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ARS Home Pacific West Area Davis, California Western Human Nutrition Research Center Immunity and Disease Prevention Research People Danielle Lemay





Lemay Labheadline bar **LEMAY LAB** /ARSUserFiles/52247/Lemay Lab 2022.jpg **March****2022**   /ARSUserFiles/52247/lemaylab2019c.JPG **2019**   Research Scientist
                              **Danielle G. Lemay, Ph.D.**
Lead Scientist / Research Molecular Biologist
Associate Adjunct Professor, UC Davis Department of Nutrition
Nutrition Lead, USDA/NSF AI Institute for Next-Generation Food Systems(AIFS)
Faculty Member, UC Davis Genome Center
Office: (530) 752-4748
Email address: danielle.lemay@usda.gov
Google Scholar page
**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.
**Lemay Lab Themes**
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 in order to build models for personalized nutrition.
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
                              **ARS Employees**
Zeynep Alkan, Chemist (Lab Manager)
**Postdoctoral Research Associates**
Jules Larke, PhD, 2021-Present
Andrew Oliver, PhD, 2021-Present
**Graduate Students**
Yirui Tang Villanueva, 2021-Present
Sarah Blecksmith, PhD student, Graduate Group in Nutritional Biology, 2020-Present
Yasmine Bouzid, PhD student, Graduate Group in Nutritional Biology, 2019-Present
**UC Davis Junior Specialist**
Yirui Tang, 2021
Sarah Spearman, 2020 – Present
**Undergraduate Students**
Occasionally seeking interns.
**Alumni**
Yue Jin, AIFS Undergraduate, Winner of Meyer Award, 2021-2022
Elizabeth Chin, PhD, Postdoctoral Research Computational Biologist, Winner of ASN Postdoc Research Competition, Winner of NNDC Young Investigator Competition, 2018-2022
Ismael Acedo, PhD student, Integrated Genetics and Genomics Graduate Group, 2019-2021
Zhengyao "Zeya" Xue, PhD, Postdoctoral Research Associate 2019-2020
Emily Yamashita, Undergraduate, 2018-2019, Graduated 2019
Gabriel Simmons, 2019, co-mentored with Ilias Tagkopoulis, Graduated 2019
Michelle Treiber, UC Davis Junior Specialist (Bioinformatics), 2017-2018
Samuel Westreich, PhD, Integrative Genetics and Genomics, Winner of UC Davis Grad Slam Competition, Graduated December 2017
Chad Masarweh, PhD student rotation, Microbiology, Winter Quarter 2017
Yuchen Li, Statistics, PhD student project, Spring Quarter 2017
Eric Kwok, BS, Genetics, Graduated 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, Graduated 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
 Selected Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Association of lactase persistence genotypes (rs4988235) and ethnicity with dairy intake in a healthy U.S. population-(Peer Reviewed Journal) Chin, E.L., Huang, L., Bouzid, Y.Y., Kirschke, C.P., Durbin-Johnson, B., Baldiviez, L.M., Bonnel, E.L., Keim, N.L., Korf, I., Stephensen, C.B., Lemay, D.G. 2019. Association of lactase persistence genotypes (rs4988235) and ethnicity with dairy intake in a healthy U.S. population. Nutrients.  https://doi.org/10.3390/nu11081860.The fecal resistome of dairy cattle is associated with diet during nursing-(Peer Reviewed Journal) Liu, J., Taft, D.H., Gomez, M.X., Johnson, D., Treiber, M.L., Lemay, D.G., Depeters, E., Mills, D.A. 2019. The fecal resistome of dairy cattle is associated with diet during nursing. Nature Magazine. https://doi.org/10.1038/s41467-019-12111-x.Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal-(Peer Reviewed Journal) Lemay, D.G., Huang, S., Huang, L., Alkan, Z., Kirschke, C.P., Burnett, D.J., Wang, Y., Hwang, D.H. 2019. Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal. Journal of Nutritional Biochemistry. 72:108209. https://doi.org/10.1016/j.jnutbio.2019.06.007.Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization-(Peer Reviewed Journal) Westreich, S.T., Ardeshir, A., Alkan, Z., Kable, M.E., Korf, I., Lemay, D.G. 2019. Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization. BMC Microbiome. 7:41. https://doi.org/10.1186/s40168-019-0664-z.Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms-(Peer Reviewed Journal) Sanctuary, M., Kain, J., Chen, S., Kalentra, K., Lemay, D.G., Rose, D., Yang, H., Tancredi, D.J., German, B.J., Slupsky, C., Ashwood, P., Mills, D., Smilowtz, J.T., Angkustsiri, K. 2019. Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms. PLoS One. 14(1):1-30. https://doi.org/10.1371/journal.pone.0210064.The collaborative effect of scientific meetings: a study of the international milk genomics consortium-(Peer Reviewed Journal) Kwok, E., Porter, M., Korf, I., Pasin, G., German, B.J., Lemay, D.G. 2018. The collaborative effect of scientific meetings: a study of the international milk genomics consortium. PLoS One. 10.1371. https://doi.org/10.1371/journal.pone.0201637.SAMSA2: a standalone metatranscriptome analysis pipeline-(Peer Reviewed Journal) Westreich, S.T., Treiber, M.L., Mills, D.A., Lemay, D.G. 2018. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics. 19:175. https://doi.org/10.1186/s12859-018-2189-z.The transcriptome of estrogen-independent mammary growth reveals that not all mammary glands are created equally-(Peer Reviewed Journal) Berryhill, G.E., Lemay, D.G., Trott, J.F., Aimo, L., Lock, A.L., Hovey, R.C. 2017. The transcriptome of estrogen-independent mammary growth reveals that not all mammary glands are created equally. Endocrinology. doi: 10.1210/en.2017-00395.21st century toolkit for optimizing population
health through precision nutrition-() O'Sullivan, A., Henrick, B., Dixon, B., Barile, D., Zivkovic, A., Smilowitz, L., Lemay, D.G., Martin, W., German, B.J., Elizabeth, S. 2017. 21st century toolkit for optimizing population health through precision nutrition. Critical Reviews in Food Science and Nutrition. 57/45.Using metatranscriptomics to determine effects of dietary supplementation with bovine milk oligosaccharides in healthy adults-(Abstract Only) Westreich, S.T., Barile, D., Salcedo, J., Mills, D.A., Smilowitz, J.T., Korf, I., Lemay, D.G. 2017. Using metatranscriptomics to determine effects of dietary supplementation with bovine milk oligosaccharides in healthy adults. Experimental Biology. 31/940.The metatranscriptome of the rhesus macaque: investigating potential causes of idiopathic chronic diarrhea-(Abstract Only) Westreich, S.T., Ardeshir, A., Kable, M.E., Korf, I., Lemay, D.G. 2016. The metatranscriptome of the rhesus macaque: investigating potential causes of idiopathic chronic diarrhea. Experimental Biology. 31/650.
 Prominent ProjectsImpact of Diet on Intestinal Microbiota, Gut Health and Immune FunctionIn-House Appropriated (D)Accession Number:432895Health Promoting Roles of Food Bio-Active Phenolic Compounds on Obesity-Altered Metabolic Functions and PhysiologyNon-Assistance Cooperative Agreement (S)Accession Number:435078Assessment of Intestinal Permeability in Human ParticipantsNon-Assistance Cooperative Agreement (S)Accession Number:436717Assessment of Antimicrobial Resistance Genes in Human Fecal SamplesNon-Assistance Cooperative Agreement (S)Accession Number:436885Mothers, Infants and Lactation Quality-Extra Analyses (MILQ II) Project IITrust Fund Cooperative Agreement (T)Accession Number:437095Association of Dairy Intake With Protection Against Gastrointestinal InflammationTrust Fund Cooperative Agreement (T)Accession Number:436064
 Methods, Technique and Software
                              **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:
• Metagenomics/metatranscriptomics assessment of human gut microbial communities
• Stool and plasma biomarkers of gastrointestinal health
• Trans-epithelial resistance of intestinal epithelial cells; inflammatory response
We also apply machine learning methods for dietary analysis and human health outcomes.
**Software**
SAMSA2: a standalone metatranscriptome analysis pipeline
SAMSA: a comprehensive metatranscriptome analysis pipeline
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.
The Globulator Given images of slides of milk, the Globulator software automates the quantification of milk fat globules and nucleic acids (DNA, RNA)."


        
        
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            Last Modified:
7/18/2022

    

    
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