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Lemay Lab
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RESEARCH INTERESTS:
Does what you eat affect your gastrointestinal health? Should dietary guidance depend on your gut microbiome? Dr. Lemay is interested in how dietary components, especially fermentable carbohydrates, affect host response and whether that response is modulated by the functional capabilities of resident microbiota. The lab also applies big data techniques, such as sequencing technologies and machine learning, to understand the effects of diet on human health.

 

The Lemay Lab’s themes include:

  1. Effect of diet on intestinal inflammation
    • Ex vivo experiments to determine effect of fermentations (from Kable Lab) and/or dietary components on intestinal epithelial cells
    • Assessment of gut barrier function and/or GI inflammation in clinical trials
  2. Methods of quantifying microbial consortia function (functional metagenomics, metatranscriptomics); application of these methods to understand diet-microbe host relationships
  3. Stool and plasma markers for GI inflammation and/or GI barrier function
  4. Application of big data techniques (omics and machine learning) to dietary data and nutritional phenotyping.

    Historically, the Lemay Lab has focused on milk science—everything from how genes are regulated to produce milk to how dairy consumption affects the consumer. We continue to work on milk-themed projects but will more broadly include studies of other dietary components in the future.

RESEARCH TEAM

Danielle G. Lemay, Ph.D.
Research Molecular Biologist
Visiting Assistant Professor, UC Davis Department of Nutrition
Associate Professional Researcher, UC Davis Genome Center
Head of Bioinformatics Initiatives, Foods For Health Institute, UC Davis
430 West Health Sciences Drive
Davis, CA 95616
Office (530) 752-4748
Lab: WHNRC Room 235
Email address: Danielle.Lemay@ars.usda.gov

Zeynep Alkan
Chemist (Lab Manager)
Lab: WHNRC Rm 235, (530)752-4725)
Email address: Zeynep.Alkan@ars.usda.gov

Michelle Treiber
Junior Specialist
Lab: WHNRC Rm 235, (530)752-4725

Graduate Students:
PhD student, Sam Westreich, Integrative Genetics and Genomics
PhD student, Hannah Lyman, Integrative Genetics and Genomics

UC Davis Graduate student rotations or projects:
Chad Masarweh, Microbiology, Winter Quarter 2017
Yuchen Li, Statistics, Spring Quarter 2017

Alumni:
Eric Kwok, BS, Genetics, Grad 2017
Michelle Treiber, BS, Genetics, Grad 2017
Seren Pollard, Undergraduate Intern from University College Dublin 2017
Shannon Joslin, PhD program, Genetics, July 2016- June 2017
Kristen Beck, PhD, Biochemistry, Molecular, Cellular and Developmental Biology, Grad 2015
Pedro Ivo Silva, undergraduate intern summer 2013
Matthew Porter, MS student summer 2013
Gina Turco, PhD student rotation, 2012
Stella Hartono, PhD student rotation, 2011

 

RESEARCH STUDIES

Assessing the Impact of Diet on Inflammation in Healthy and Obese Adults in a Cross-Sectional Phenotyping and a Longitudinal Intervention Trial (USDA Agricultural Research Service)

Charles Stephensen (PI), 10/01/13-10/01/18

Role: Co-Investigator

The goal of this study is to identify lifestyle, biological, and environmental factors associated with the variance in metabolic health and immune responses to dietary challenges in generally healthy US adults. The role of the Lemay Lab in this project is to assess the effects of diet on markers of gastrointestinal health and to apply machine learning techniques to analyze project-wide data.

 

Milk, Health, and Genetics (California Dairy Research Foundation)

Danielle Lemay (PI), 01/01/17-12/31/18

The goal of this project is to determine how lactose persistence genetics affects disease risk using meta-analysis of genome-wide association studies (GWAS) and the association of fluid milk intake with markers of cardiovascular, bone, prostate, and gut health in a Californian cohort.

 

Cardiovascular and Immune Benefits to Elders From Increased Dairy Consumption (California Dairy Research Foundation)

Marta Van Loan (PI), 01/01/17-12/31/18

Role: Co-PI

The goal of this project is to evaluate, based on a suite of established biomarkers, the cardiovascular and immune benefits of daily supplementation of diets with whey powder in an elderly population.

 

Activation of Probiotic Bifidobacteria by Milk Glycans (NIH NCCAM R01AT008759)

David A Mills (PI), 9/30/2014 – 8/30/2019

Role: Co-Investigator

The overall goal of this project is to characterize the mechanisms by which infant bifidobacteria and milk glycans interact to promote the intestinal health of the host.

 

Characterization Of Cis-Regulatory Elements Associated With Mammary Gland Function (USDA NIFA 2011-03183)

Monique Rijnkels (PI), 4/15/2012-03/31/2018

Role: Co-Investigator

The goal of this project is to identify and characterize cis-regulatory elements in the bovine genome that influence gene expression in the mammary gland utilizing sequencing technologies (RNA-Seq, DNase-Seq, ATAC-Seq, WGBS).

 

Development of tools to analyze infant fecal metagenomes: A sub-study of the Health Innovation Partnership grant (China Mengnui Dairy Company)

Bethany Henrick (PI) of Health Innovation Partnership grant. Lemay (PI) of substudy.

The goal of the main study is to create proof-of-principle, knowledge-based precision diets for weaning infants that improves metabolic, cognitive and immune-based health. The role of the Lemay Lab is to develop tools to analyze infant fecal metagenomes.

 

ADDITIONAL CURRENT COLLABORATIONS:

METHODS AND TECHNIQUE
The Lemay Lab develops methods for omics experiments, especially functional metagenomics and metatranscriptomics, and for multi-omics integration and analysis.

Endpoints analyzed in the Lemay Lab:

We also apply machine learning methods for dietary analysis and human health outcomes.

 

SOFTWARE
SAMSA2: a standalone metatranscriptome analysis pipeline https://github.com/transcript/samsa2

SAMSA: a comprehensive metatranscriptome analysis pipeline https://github.com/transcript/SAMSA

The Gene Neighborhood Scoring Tool (G-NEST) G-NEST combines genome location, gene expression, and evolutionary sequence  conservation data to score putative gene neighborhood locations in eukaryotic genomes. G-NEST source code is available at <https://github.com/dglemay/G-NEST>
The Globulator Given images of slides of milk, the Globulator software automates the quantification of milk fat globules and nucleic acids (DNA, RNA)." The Globulator software is available at https://github.com/srhartono/Globulator

PUBLICATIONS
ST Westreich, ML Treiber, DA Mills, I Korf, DG Lemay. SAMSA2: A standalone metatranscriptome analysis pipeline. bioRxiv, 2017

ill GE, Lemay DG, Trott JF, Aimo L, Lock AL, Hovey RC. The transcriptome of estrogen-independent mammary growth in female mice reveals that not all mammary glands are created equally. Endocrinology. 2017 Jul 27. doi:10.1210/en.2017-00395. [Epub ahead of print] PubMed PMID: 28938404.

 

Aifric O'sullivan, Bethany Henrick, Bonnie Dixon, Daniela Barile, Angela Zivkovic, Jennifer Smilowitz, Danielle Lemay, William Martin, J Bruce German, Sara Elizabeth Schaefer. 21st Century Toolkit for Optimizing Population Health through Precision Nutrition. Critical Reviews in Food Science and Nutrition. Published online: 05 Jul 2017. http://dx.doi.org/10.1080/10408398.2017.1348335

 

Smilowitz JT, Lemay DG, Kalanetra KM, Chin EL, Zivkovic AM, Breck MA, German JB, Mills DA, Slupsky C, Barile D. Tolerability and safety of the intake of bovine milk oligosaccharides extracted from cheese whey in healthy human adults. J Nutr Sci. 2017 Feb 20;6:e6. doi: 10.1017/jns.2017.2. eCollection 2017. PubMed PMID: 28620481; PubMed Central PMCID: PMC5465862.

 

Lewis ZT, Sidamonidze K, Tsaturyan V, Tsereteli D, Khachidze N, Pepoyan A, Zhgenti E, Tevzadze L, Manvelyan A, Balayan M, Imnadze P, Torok T, Lemay DG, Mills DA. The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia. Sci Rep. 2017 Feb 2;7:40932. doi: 10.1038/srep40932. PubMed PMID:28150690; PubMed Central PMCID: PMC5288704.

 

Garrido D, Ruiz-Moyano S, Kirmiz N, Davis JC, Totten SM, Lemay DG, Ugalde JA, German JB, Lebrilla CB, Mills DA. A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596. Sci Rep. 2016 Oct 19;6:35045. doi: 10.1038/srep35045. PubMed PMID: 27756904; PubMed Central PMCID: PMC5069460.

 

Westreich ST, Korf I, Mills DA, Lemay DG. SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics. 2016 Sep 29;17(1):399. PubMed PMID: 27687690.

 

Garrido D, Ruiz-Moyano S, Lemay DG, Sela DA, German JB, Mills DA. Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria. Sci Rep. 2015 Sep 4;5:13517. doi: 10.1038/srep13517. PMID:26337101

 

Underwood MA, Gaerlan S, De Leoz ML, Dimapasoc L, Kalanetra KM, Lemay DG, German JB, Mills DA, Lebrilla CB. Human milk oligosaccharides in premature infants: absorption, excretion, and influence on the intestinal microbiota. Pediatr Res. 2015 Aug 31. doi: 10.1038/pr.2015.162. [Epub ahead of print] PMID:26322410

 

Wickramasinghe S, Pacheco AR, Lemay DG, Mills DA. Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells. BMC Microbiology. 2015 Aug 25;15:172. doi: 10.1186/s12866-015-0508-3. PMID: 26303932

 

Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG. Comparative proteomics of human and macaque milk reveals species-specific nutrition during postnatal development. J Proteome Res. 2015 May 1;14(5):2143-57. doi: 10.1021/pr501243m. Epub 2015 Apr 6. PubMed PMID: 25757574.

 

Lewis ZT, Totten SM, Smilowitz JT, Popovic M, Parker E, Lemay DG, Van Tassell ML, Miller MJ, Jin YS, German JB, Lebrilla CB, Mills DA. Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants. Microbiome. 2015 Apr 10;3:13. doi: 10.1186/s40168-015-0071-z. eCollection 2015. PubMed PMID: 25922665.

 

Hamilton MK, Boudry G, Lemay DG, Raybould HE. Changes in intestinal barrier function and gut microbiota in high-fat diet-fed rats are dynamic and region dependent. Am J Physiol Gastrointest Liver Physiol. 2015 May 15;308(10):G840-51. doi: 10.1152/ajpgi.00029.2015. Epub 2015 Mar 6. PubMed PMID: 25747351.

 

Grapov D, Lemay DG, Weber D, Phinney BS, Azulay Chertok IR, Gho DS, German JB, Smilowitz JT. The human colostrum whey proteome is altered in gestational diabetes mellitus. J Proteome Res. 2015 Jan 2;14(1):512-20. doi: 10.1021/pr500818d. Epub 2014 Dec 1. PubMed PMID: 25338220.

 

Schennink A, Trott JF, Manjarin R, Lemay DG, Freking BA, Hovey R. Comparative genomics reveals tissue-specific regulation of prolactin receptor gene expression. J Mol Endocrinol. 2015 Feb;54(1):1-15. doi: 10.1530/JME-14-0212. Epub 2014 Oct 30. PubMed PMID: 25358647.

 

Lemay DG, Hovey RC, Hartono SR, Hinde K, Smilowitz JT, Ventimiglia F, Schmidt KA, Lee JW, Islas-Trejo A, Silva PI, Korf I, Medrano JF, Barry PA, German JB. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics. 2013 Dec 12;14:872. doi: 10.1186/1471-2164-14-872. PMID: 24330573.

 

Lemay DG, Pollard KS, Martin WF, Zadrowski CF, Hernandez J, Korf I, German JB, Rijnkels M. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome, PLoS One, 2013 Sep 26;8(9):e75030.

 

Lemay DG, Ballard OA, Hughes MA, Morrow AL, Horseman ND, Nommsen-Rivers LA. RNA sequencing of the human milk fat layer transcriptome reveals distinct gene expression profiles at three stages of lactation. PLoS One 2013; 8(7): e67531

 

Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, Li W, Lemay DG. Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One. 2013; 8(1):e53270.

 

Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics 2012; Sep 28;13:253. PMID: 23020263

 

Neville MC, Anderson SM, McManaman JL, Badger TM, Bunik M, Contractor N, Crume T, Dabelea D, Donovan SM, Forman N, Frank DN, Friedman JE, German JB, Goldman A, Hadsell D, Hambidge M, Hinde K, Horseman ND, Hovey RC, Janoff E, Krebs NF, Lebrilla CB, Lemay DG, Maclean PS, Meier P, Morrow AL, Neu J, Nommsen-Rivers LA, Raiten DJ, Rijnkels M, Seewaldt V, Shur BD, Vanhouten J, Williamson P. Lactation and Neonatal Nutrition: Defining and Refining the Critical Questions. J Mammary Gland Biol Neoplasia. 2012 Jun;17(2):167-88. doi: 10.1007/s10911-012-9261-5. Epub 2012 Jul 1. PMID: 22752723

 

Argov-Argaman N, Smilowitz JT, Bricarello DA, Barboza M, Lerno L, Froehlich JW, Lee H, Zivkovic AM, Lemay DG, Freeman S, Lebrilla CB, Parikh AN, German JB. Lactosomes: Structural and Compositional Classification of Unique Nanometer-Sized Protein Lipid Particles of Human Milk. J Agric Food Chem. 2010 Oct 6. PMID: 20925428

 

Lemay DG, Rijnkels M, German JB. Lessons from the bovine genome: implications for human nutrition and research. J Nutr. 2009;139(7):1271-2. PMCID: 2698669.

 

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, and Rijnkels M. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biology 2009;10(4):R43. PMCID: 2688934. (Reviewed in Nature Reviews Genetics 10, 346-347 June 2009) (Reviewed in Journal of Biology 2009, 8:37)

 

Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics. 2009;10:193. PMCID: 2680899.

 

The Bovine Genome Sequencing and Analysis Consortium. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009;324(5926):522-8. (Cover article)

 

Argov N, Lemay DG and German JB Milk fat globule structure and function: nanoscience comes to milk production Trends Food Sci Technol. 2008;19(12): 617-623.

 

Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB: Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol 2007, 1:56.

 

Lemay DG, Zivkovic AM, German JB: Building the bridges to bioinformatics in nutrition research. Am J Clin Nutr. 2007, 86:1261-1269.

 

Lange MC, Lemay DG, German JB: A multi-ontology framework to guide agriculture and food towards diet and health. J. Sci. Food Agric. 2007, 87(8):1427-1434. doi: 10.1002/jsfa.2832.

 

Lemay D.G., Dillard C.J. and German J.B. (2007) Food structure for nutrition. In: Food Colloids: Self‑Assembly and Material Science. Dickinson E. and Leser M. (eds.) Royal Society of Chemistry, London, England, Chapter 1, pp. 1–15.

 

Lemay DG, Hwang DH: Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics. J Lipid Res. 2006, 47:1583-1587. (Cover article)

 

Lee JY, Lowell CA, Lemay DG, Youn HS, Rhee SH, Sohn KH, Jang B, Ye J, Chung JH, Hwang DH: The regulation of the expression of inducible nitric oxide synthase by Src-family tyrosine kinases mediated through MyD88-independent signaling pathways of Toll-like receptor 4. Biochem Pharmacol. 2005, 70:1231-1240.

 

Weatherill AR, Lee JY, Zhao L, Lemay DG, Youn HS, Hwang DH: Saturated and polyunsaturated fatty acids reciprocally modulate dendritic cell functions mediated through TLR4. J Immunol. 2005, 174:5390-5397.