. Front Microbiol. 2022;13:910390.
• Silverman JD, Roche K, Holmes ZC, David LA, Mukherjee S. Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes. Journal of Machine Learning Research. 2022 Jan 1;23.
• Davey L, Malkus P, Villa M, Dolat L, Holmes Z, Letourneau J, et al. Mucin foraging enables Akkermansia muciniphila to compete against other microbes in the gut and to modulate host sterol biosynthesis. Research Square. 2022.
• Silverman JD, Bloom RJ, Jiang S, Durand HK, Dallow E, Mukherjee S, et al. Measuring and mitigating PCR bias in microbiota datasets. PLoS Comput Biol. 2021 Jul;17(7):e1009113.
• Becken B, Davey L, Middleton DR, Mueller KD, Sharma A, Holmes ZC, et al. Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila. mBio. 2021 May;12(3):e00478–e00421.
• McCann JR, Bihlmeyer NA, Roche K, Catherine C, Jawahar J, Kwee LC, et al. The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. Obesity (Silver Spring). 2021 Mar;29(3):569–78.
• Levade I, Saber MM, Midani FS, Chowdhury F, Khan AI, Begum YA, et al. Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study. J Infect Dis. 2021 Feb 3;223(2):342–51.
• David LA, Holmes ZC, Villa MM, Durand HK, Jiang S, Dallow EP, et al. Individual Variation in Prebiotic Response. In: IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL. 2021. p. S11–S11.
• Letourneau J, Holmes Z, Dallow E, Durand H, Jiang S, Gupta S, et al. Ecological memory of prior nutrient exposure in the human gut microbiome. 2021;
• Holmes Z, Villa M, Durand H, Jiang S, Dallow E, Petrone B, et al. Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. 2021;
• Cholan PM, Han A, Woodie BR, Watchon M, Kurz AR, Laird AS, et al. Conserved anti-inflammatory effects and sensing of butyrate in zebrafish. Gut Microbes. 2020 Nov 9;12(1):1–11.
• Holmes ZC, Silverman JD, Dressman HK, Wei Z, Dallow EP, Armstrong SC, et al. Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition. mBio. 2020 Aug 11;11(4).
• Villa MM, Bloom RJ, Silverman JD, Durand HK, Jiang S, Wu A, et al. Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture. mSystems. 2020 Jun 30;5(3).
• Nimmagadda SN, Midani FS, Durand H, Reese AT, Murdoch CC, Nicholson BP, et al. Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection. 2020 Apr 17;
• Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, et al. The emergence of microbiome centres. Nat Microbiol. 2020 Jan;5(1):2–3.
• Silverman JD, Roche K, Mukherjee S, David LA. Naught all zeros in sequence count data are the same. Computational and structural biotechnology journal. 2020 Jan;18:2789–98.
• Levade I, Saber M, Midani F, Chowdhury F, Khan A, Begum Y, et al. PredictingVibrio choleraeinfection and disease severity using metagenomics in a prospective cohort study. 2020;
• Suarez L, Skinner A, Truong T, McCann J, David L, Rawls J, et al. The Selection of Obesity Treatment Among Adolescents in a Pediatric Weight Management Program. In: OBESITY. 2020. p. 33–33.
• Reese AT, Kartzinel TR, Petrone BL, Turnbaugh PJ, Pringle RM, David LA. Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept. mSystems. 2019 Oct 8;4(5).
• Washburne AD, Silverman JD, Morton JT, Becker DJ, Crowley D, Mukherjee S, et al. Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data. Ecological Monographs. 2019 May 1;89(2).
• David L. Personalizing Food to the Gut Microbiome. In: FASEB JOURNAL. 2019.
• Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, et al. Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol. 2018 Dec;3(12):1441–50.
• Silverman JD, Durand HK, Bloom RJ, Mukherjee S, David LA. Correction to: Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome. 2018 Nov 27;6(1):212.
• Silverman JD, Durand HK, Bloom RJ, Mukherjee S, David LA. Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome. 2018 Nov 12;6(1):202.
• Midani FS, Weil AA, Chowdhury F, Begum YA, Khan AI, Debela MD, et al. Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection. J Infect Dis. 2018 Jul 13;218(4):645–53.
• Reese AT, Cho EH, Klitzman B, Nichols SP, Wisniewski NA, Villa MM, et al. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. Elife. 2018 Jun 19;7.
• David LA. Toward Personalized Control of Human Gut Bacterial Communities. mSystems. 2018;3(2).
• Reese AT, Lulow K, David LA, Wright JP. Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms. Ecol Evol. 2018 Jan;8(2):1196–205.
• Silverman J, Durand H, Bloom R, Mukherjee S, David L. Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. 2018;
• Silverman JD, Washburne AD, Mukherjee S, David LA. A phylogenetic transform enhances analysis of compositional microbiota data. Elife. 2017 Feb 15;6.
• Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, et al. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ. 2017;5:e2969.
• Zhang Y, Zhao Y, David L, Henao R, Carin L. Dynamic poisson factor analysis. In: Proceedings - IEEE International Conference on Data Mining, ICDM. 2016. p. 1359–64.
• David LA, Materna AC, Friedman J, Baptista MIC, Blackburn MC, Perrotta A, et al. Erratum to: Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2016 May 31;17(1):117.
• Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, et al. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology. 2016 Mar;63(3):764–75.
• Washburne A, Silverman J, Leff J, Bennett D, Darcy J, Mukherjee S, et al. Phylogenetic factorization of compositional data. 2016;
• Silverman J, Washburne A, Mukherjee S, David L. A phylogenetic transform enhances analysis of compositional microbiota data. 2016;
• Boursier J, Mueller O, Barret M, Machado MV, Fizanne L, Guy CD, et al. Increasing severity of NAFLD is associated with gut dysbiosis and modification of the metabolic function of the gut microbiota. In: HEPATOLOGY. WILEY-BLACKWELL; 2015. p. 1274A-1274A.
• Wong S, Stephens WZ, Burns AR, Stagaman K, David LA, Bohannan BJM, et al. Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. mBio. 2015 Sep 29;6(5):e00687–e00615.
• David LA, Weil A, Ryan ET, Calderwood SB, Harris JB, Chowdhury F, et al. Gut microbial succession follows acute secretory diarrhea in humans. mBio. 2015 May 19;6(3):e00381–e00315.
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559–63.
• David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2014;15(7):R89.
• Szabo G, Preheim SP, Kauffman KM, David LA, Shapiro J, Alm EJ, et al. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J. 2013 Mar;7(3):509–19.
• Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011 Oct 30;480(7376):241–4.
• David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature. 2011 Jan 6;469(7328):93–6.
• Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, Alm EJ, et al. Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol. 2011 Jan;13(1):265–75.
• Shapiro BJ, David LA, Friedman J, Alm EJ. Looking for Darwin's footprints in the microbial world. Trends Microbiol. 2009 May;17(5):196–204.
• Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science. 2008 May 23;320(5879):1081–5.
• Dubin-Thaler BJ, Hofman JM, Cai Y, Xenias H, Spielman I, Shneidman AV, et al. Quantification of cell edge velocities and traction forces reveals distinct motility modules during cell spreading. PLoS One. 2008;3(11):e3735.
• David LA, Wiggins CH. Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. Ann N Y Acad Sci. 2007 Dec;1115:90–101.
• Glenn CF, Chow DK, David L, Cooke CA, Gami MS, Iser WB, et al. Behavioral deficits during early stages of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty. J Gerontol A Biol Sci Med Sci. 2004 Dec;59(12):1251–60.

In The News

• Duke Test Labs Explore Our Friendly (and Unfriendly) Neighborhood Microbes (Oct 31, 2023 | Pratt School of Engineering)
• DNA Barcoding Identifies the Plants a Person Has Eaten (Jun 27, 2023 | Duke Today)
• Three of 25 Science Diversity Leadership Awards Come to Duke (Oct 19, 2022 | )
• It Doesn’t Matter Much Which Fiber You Choose – Just Get More Fiber! (Jul 29, 2022 | )
• Meet the Newly Tenured Faculty of 2021 (Sep 21, 2021 | Office of Faculty Advancement)
• How Much Fiber Should You Eat? A Duke Graduate Student Forages for the Answer (Sep 13, 2021 | School of Medicine Magnify)
• 'I Wanted to Be a Part of a Movement:' School of Medicine's Plan for Change (Aug 3, 2021 | School of Medicine)
• School of Medicine Researchers Honored for Study of the Pathogenesis of Infectious Disease (May 25, 2021 | School of Medicine)
• Everybody's Microbiome Is Different. So How Do You Study It Usefully? (Jul 1, 2020 | Center for Genomic and Computational Biology)
• Poop: It's a Great Thing to Study (Jan 7, 2020 | )
• Our Microbes Are Starving, and That’s a Good Thing (Oct 29, 2018 | )
• AI Detects Patterns Of Gut Microbes for Cholera Risk (May 7, 2018 | )
• Microbes Evolved to Colonize Different Parts of the Human Body (Mar 20, 2017 | )
• Ten Scientists to Watch: Lawrence Davids gut check gets personal (Sep 22, 2016 | Science News)
• A Little Dirt Won't Hurt You (Jun 17, 2016 | )
• New Collaborative Seed Grant Program Gives Eight Awards (Mar 16, 2016 | )
• Lawrence David Named Searle Scholar (Apr 15, 2015 | )
• Q-and-A: Scientist studied his poop for a year to learn about gut bugs (Jul 25, 2014 | National Geographic)
• Lawrence David Gets to the Gut of the Matter (May 13, 2014 | Duke Research Blog)
• Five Science Faculty Win Sloan Fellowships (Feb 18, 2014 | )
• Changes in diet can alter gut bacteria within 24 hours (Dec 12, 2013 | Fox News, LiveScience)
• MIcrobes R Us (Oct 23, 2013 | )