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





Danielle  Lemay    Research Molecular Biologist **RESEARCH SCIENTIST**
430 West Health Sciences Drive
University of California, Davis
Davis, CA 95616

Phone:(530) 752-4748
/ARSUserFiles/52247/Lemay Headshot_resized.jpg **LEMAY LAB**
 
 Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Surveying nutrient assessment with photographs of meals (SNAPMe): a benchmark dataset of food photos for dietary assessment-(Peer Reviewed Journal) Larke, J.A., Chin, E.L., Bouzid, Y.Y., Nguyen, T.T., Vainberg, Y., Lee, D., Pirsiavash, H., Smilowitz, J.T., Lemay, D.G. 2023. Surveying nutrient assessment with photographs of meals (SNAPMe): a benchmark dataset of food photos for dietary assessment. The American Journal of Clinical Nutrition. 15(23) 4972. https://doi.org/10.3390/nu15234972.TaxaHFE a machine learning approach to collapse microbiome datasets using taxonomic structure-(Peer Reviewed Journal)Association of estimated daily lactose consumption, lactase persistence genotype (rs4988235), and gut microbiota in healthy U.S. adults-(Peer Reviewed Journal) Kable, M.E., Chin, E., Huang, L., Stephensen, C.B., Lemay, D.G. 2023. Association of estimated daily lactose consumption, lactase persistence genotype (rs4988235), and gut microbiota in healthy U.S. adults. Journal of Nutrition. https://doi.org/10.1016/j.tjnut.2023.06.025.Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals-(Peer Reviewed Journal) Durham, S.D., Wei, Z., Lemay, D.G., Lange, M., Barile, D. 2023. Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals. Scientific Reports. 13. Article 10345. https://doi.org/10.1038/s41598-023-36866-y.TaxaHFE a machine learning approach to collapse microbiome datasets using taxonomic structure-(Pre-print Publication) Oliver, A., Lemay, D.G. 2023. TaxaHFE a machine learning approach to collapse microbiome datasets using taxonomic structure. bioRxiv. 10.1101/543755. https://doi.org/10.1101/2023.06.06.543755.In vitro examination of the effect of honey on the survival of the foodborne pathogen enterotoxigenic E. coli in a small intestine microbial mock community-(Abstract Only)Increasing fiber in dairy cow feed is associated with altered milk composition which may support a more beneficial milk microbial community for cows and humans-(Abstract Only)Associations among milk microbiota, milk fatty acids, milk glycans, and inflammation from lactating Holstein cows-(Peer Reviewed Journal) Coates, L.C., Durham, S., Storms, D.H., Magnuson, A.D., Van Hekken, D.L., Plumier, B.M., Finley, J.W., Fukagawa, N.K., Tomasula, M.M., Lemay, D.G., Picklo, M., Barile, D., Kalscheur, K., Kable, M.E. 2023. Associations among milk microbiota, milk fatty acids, milk glycans, and inflammation from lactating Holstein cows. Microbiology Spectrum. 11(3). Article e04020-22. https://doi.org/10.1128/spectrum.04020-22.Dietary intake of monosaccharides from foods is associated with characteristics of the gut microbiota and gastrointestinal inflammation in healthy US adults-(Peer Reviewed Journal) Larke, J.A., Bacalzo, N., Castillo, J.J., Couture, G., Chen, Y., Xue, Z., Alkan, Z., Kable, M.E., Lebrilla, C.B., Stephensen, C.B., Lemay, D.G. 2022. Dietary intake of monosaccharides from foods is associated with characteristics of the gut microbiota and gastrointestinal inflammation in healthy US adults. Journal of Nutrition. 153(1):106-119. https://doi.org/10.1016/j.tjnut.2022.12.008.A benchmark dataset of food photos with food records for evaluation of computer vision algorithms in the context of dietary assessment-(Database / Dataset) Chin, E.L., Larke, J.A., Bouzid, Y.Y., Nguyen, T.T., Vainberg, Y., Smilowitz, J.T., Lemay, D.G. 2022. A benchmark dataset of food photos with food records for evaluation of computer vision algorithms in the context of dietary assessment. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1528346.Low intake of dietary fiber is associated with gastrointestinal inflammation in healthy U.S. adults-(Abstract Only) Bouzid, Y.Y., Alkan, Z., Stephensen, C.B., Lemay, D.G. 2022. Low intake of dietary fiber is associated with gastrointestinal inflammation in healthy U.S. adults. Current Developments in Nutrition. 6/974. https://doi.org/10.1093/cdn/nzac068.003.Carbohydrate active enzyme profiles of gut microbiomes from low and adequate fiber consumers in a healthy U.S. cohort-(Abstract Only) Blecksmith, S.E., Xue, Z., Tang, Y., Alkan, Z., Stephensen, C.B., Kable, M.E., Lemay, D.G. 2022. Carbohydrate active enzyme profiles of gut microbiomes from low and adequate fiber consumers in a healthy U.S. cohort. Current Developments in Nutrition. 6/999. https://doi.org/10.1093/cdn/nzac069.004.Diversity of monosaccharide composition of diets consumed by healthy U.S. adults is highly variable and positively associated with the healthy eating index-(Abstract Only) Larke, J.A., Chin, E.L., Castillo, J.J., Bacalzo, N., Couture, G., Stephensen, C.B., Labrilla, C.B., Lemay, D.G. 2022. Diversity of monosaccharide composition of diets consumed by healthy U.S. adults is highly variable and positively associated with the healthy eating index. Current Developments in Nutrition. 6/519. https://doi.org/10.1093/cdn/nzac077.022.A low starch and high fiber diet intervention impacts the microbial community of raw bovine milk-(Peer Reviewed Journal) Coates, L.C., Storms, D.H., Finley, J.W., Fukagawa, N.K., Lemay, D.G., Kalscheur, K., Kable, M.E. 2022. A low starch and high fiber diet intervention impacts the microbial community of raw bovine milk. Current Developments in Nutrition. 6(6). Article nzac086. https://doi.org/10.1093/cdn/nzac086.Association of diet and antimicrobial resistance in healthy U.S. adults-(Peer Reviewed Journal) Oliver, A., Xue, Z., Villanueva, Y.T., Durbin-Johnson, B., Alkan, Z., Taft, D.H., Liu, J., Korf, I., Laugero, K.D., Stephensen, C.B., Mills, D.A., Kable, M.E., Lemay, D.G. 2022. Association of diet and antimicrobial resistance in healthy U.S. adults. mBio. 13(3). Article e00101-22. https://doi.org/10.1128/mbio.00101-22.The development of the Davis Food Glycopedia - A glycan encyclopedia
of food-(Peer Reviewed Journal) Castillo, J.J., Couture, G., Bacalzo, N.P., Chen, Y., Chin, E.L., Blecksmith, S.E., Bouzid, Y.Y., Vainberg, Y., Masarweh, C., Zhou, Q., Smilowitz, J.T., German, J.B., Mills, D.A., Lemay, D.G., Lebrilla, C.B. 2022. The development of the Davis Food Glycopedia - A glycan encyclopedia of food. Nutrients. 14(8). Article 1639. https://doi.org/10.3390/nu14081639.In vitro examination of the effect of honey in the gastrointestinal tract-(Abstract Only) Traxler, S., Spearman, S., Storms, D.H., Lemay, D.G., Kable, M.E. 2022. In vitro examination of the effect of honey in the gastrointestinal tract. Current Developments in Nutrition. 6/1031. https://doi.org/10.1093/cdn/nzac069.036.Dietary fiber to starch ratio affects bovine milk Oligosaccharide profiles-(Peer Reviewed Journal) Durham, S.D., Lemay, D.G., Wei, Z., Kalscheur, K., Finley, J.W., Fukagawa, N.K., Barile, D. 2022. Dietary fiber to starch ratio affects bovine milk Oligosaccharide profiles. Current Developments in Nutrition. 6/6. https://doi.org/10.1093/cdn/nzac033.Special report: AI Institute for next generation food systems (AIFS)-(Review Article) Tagkopoulos, I., Brown, S.F., Liu, X., Zhao, Q., Zohdi, T., Earles, J.M., Nitin, N., Runcie, D.E., Lemay, D.G., Smith, A.D., Ronald, P.C., Feng, H., Youtsey, G.D. 2022. Special report: AI Institute for next generation food systems (AIFS). Computers and Electronics in Agriculture. 196. Article 106819. https://doi.org/10.1016/j.compag.2022.106819.Tree-based analysis of dietary diversity captures associations between fiber intake and gut microbiota composition in a healthy U.S. adult cohort-(Peer Reviewed Journal) Kable, M.E., Chin, E.L., Storms, D.H., Lemay, D.G., Stephensen, C.B. 2021. Tree-based analysis of dietary diversity captures associations between fiber intake and gut microbiota composition in a healthy U.S. adult cohort. Journal of Nutrition. 152(3):779-788. https://doi.org/10.1093/jn/nxab430.Unique transcriptomic changes underlie hormonal interactions during mammary histomorphogenesis in female pigs-(Peer Reviewed Journal) Trott, J.F., Schennink, A., Horigan, K.C., Lemay, D.G., Cohen, J.R., Famula, T.R., Dragon, J.A., Hovey, R.C. 2021. Unique transcriptomic changes underlie hormonal interactions during mammary histomorphogenesis in female pigs. Endocrinology. 163(3). Article bqab256. https://doi.org/10.1210/endocr/bqab256.Machine learning identifies stool pH as predictor of bone mineral density in healthy multiethnic US adults-(Peer Reviewed Journal) Chin, E.L., Van Loan, M., Spearman, S., Bonnel, E.L., Laugero, K.D., Stephensen, C.B., Lemay, D.G. 2021. Machine learning identifies stool pH as predictor of bone mineral density in healthy multiethnic US adults. Journal of Nutrition. 151(11):3379-3390. https://doi.org/10.1093/jn/nxab266.Effect of manual data cleaning on nutrient intakes using the
automated self-administered 24-hour dietary assessment tool (ASA24)-(Abstract Only) Bouzid, Y.Y., Arsenault, J.E., Bonnel, E.L., Cervantes, E., Kan, A., Burnett, D.J., Keim, N.L., Lemay, D.G., Stephensen, C.B. 2021. Effect of manual data cleaning on nutrient intakes using the automated self-administered 24-hour dietary assessment tool (ASA24) . Current Developments in Nutrition. 5/3. https://doi.org/10.1093/cdn/nzab005.Manual data cleaning modifications can significantly change nutrient values recorded in automated self-administered 24-hour recalls (ASA24)-(Peer Reviewed Journal)Technician-scored stool consistency spans the full range of the bristol scale in a healthy US population and differs by diet and chronic stress load-(Peer Reviewed Journal) Lemay, D.G., Baldiviez, L.M., Chin, E.L., Spearman, S., Cervantes, E., Woodhouse, L.R., Keim, N.L., Stephensen, C.B., Laugero, K.D. 2021. Technician-scored stool consistency spans the full range of the Bristol scale in a healthy US population and differs by diet and chronic stress load. Journal of Nutrition. 151(6):1443-1452. https://doi.org/10.1093/jn/nxab019.Association of the lactase persistence haplotype block with disease risk in populations of european descent-(Peer Reviewed Journal) Joslin, S.E., Durbin-Johnson, B.P., Britton, M.T., Settles, M.L., Korf, I., Lemay, D.G. 2020. Association of the lactase persistence haplotype block with disease risk in populations of European descent. Frontiers in Genetics. 11. Article: 558762. https://doi.org/10.3389/fgene.2020.558762.Association of estimated daily lactose consumption, lactase persistence genotype (rs4988235), and gut microbiota in healthy U.S. adults-(Abstract Only) Kable, M.E., Chin, E.L., Huang, L., Stephensen, C.B., Lemay, D.G. 2020. Association of estimated daily lactose consumption, lactase persistence genotype (rs4988235), and gut microbiota in healthy U.S. adults. Current Developments in Nutrition. 4/2/1566. https://doi.org/10.1093/cdn/nzaa062_023.Reservoirs of antimicrobial resistance genes in retail raw milk-(Peer Reviewed Journal) Liu, J., Zhu, Y., Jay-Russell, M., Lemay, D.G., Mills, D.A. 2020. Reservoirs of antimicrobial resistance genes in retail raw milk. Microbiome. 8(99). https://doi.org/10.1186/s40168-020-00861-6.Harnessing AI to transform agriculture and inform agricultural research-(Peer Reviewed Journal) Peters, D.C., Rivers, A.R., Hatfield, J.L., Lemay, D.G., Liu, S.Y., Basso, B. 2020. Harnessing AI to transform agriculture and inform agricultural research. IEEE IT Professional. 22(3):16-21. https://doi.org/10.1109/MITP.2020.2986124.Multimodal AI to improve agriculture-(Peer Reviewed Journal) Parr, C.J, Lemay, D.G., Owen, C.L., Woodward Greene, M.J., Sun, J. 2021. Multimodal AI to improve agriculture. IEEE IT Professional. 23(3):53-57. https://doi.org/10.1109/MITP.2020.2986122.Estimated daily Lactose consumption in healthy U.S. adults in relation to lactase persistence genotype (rs4988235)-(Abstract Only)Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes-(Peer Reviewed Journal) Treiber, M.L., Taft, D.H., Korf, I., Mills, D.A., Lemay, D.G. 2020. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinformatics. 21(74). https://doi.org/10.1186/s12859-020-3416-y.Fecal metatranscriptomics and glycomics suggests that bovine milk oligosaccharides are fully utilized by healthy adults-(Peer Reviewed Journal) Westreich, S.T., Salcedo, J., Durbin-Johnson, B., Smilowitz, J.T., Korf, I., Mills, D.A., Daniela, B., Lemay, D.G. 2020. Fecal metatranscriptomics and glycomics suggests that bovine milk oligosaccharides are fully utilized by healthy adults. Journal of Nutritional Biochemistry. 79. https://doi.org/10.1016/j.jnutbio.2020.108340.Nutrient estimation from 24-hour food recalls using machine learning and database mapping: a case study with lactose-(Peer Reviewed Journal) Chin, E.L., Simmons, G., Bouzid, Y.Y., Kan, A., Burnett, D.J., Tagkopoulos, L., Lemay, D.G. 2019. Nutrient estimation from 24-hour food recalls using machine learning and database mapping: a case study with lactose. Nutrients. 11(12):3045. https://doi.org/10.3390/nu11123045.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. 11(8):1860. 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 Communications. 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-(Trade Journal) 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.  ProjectsWHNRC Fiber Intervention Study: Dietary AssessmentCooperative Agreement (A)Accession Number:438315Effect of Diet on Gut Microbiome, Gastrointestinal Health, and Immune FunctionIn-House Appropriated (D)Accession Number:446030AI Institute for Next Generation Food SystemsReimbursable Cooperative Agreement (R)Accession Number:438876Valorization of Dairy Sidestreams to Fight Calcium Deficits in Postmenopausal WomenReimbursable Cooperative Agreement (R)Accession Number:437629Effect of Yogurt on Mucosal Immunity in the Gastrointestinal TractReimbursable Cooperative Agreement (R)Accession Number:443499Advancing Methods and Applications in Metagenomics Sequence AnalysisNon-Assistance Cooperative Agreement (S)Accession Number:444878Modernizing Dietary Assessment: Adapting Deep Learning to Predict Ingredients from Food PhotosNon-Assistance Cooperative Agreement (S)Accession Number:441170Assessment of Intestinal Permeability in AdultsNon-Assistance Cooperative Agreement (S)Accession Number:441392Mothers, Infants and Lactation Quality-Extra Analyses (MILQ II) Project IITrust Fund Cooperative Agreement (T)Accession Number:437095  ARS News ArticlesitemStudy Gives Insight into Diet, Gut Bacteria and Chronic DiarrheaitemDiets High in Fiber Associated with Less Antibiotic Resistance in Gut BacteriaitemHumans More Unique than Expected When It Comes to Digesting Fatty Meals


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