Publications

* indicates equal author contributions; underline members of the David Lab.

  1. ZC HolmesJD SilvermanHK DressmanZ WeiEP DallowSC ArmstrongPC SeedJF RawlsLA David. “Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition.” mBio Aug 2020, 11 (4) e00914-20; DOI: 10.1128/mBio.00914-20 [link]
  2. MM Villa*RJ Bloom*, JD Silverman, HK Durand, S Jiang, A Wu, EP Dallow, S Huang, L You, and LA David.”Interindividual variation in dietary carbohydrate metabolism by gut Bacteria revealed with droplet microfluidic culture.” Msystems 5.3 (2020). [link]
  3. SN Nimmagadda, FS Midani, HK Durand, AT Reese, C Murdoch, BP Nicholson, T Veldman, TW Burke, AK Zaas, CW Woods, G Ginsburg, LA David. “Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection” medRxiv 2020.04.11.20061911. [link]
  4. JD Silverman, K Roche, S Mukherjee, LA David. “Naught all zeros in sequence count data are the same.” Mar 2020. bioRxiv 477794. [link]
  5. AT Reese, TR Kartzinel, BL Petrone, PJ Turnbaugh, RM Pringle, LA David. “Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.” mSystems Oct 2019, 4 (5) e00458-19; DOI: 10.1128/mSystems.00458-19. [link]
  6. JD Silverman, HK Durand, RJ Bloom, S Mukherjee, and LA David. Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome6:202, Nov 2018. [link]
  7. AT Reese, FC Pereira, A Schintlmeister, D Berry, M Wagner, LP Hale, A Wu, S Jiang, HK Durand, X Zhou, RT Premont, AM Diehl, TM O’Connell, SC Alberts, TR Kartzinel, RM Pringle, RR Dunn, JP Wright & LA David. Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology,  Vol. 3, pages 1441–1450 (2018). [link]
  8. AT Reese, EH Cho, B Klitzman, SP Nichols, NA Wisniewski, MM Villa, HK Durand, S Jiang, FS Midani, SN Nimmagadda, TM O’Connell, JP Wright, MA Deshusses, LA David. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLIFE, 10.7554/eLife.35987, Jun 2018. [link]
  9. FS Midani*, AA Weil*, F Chowdhury, YA Begum, AI Khan, MD Debela, HK Durand, AT Reese, SN Nimmagadda, JD Silverman, CN Ellis, ET Ryan, SB Calderwood, JB Harris, F Qadri, LA David, RC LaRocque; Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection, The Journal of Infectious Diseases, jiy192, [linkm_cover JID
  10. David, LA. 2018. Toward personalized control of the human gut bacterial communities. mSystems 3:e00165-17. [link]
  11. AT Reese, K Lulow, LA David, JP Wright. Plant community and soil conditions individually affect soil microbial community assembly in experimental old-field microcosms. Submitted, 2016.
  12. JD Silverman, A Washburne, S Mukherjee, LA David. A phylogenetic transform enhances analysis of compositional microbiota data. eLife, 10.7554/eLife.21887, Feb 2017. [link]
  13. AD Washburne, J Silverman, JW Leff, DJ Bennett, J Darcy, S Mukherjee, N Fierer, LA David. Phylogenetic factorization of microbiome data yields lineage-level associations in microbiome datasets. PeerJ, 5:e2969, Feb 2017. [link]
  14. J Boursier, O Mueller, M Barret, M Machado, L Fizanne, F Araujo-Perez, C Guy, P Seed, J Rawls, LA David, G Hunault, F Oberti, P Cales, AM Diehl. The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology, 63(3):764-775, Mar 2016. [link]
  15. S Wong, WZ Stephens, AR Burns, K Stagaman, LA David, BJM Bohannan, K Guillemin, JF Rawls. Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. mBio, 6(5):e00687-15, Sept 2015. [link]
  16. LA Davidcover_nature, A Weil, ET Ryan, SB Calderwood, JB Harris, F Chowdhury, Y Begum, F Qadri, RC LaRocque, PJ Turnbaugh. Gut microbial succession follows acute secretory diarrhea in humans. mBio,6(3):e00381-15, Apr 2015. [link]
  17. LA David, AC Materna, J Friedman, I Baptista, MC Blackburn, A Perrotta, SE Erdman, EJ Alm. Host lifestyle affects human microbiota on daily timescales. Genome Biol, 15:R89, Jul 2014. [link]
  18. LA David, CF Maurice, RN Carmody, DB Gootenberg, JE Button, BE Wolfe, AV Ling, AS Devlin, Y Varma, MA Fischbach, SB Biddinger, RJ Dutton, PJ Turnbaugh. Diet rapidly and reproducibly alters the gut microbiome. Nature, 505(7484):559-563, Jan 2014.  [link]
  19. G Szabo, SP Preheim, KM Kauffman, LA David, J Shapiro, EJ Alm, MF Polz. Reproducibility of Vibrionaceae Population Structure in Coastal Bacterioplankton. ISME J, 7: 509-519, Mar 2013. [link]
  20. CS Smillie*, MB Smith*, J Friedman, OX Cordero, LA David, EJ Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480(7376):241-244, Dec, 2011. [link]angst_cover
  21. LA David, EJ Alm. Rapid evolutionary innovation during an Archean Genetic Expansion. Nature, 469(7328):93-96, Jan 2011. [link]
  22. SP Preheim, Y Boucher, H Wildschutte, LA David, D Veneziano, EJ Alm and MF Polz. Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol, 13:265-275, Jan 2011. [link]
  23. BJ Shapiro, LA David, J Friedman, EJ Alm. Looking for Darwin’s footprints in the microbial world. Trends Microbiol. 17(5):196-204, May 2009. [link]
  24. BJ Dubin-Thaler, JM Hofman, Y Cai, H Xenias, I Spielman, AV Shneidman, LA David, HG Dobereiner, CH Wiggins, MP Sheetz. Quantification of Cell Edge Velocities and Traction Forces Reveals Distinct Motility Modules during Cell Spreading. PLoS ONE, 3(11), Nov 2008. [link]
  25. DE Hunt*, LA David*, D Gevers, SP Preheim, EJ Alm, MF Polz. Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton. Science, 320(5879):1081-85, May 2008. [link]science_cover
  26. LA David, CH Wiggins. Benchmarking of dynamic Bayesian Networks from stochastic time-series data. Ann NY Acad Sci., 1115 90-101, Dec 2007. [link]
  27. CF Glenn, DK Chow, L David, C Cooke, M Gami, W Iser, K Hanselman, I Goldberg and CA Wolkow. Behavioral deficits during early states of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty. J Gerontol A Biol Sci Med Sci., 59(12):1251-60, Dec 2004. [link]