| Lemay Lab |
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LEMAY LAB
March 2022
2019
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 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.
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
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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Impact of Diet on Intestinal Microbiota, Gut Health and Immune Function In-House Appropriated (D) Accession Number:432895 Health Promoting Roles of Food Bio-Active Phenolic Compounds on Obesity-Altered Metabolic Functions and Physiology Non-Assistance Cooperative Agreement (S) Accession Number:435078 Assessment of Intestinal Permeability in Human Participants Non-Assistance Cooperative Agreement (S) Accession Number:436717 Assessment of Antimicrobial Resistance Genes in Human Fecal Samples Non-Assistance Cooperative Agreement (S) Accession Number:436885 Mothers, Infants and Lactation Quality-Extra Analyses (MILQ II) Project II Trust Fund Cooperative Agreement (T) Accession Number:437095 Association of Dairy Intake With Protection Against Gastrointestinal Inflammation Trust Fund Cooperative Agreement (T) Accession Number:436064
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)."
