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  • Hutkins, R., J. Krumbeck, L. B Bindels, P. Cani, G. Fahey, Jr, Y, Goh, B. Hamaker, E. Martens, D. A. Mills, R. Rastal, E. Vaughan.  2016.  Prebiotics: why definitions matter.   Current Opinion in Biotechnology 37:1-7.
  • Dallas, D. C., F. Citerne, T. Tian, V. L. M.  Silva, K. M. Kalanetra, S. A. Frese, R. C. Robinson, D. A. Mills and D. Barile.  2016. Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.  Food Chemistry 197: 273–284.


  • Charbonneau, M. R., D. O’Donnell, L. V. Blanton, S. M. Totten, J. Davis, M. J. Barratt, J. Cheng, J. Guruge, M. Talcott, J. R. Bain, M. J. Muehlbauer, O. Ilkayeva, C. Wu, T. Struckmeyer, D. Barile, K. Maleta, K. Dewey, P. Ashorn, C. B. Newgard, C. Lebrilla, D. A. Mills, J. I. Gordon. 2015. Sialylated milk oligosaccharides promote growth in gnotobiotic mice and piglets harboring a stunted Malawian infant gut microbiota. Cell. (In Press).
  • Powell, W.T., R. A. Borghese, K. M. Kalanetra, M. Mirmiran, D. A Mills, and M. A. Underwood. Probiotic administration in infants with gastroschisis. Journal of Pediatric Gastroenterology and Nutrition. (In Press).
  • Sohn, K. K. Kalanetra, D. A. Mills and M. A. Underwood. 2015. Buccal administration of human colostrum: impact on the oral microbiota of premature infants. Journal of Perinatology (In Press).
  • Lewis, Z. T., G. Shani, C. Masarweh, M. Popovic, S. A. Frese, D. A. Sela, M. A. Underwood and D. A. Mills. 2015. Validating bifidobacterial species and subspecies identity in commercial probiotic products.  Pediatrics Research (In Press).
  • Underwood, M. A., S. Gaerlan, M. L. De Leoz, L. Dimapasoc, K. M. Kalanetra, D. G. Lemay, J. B. German, D. A. Mills, and C. B. Lebrilla.  2015.  Human milk oligosaccharides in premature infants: absorption, excretion and influence on the intestinal microbiota. Pediatric Research (In Press).
  • Kirmiz, N, and D. A. Mills. 2015. Intestinal microbiota in breast-fed infants: insights into infant-associated bifidobacteria and human milk glycans.  In:  R. R. Watson Ed.  Bioactive Foods in Promoting Health: Probiotics, Prebiotics, and Synbiotics 2nd Edition. Elsevier  (In Press).
  • Karav, S., J. M. L. N. de Moura Bell, A. Le Parc, Y. Liu, D. A. Mills, D. E. Block and D. Barile. 2015.  Characterizing the release of bioactive N-glycans from dairy products by a novel endo-β-N-acetylglucosaminidase. Biotechnology Progress 31:1331-1339.
  • Le Parc, A., S. Karav, J. M. L. N. de Moura Bell, A. Le Parc, Y. Liu, D. A. Mills, D. E. Block and D. Barile. 2015. A novel endo-β-N-acetylglucosaminidase releases specific N-glycans depending on different reaction conditions. Biotechnology Progress 31:1323-1330.
  • Wickramasinghe, S, A. R. Pacheco, D. G. Lemay, and D. A. Mills. 2015. Bifidobacteria grown in human milk oligosaccharides down regulate the expression of inflammation-related genes in Caco-2 cells.  BMC Microbiology15:172.
  • Pudlo, N., K. Urs, S. S. Kumar, J. B. German, D. A. Mills and E. C. Martens.  2015. Symbiotic human gut bacteria with variable metabolic priorities for host mucosal glycans.  mBio 6: e01282-15.
  • Frese, SA, K, Parker, C. C. Calvert and D. A. Mlls. 2015.  Diet shapes the microbiome of pigs during nursing and weaning. Microbiome 3:28.
  • Garrido, D. S. Ruiz-Moyano, D. G. Lemay, D. A. Sela, J B. German and D. A Mills. 2015. Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria. Nature Scientific Reports 5:13517.
  • Kim, S. R., T. V. Nguyen, N. R. Seo, S. Jung, H. J. An, D. A. Mills, and J.-H. Kim. 2015. Comparative proteomics: assessment of biological variability and dataset comparability.  BMC Bioinformatics. 16:121.
  • Frese, S. A. and D. A. Mills.  2015.  Birth of the infant gut microbiome: Moms deliver twice!  Cell Host and Microbe 17:543–544.
  • Swadener, M. L. and D. A. Mills. 2015. A new look at an old practice: How SO2 additions influence microbial diversity during fermentation. Wine & Viticulture Journal 3:32-34.
  • Frese, S. and D. A. Mills.  2015. Should infants cry over spilled milk? Fecal glycomics as an indicator of a healthy infant gut microbiome.  Journal of Pediatric Gastroenterology and Nutrition 60:695.
  • Karav, S., A. Le Parc-Le Bouedec, J. M. L. N. de Moura Bell, C. Rouquié, D. A. Mills, D. Barile and D. E. Block. 2015. Kinetic characterization of a novel endo-beta-N-acetylglucosaminidase on concentrated bovine colostrum whey to release bioactive glycans. Enzyme and Microbial Technology 77:46–53.
  • Subramanian, S., L. Blanton, S. A. Frese, M. Charbonneau, D. A. Mills, and J. I. Gordon.  2015. Cultivating healthy growth and nutrition through the gut microbiota. Cell 161:36-48.
  • Zarraonaindia, I., S. M. Owens, K. West, J. Hampton-Marcell, S.Lax, N. A. Bokulich, D. A. Mills, G Martin, S. Taghavid, D. van der Lelie and J. A. Gilbert.  2015.  The soil microbiome influences grapevine-associated microbiota. mBio 6:e02527-14.
  • Lewis, Z. T., S. M. Totten, J. T. Smilowitz, M. Popovic, E. Parker, D. G. Lemay, M. L. Van Tassell, M. J. Miller, Y. S. Jin,  J. B. German, C. B. Lebrilla and D. A. Mills. 2015. Maternal fucosyltransferase 2 status impacts gut bifidobacterial communities of breastfed infants. Microbiome 3:13.
  • Bokulich, N. A., J. Bergsveinson, B. Ziola, D. A. Mills. 2015. Mapping microbial ecosystems and spoilage-gene flow in brewery environments highlights patterns of contamination and resistance. Elife 4:e04634.
  • Porcellato, D., M. E. Johnson. K. Houck. S. B. Skeie. D. A. Mills. K. M. Kalanetra, J. L. Steele. 2015. Potential of Lactobacillus curvatus LFC1 to produce slits in Cheddar cheese. Food Microbiology 49: 65–73.
  • Bokulich, N. A., L. Amiranashvili, K. Chitchyan, N. Ghazanchyan, K. Darbinyan, N. Gagelidze, T. Sadunishvili, V. Goginyan, G. Kvesitadze, T. Torok and D. A. Mills. 2015. Microbial biogeography of the transnational fermented milk Matsoni. Food Microbiology 50:12–19.
  • McInniss, E. A., K. M. Kalanetra, D. A. Mills and E. A. Maga.  2015.  Impact of lysozyme on the microbiota of raw goat milk. Food Microbiology 46:121-131.
  • Bokulich, N. A., M. Swadener, K. Sakamoto, D. A. Mills and Linda F. Bisson. 2015. Sulphur dioxide treatment alters wine microbial diversity and fermentation progression in a dose-dependent fashion. American Journal of Enology and Viticulture. 66:73-79.
  • Pacheco, A. R., D. Barile, M. A. Underwood, D. A. Mills. 2015.  Impact of the milk glycobiome on the neonate gut microbiota. Annual Reviews in Animal Sciences 3: 419-445.
  • Underwood, M. A., J. B. German, C. B. Lebrilla, D. A. Mills. 2015. Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut.  Pediatric Research 77:229-235.
  • German, J. B., J. T. Smilowitz, C. B. Lebrilla, D. A. Mills, S.L. Freeman. 2015. Metabolomics and milk: The development of the microbiota in breast fed infants.  In, S. Kochhar and F.-P. Martin, Eds, Metabonomics and Gut Microbiota in Nutrition and Disease, Springer, New York, NY pp 147-167.
  • De Leoza, M. L. A., K. M. Kalanetra, N. A. Bokulich, J. S. Strum, M. A. Underwood, J. B. German, D. A. Mills, and C. B. Lebrilla.  2015. Human milk glycomics and gut microbial genomics in infant feces shows correlation between human milk oligosaccharides and gut microbiota: A proof-of-concept study. Journal of Proteome Research 14:491–502.


  • Choy, Y. Y., P. Quifer-Rada, D. M. Holstege, S. A. Frese, C. C. Calvert, D. A. Mills, R. M. Lamuela-Raventos and A. L. Waterhouse.  2014. Phenolic metabolites and substantial microbiome changes in pig feces by ingesting grape seed proanthocyanidins.  Food & Function 5: 2298-2308.
  • Underwood, M., J. Arriola, C. Gerber, A. Kaveti, K. Kalanetra, A. Kananurak, C. Bevins, D. A. Mills, and B. Dvorak. 2014. Bifidobacterium longum subsp. infantis in experimental necrotizing enterocolitis: alterations in inflammation, innate immune response, and the microbiota.  Pediatric Research 76: 326–333.
  • Huda, M N., Z. Lewis, K. Kalanetra, M. Rashid, S. Ahmad, R. Raqib, F. Qadri, M. A. Underwood, D. A. Mills and C. Stephensen. 2014. Stool microbiota and vaccine responses of infants.  Pediatrics 134:2 e362-e372.
  • Ravel, J., M. J. Blaser, J. Braun, E. Brown, F. D Bushman, E. B. Chang, J. Davies, K. G. Dewey, T. Dinan, M. Dominguez-Bello, S. E Erdman, B. B. Finlay, W. S. Garrett, G. B. Huffnagle, C. Huttenhower, J. Jansson, I. B. Jeffery, C. Jobin, A. Khoruts, H. H. Kong, J. W. Lampe, R. E. Ley, D. R. Littman, S. K. Mazmanian, D. A. Mills, A. S. Neish, E. Petrof, D. A. Relman, R. Rhodes, P. J. Turnbaugh, V. B. Young, R. Knight and O. White.  2014.  Human microbiome science: vision for the future: Bethesda, MD, July 24 to 26, 2013.  Microbiome 2:16.
  • Smilowitz, J. T., C. B. Lebrilla, D. A. Mills, J. B. German and S. L. Freeman.  2014. Breast milk oligosaccahrides:  Structure function relationships in the neonate.  Annual Review of Nutrition 34:143-69.
  • Lee H., D. Garrido D., D. A. Mills, D. Barile. 2014. Hydrolysis of milk gangliosides by infant-gut associated bifidobacteria determined by microfluidic chips and high-resolution mass spectrometry. Electrophoresis 11:1742-1750.
  • Ozcan, S. B. J. Kim, G. Ro, J.-H. Kim, L. T. Bereuter, C. Reiter, L. Dimapasoc, D. Garrido, D. A. Mills, R. Grimm, C. B. Lebrilla and  H. J. An. 2014. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Nature Scientific Reports 4:4983.
  • Sela, D. A. and D. A. Mills.  2014. The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk.  The American Journal of Clinical Nutrition 99:697S-703S.
  • Underwood, M. A., K. M. Kalanetra, N. A. Bokulich, M. Mirmiran, D. Barile, D. J. Tancredi, J. B. German, C. B. Lebrilla and D. A. Mills.  2014. Prebiotic oligosaccharides in premature infants.   Journal of Pediatric Gastroenterology & Nutrition 58:352-360.


  • Peacock, K., R. L. Ruhaak, M. K. Tsui, D. A. Mills, C. B. Lebrilla. Isomer-specific consumption of galactooligosaccharides by bifidobacterial species. 2013. Journal of Agricultural and Food Chemistry 61:12612-12619.
  • Ruiz-Moyano, S., S. M. Totten, D. A. Garrido, J. T. Smilowitz, J. B. German, C. B. Lebrilla and D. A. Mills.  2013.  Variation in consumption of human milk oligosaccharides by infant-gut associated strains of Bifidobacterium breve.  Applied and Environmental Microbiology 79:6040-6049.
  • Underwood, M., K. Kalanetra, N. Bokulich, Z. T. Lewis, M. Mirmiran, D. Tancredi and D. A. Mills.  2013. A comparison of two probiotic strains of bifidobacteria in premature infants.  Journal of Pediatrics 163:1585-1591.
  • Ellis, C. L., N. A. Bokulich, K. M. Kalanetra, M. Mirmiran, J. Elumalai, L. Haapanen, T. Schegg, J. C. Rutledge, G. Raff, D. A. Mills, M. A. Underwood. 2013.  Probiotic administration in congenital heart disease: A pilot study.  Journal of Perinatology 33:691-697.
  • Zivkovic, A. M., Z. T. Lewis, J. B. German and D. A. Mills. 2013. Establishment of a milk-oriented microbiota (MOM) in early life:  How babies meet their MOMs.  Functional Food Reviews 5:3-12.
  • Bokulich, N. A. and D. A. Mills. 2013. House microbiome drives microbial landscapes of artisan cheesemaking plants.  Applied and Environmental Microbiology 79:5214-5223.
  • Bokulich, N. A., D. A. Mills and M. Underwood.  2013.  Surface microbes in the neonatal intensive care unit: Changes with routine cleaning and over time. Journal of Clinical Microbiology 51:2617-2624.
  • Bokulich, N. A., M. Ohta, P. M. Richardson and D. A. Mills.  2013. Monitoring seasonal changes in winery-resident microbiota.  PLoS One8:e66437.
  • De Leoz, M. L., S. Wu, J. S. Strum, M. R. Niñonuevo, S. C. Gaerlan, M. Mirmiran, J. B. German, D. A. Mills, C. B. Lebrilla, M. A. Underwood. A quantitative and comprehensive structural method to analyze human milk oligosaccharides in the urine and feces of infants. Analytical and Bioanalytical Chemistry 405:4089-4105.
  • Garrido, D. A., D. C. Dallas and D. A. Mills.  2013. Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications.  Microbiology 159:649-664.
  • Bokulich, N. A. and D. A. Mills.  2013. Improved internal transcribed spacer primer selection enables quantitative, ultra-high-throughput fungal community profiling.  Applied and Environmental Microbiology 79:2519-2526.
  • Kim, J.-H., H. J. An, D. A. Garrido, J. B. German, C. B. Lebrilla and D. A. Mills.  2013. Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans.  PLoS ONE 8(2): e57535.
  • Lewis, Z. T., N. A. Bokulich, K. M. Kalanetra, S. Ruiz-Moyano, M. A Underwood and D. A Mills.  2013. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.  Anaerobe 19:62-69.
  • Ramsey, M. S. and D. A. Mills.   2013.  Winery Biofilms:  A source for contamination throughout the winery.  Practical Winery and Vineyard Journal.  Winter Issue.
  • Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, J. G. Caporaso.  2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10:57-59.
  • Garrido, D., S. Ruiz-Moyano, J. Jimenez-Espinoza, H-J. Eom, D. E. Block and D. A. Mills.  2013. Utilization of galactooligosaccharides by Bifidobacterium longum subsp. infantis isolates.  Food Microbiology 33:262–270.


  • Ma, B. W., N. A. Bokulich, P. A. Castillo, A. Kananurak, M. A. Underwood, D. A. Mills, C. L. Bevins.  2012. Routine habitat change: A source of unrecognized transient alteration of intestinal microbiota in laboratory mice.  PLoS One 7(10): e47416.
  • De Leoz, M. L., S. Gaerlan, J. Strum, L. Dimapasoc, M. Mirmiran, D. Tancredi, J. Smilowitz, K. Kalanetra, D. A. Mills, J. B.  German, C. B. Lebrilla,  M. Underwood.  2012. Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm. Journal of Proteome Research 11:4662-4672.
  • Strum, J., J-H Kim, S. Wu, M. L. De Leoz, K. Peacock, R. Grimm, J. B. German, D. A. Mills, C. B. Lebrilla. 2012. Rapid identification and accurate quantitation of biological oligosaccharide mixtures.  Analytical Biochemistry 84:7793-7801.
  • Chichlowski, M., G. De Lartigue, J. B. German, H. E. Raybould and D. A. Mills. 2012.  Select bifidobacteria cultured on human milk oligosaccharides affect intestinal epithelial function. Journal of Pediatric Gastroenterology and Nutrition 55: 321-327.
  • Garrido, D., C. Nwosu, S. Ruiz-Moyano, D. Aldredge, J. B. German, C. B. Lebrilla and D. A. Mills. 2012.   Endo-beta-N-acetylglucosaminidases from infant-gut associated bifidobacteria release complex N-glycans from human milk glycoproteins.  Molecular and Cellular Proteomics 11:775-785.  Article press coverage
  • Garrido, D., S. Ruiz-Moyano and D. A. Mills. 2012.   Release and utilization of N-acetyl-D-glucosamine from human milk oligosaccharides by Bifidobacterium longum subsp. infantis.  Anaerobe 18:430-435.
  • Bokulich, N, and D. A. Mills. 2012. Next-generation approaches to the microbial ecology of food fermentations.  Journal of Biochemistry and Molecular Biology 45:377-389.
  • Gordon, J. I., K. Dewey, D. A. Mills and R M. Medzhitov. 2012.   The human gut microbiota and undernutrition.  Science Translational Medicine 4:137ps12.
  • Bokulich, N., C. H. Hwang, L. Shuwen, K. Boundy-Mills and D. A. Mills.  2012. Profiling the yeast ecology of wine using terminal restriction fragment length polymorphism analysis.  American Journal of Enology and Viticulture 63:185-194. (AJEV best Paper award).
  • Garrido, D., D. Barile and D. A. Mills.  2012. A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract.  Advances in Nutrition 3:415S-421S.
  • Bokulich, N. A., C. M. L. Joseph, G. Allen, A. K. Benson and D. A. Mills. 2012. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One 7:e36357.
  • Bokulich, N. A., C. Bamforth, and D. A. Mills. 2012. Brewhouse-resident microbiota responsible for fermentation of American coolship ale. PLoS One 7:e35507.
  • Bokulich, N. A. and D. A. Mills.  2012.  Differentiation of mixed lactic acid bacteria communities in beverage fermentations using targeted terminal restriction fragment length polymorphism.  Food Microbiology 31:126-131.
  • Ruiz-Moyano, S., N. Tao, M. Underwood and D. A. Mills.  2012.  Rapid discrimination of Bifidobacterium animalis subspecies by matrix-assisted desorption ionization time of flight (MALDI-TOF) mass spectrometry.  Food Microbiology 30:432-437.
  • Sela, D. A., D. Garrido, L. Lerno, S. Wu, K. Tan, H-J. Eom, A. Joachimiak, C. B. Lebrilla and D. A. Mills. 2012.  Bifidobacterium longum subsp. infantis ATCC15697 α-fucosidases are active on fucosylated human milk oligosaccharides.  Applied and Environmental Microbiology 78:795-803.



  • Marcobal A., M. Barboza, E. D. Sonnenburg, N. Pudlo, E. C. Martens, P. Desai, C. B. Lebrilla, B. C. Weimer, D. A. Mills, J. B. German and J. L. Sonnenburg.  2011. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways.  Cell Host and Microbe 10: 507-514.
  • Liu S., T. D. Leathers, A. Copeland, O. Chertkov, L. Goodwin, and D. A. Mills. 2011. Genome sequence of Lactobacillus buchneri NRRL B-30929, a novel strain from a commercial ethanol plant. Journal of Bacteriology 193:4019-4020. (July issue cover)
  • Sela, D. A., Y. Li, L. Lerno, S. Wu, A. M. Marcobal, J. B. German, Xi Chen, C. B. Lebrilla and D. A. Mills. 2011. An infant-associated bacterial commensal utilizes breast milk sialyoligosaccharides.  Journal of Biological Chemistry 286:11909-11918.
  • pnas cover imageGarrido, D., J.-H. Kim, J. B. German, H. E. Raybould, and D. A. Mills. 2011. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans.  PLoS One 6:e175315.
  • Chichlowski, M., J. B. German, C. B. Lebrilla and D. A. Mills. 2011. The influence of milk oligosaccharides on the microbiota of infants:  Opportunities for formulas.  Annual Reviews in Food Science and Technology 3:331-351.
  • Zivkovic, A., J. B. German, C. B. Lebrilla and D. A. Mills.  2011. The human milk glycobiome and its impact on the infant gastrointestinal microbiota.  Proceedings of the National Academy of Sciences 108:4653-4658.  see comment in New York Times (March issue cover)


  • Turroni, F. F. Bottacini, E. Foroni, I. Mulder, J.-H. Kim, A. Zomer, B.S. Garcia, A. Bidossi, A. Ferrarini, V. Giubellini, M. Delledonne, B. Henrissat, P. Coutinho, M. Oggioni, G. F. Fitzgerald, D. A. Mills, A. Margolles, D. Kelly, D. van Sinderen and M. Ventura.  2010.  Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host derived glycan foraging.  Proceedings of the National Academy of Sciences 45:19514-19519.
  • LoCascio, R. G., P. Desai, D. A. Sela, B. Weimer, and D. A. Mills  2010. Comparative genomic hybridization of Bifidobacterium longum strains reveals broad conservation of milk utilization genes in subsp. infantis. Applied and Environmental Microbiology 76:7373-7381. see comment by ASM
  • Kim, J-H.  D. E. Block and D. A. Mills.  2010. Simultaneous consumption of pentose and hexose sugars: An optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Applied Microbiology and Biotechnology 88:1077-1085.
  • Kim, J-H.  D. E. Block, S. P. Shoemaker and D. A. Mills.  2010. Atypical ethanol production by carbon catabolite derepressed lactobacilli. BioResource Technology 101:8790-8797.
  • Marcobal, A., M. Barboza, J. Froehlich, D. E. Block, J. B. German, C. B. Lebrilla, and D. A. Mills. 2010.  Consumption of human milk oligosaccharides by gut-related microbes.  Journal of Agricultural and Food Chemistry 58:5334-40.
  • TIMcoverGerman, J. B., C. Lebrilla and D. A. Mills.   2010.  Milk’s emerging health ingredients.  Prepared Foods May issue.
  • Sela. D. A. and D. A. Mills.  2010.  Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides.  Trends in Microbiology 18:298-307. (July issue cover)
  • Kim, J-H. D. E. Block, S. P. Shoemaker and D. A. Mills.  2010.  Conversion of rice straw to bio-based chemicals: an integrated process using Lactobacillus brevis.  Applied Microbiology and Biotechnology 86:1375-1385.
  • Sela, D. A., N. P. J. Price and D. A. Mills.  2010.  Metabolism of bifidobacteria.  In B. Mayo and D. van Sinderen Eds.  Bifidobacteria: Genomics and Molecular Aspects.  Caister Academic Press.


  • Barboza, M., D. A. Sela, C. Pirim, R. G. LoCascio, S. L. Freeman, J. B. German, D. A. Mills and C. B. Lebrilla. 2009. Glycoprofiling bifidobacterial consumption of galactooligosaccharides by mass spectrometry reveals strain specific, preferential consumption of glycans.  Applied and Environmental Microbiology 75:7319-7325.
  • Ventura, M.,  F. Turroni, Gipsi Lima-Mendez, Elena Foroni, A. Zomer, S. Duranti, V. Giubellini, F. Bottacini, P. Horvath, R. Barrangou, D. Sela, D. Mills and D. van Sinderen. 2009. Comparative analyses of prophage-like elements present in bifidobacterial genomes.  Applied and Environmental Microbiology 75:6929-6936.
  • Mills, D. A.   Molecular methods to characterize the microbial ecology of wine.  2009. Proceedings of the Sixth International Symposium on Viticulture and Enology, Yangling, China, p. 165-175.
  • Oddone, G. M., D. A. Mills and D. E. Block. 2009.  A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression.  Metabolic Engineering 11:367-381.
  • Oddone, G. M., D. A. Mills and D. E. Block. 2009.  Dual inducible expression of recombinant GFP and targeted antisense RNA in Lactococcus lactis.  Plasmid 62:108–118.
  • Kim, J.-H., S. Shoemaker, and D. A. Mills. 2009.  Relaxed control of sugar utilization in Lactobacillus brevisMicrobiology 155: 1351-1359.
  • Oddone, G. M., D. A. Mills and D. E. Block. 2009.  Incorporation of nisI-mediated nisin immunity improves vector-based nisin-controlled gene expression in lactic acid bacteria. Plasmid 61:151-158.
  • Zhang, G., D. A. Mills and D. E. Block. 2009. Development and optimization of chemically-defined media supporting high cell density growth of lactococci, enterococci, and streptococci.  Applied and Environmental Microbiology 75:1080-1087.  (download recipe for ZMB1 media here)
  • LoCascio, R. G., M. R. Ninoneuvo, S. R. Kronewitter, S. F. Freeman, J. B. German, C. B. Lebrilla, and D. A. Mills. 2009.  A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides.  Microbial Biotechnology 2:333-342.
  • Underwood, M. A., N. H. Salzman, S. H. Bennett, M. Barman, D. A. Mills, A. Marcobal, C. L. Bevins, M. P. Sherman.  2009. A randomized placebo-controlled comparison of two probiotics in preterm infants: Impact on weight gain, intestinal microbiota, and fecal short chain fatty acids. Journal of Pediatric Gastroenterology and Nutrition 49:216-225.
  • Marcobal, A. and D. A. Mills. 2009.  Genomics of Oenococcus oeni and other lactic acid bacteria. In Koning, H., Uden, G. and Frohlich, J. Eds. Biology of Microorganisms on Grapes, in Musts and Wine. Springer, New York.


  • Sela, D. A., J. Chapman, A. Adeuya, J.H. Kim, F. Chen, T.R. Whitehead, A. Lapidus, D.S. Rokhsar, C.B. Lebrilla, J.B German, N.P. Price, P.M. Richardson, and D.A. Mills. 2008. The complete genome sequence of Bifidobacterium longum subsp. infantis suggests adaptation for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences 105:18964-18969. (see profile in Nature).
  • German, J.B, S. L. Freeman, C. B. Lebrilla, and D. A. Mills.  Human milk oligosaccharides: Evolution, structures and bioselectivity as substrates for intestinal bacteria.   2008.  In Bier, D.M., J.B. German, and B. Lonnerdal Eds.  Personalized nutrition for the diverse needs of infants and children.  Karger, New York.
  • Lee J-H, V.N. Karamychev, S.A. Kozyavkin, D. Mills, A.R. Pavlov, N.V. Pavlova, N.N. Polouchine, P.M. Richardson, V.V. Shakhova, A.I. Slesarev, B. Weimer, D.J. O'Sullivan. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics. 9:247.
  • Marcobal, A., M. Underwood and D. A. Mills. Rapid determination of the bacterial composition of commercial probiotic products by terminal restriction fragment length polymorphism analysis. 2008. Journal of Pediatric Gastroenterology and Nutrition. 46:608-611.
  • Ninonuevo, M. P. D. Perkins, J. Francis, L. M. Lamotte, R. G. LoCascio, S. L. Freeman, D. A. Mills, J. B. German, R. Grimm and C. B. Lebrilla. 2008. Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry. Journal of Agricultural and Food Chemistry 56:618-626.
  • J. Bacteriology CoverMarcobal, A., D. Sela, Y. I. Wolf, K. Makarova and D. A. Mills. 2008. Hypermutability and its role in the evolution of the genus Oenococcus. Journal of Bacteriology 190:564-570. (January Issue Cover)
  • Seipert, R., M. Barboza, M. Niñonuevo, R. LoCascio, D. A. Mills, S. Freeman, J. B. German, C. Lebrilla. 2008. Analysis and quantitation of fructooligosaccharides using matrix-assisted laser desorption/ionization fourier transform ion cyclotron resonance mass spectrometry. Analytical Biochemistry 80:159-65.


  • Mills, D. A., T. G. Phister, E. Neeley and E. Johannsen. Wine Fermentations. In, L. Cocolin and D. Ercolini Eds, Molecular Methods and Microbial Ecology of Fermented Foods. Elsevier, New York. 2007.
  • LoCascio R. G,, M. R. Ninonuevo, S. L. Freeman, D. A. Sela, R. Grimm, C. B. Lebrilla, D. A. Mills, and J. B. German. 2007. Glycoprofiling of bifidobacterial consumption of human milk oliogosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation. Journal of Agricultural and Food Chemistry, 55: 8914-8919.
  • Ward, R. E., M. Niñonuevo, D. A. Mills, C. B. Lebrilla, and J. B. German. 2007. In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria. Molecular Nutrition and Food Research. 51:1398-1405.
  • Kim, J.-H. and D. A. Mills. 2007. Improvement of a nisin inducible expression vector for expression of heterologous genes in the lactic acid bacteria. Plasmid 58:275-283.
  • Scharfen, E. C., D. A. Mills and E. A. Maga. 2007. Utilization of human lysozyme transgenic goat milk in cheese-making: Effects on lactic acid bacteria profile. Journal of Dairy Science 90:4084-4091.
  • Oddone, G. M., Q. Q. Lan, H. Rawsthorne, D. A. Mills, and D. E. Block. 2007. Optimization of fed batch production of the model recombinant protein GFP in Lactococcus lactis. Biotechnology and Bioengineering 96:1127-1138.
  • Sela, D., H. Rawsthorne, and D. A. Mills. 2007. Characterization of the lactococcal group II intron target site in its native host. Plasmid 58:127-139.
  • Ninonuevo, M. R., R. E. Ward, R. G. LoCascio, J. B. German, S. L. Freeman, M. Barboza, D. A. Mills, and C. B. Lebrilla. 2007. Quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry. Analytical Biochemistry. 361:15-23.
  • Phister, T. G., H. Rawsthorne, L. Joseph and D. A. Mills. 2007. Quantitative real-time PCR assay for detection and enumeration of Hanseniaspora from wine and juice. American Journal of Enology and Viticulture. 58: 229-233.


  • Rawsthorne, H, K. N. Turner, and D. A. Mills. 2006. Multicopy integration of heterologous genes using the lactococcal group II intron targeted to bacterial insertion sequences. Applied and Environmental Microbiology. 72:6088-6093.
  • Lan, C., G. Oddone, D. A. Mills, and D. E. Block. 2006. Kinetics of Lactococcus lactis growth and metabolite formation under aerobic and anaerobic conditions at the presence or absence of hemin. Biotechnology and Bioengineering 95:1070-1080.
  • LoCascio, R., D. A. Mills, A. L. Waterhouse. 2006. Reduction of catechin, rutin and quercetin levels by interaction with food-related microorganisms in a resting state. Journal of the Science of Food and Agriculture. 86:2105-2112.
  • Ward, R. E., M. Ninonuevo, D. A. Mills, C. B. Lebrilla, and J. B. German. 2006. In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri. Applied and Environmental Microbiology 72:4497-4499.
  • Makarova, K., A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin, E. Koonin, A. Pavlov, N. Pavlova, V. Karamychev, N. Polouchine, V. Shakhova, I. Grigoriev, Y. Lou, D. Rohksar, S. Lucas, K. Huang, D. M. Goodstein, T. Hawkins, V. Plengvidhya, D. Welker, J. Hughes, Y. Goh, A. Benson, K. Baldwin, J.-H. Lee, I. Díaz-Muñiz, B. Dosti, V. Smeianov, W. Wechter, R. Barabote, G. Lorca, E. Altermann, R. Barrangou, B. Ganesan, Y. Xie, H. Rawsthorne, D. Tamir, C. Parker, L. McKay, F. Breidt, J. Broadbent, R. Hutkins, D. O'Sullivan, J. Steele, G. Unlu, M. Saier, T. Klaenhammer, P. Richardson, S. Kozyavkin, B. Weimer, and D. A. Mills. 2006. Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences 103:15611-15616.
  • Mills, D. A. and E. T. Neeley. 2006. Molecular methods to characterize wine microorganisms. International Wine Microbiology Symposium Proceedings, Yosemite, CA, CATI.



  • Mills, D. A. 2004. The lactic acid bacteria genome project. Journal of Food Science, 69 FMS28-30.
  • Mills, D. A. 2004. Practical Implications of the lactic acid bacteria genome project: Malolactic fermentations. Proceedings of the XVIes Entretiens Scientifiques Lallemand. pg 39-43.
  • Sanders, M. .E., F. Guarner, D. A. Mills, B. Pot, J. Rafter, B. Rastall, G. Reid, Y. Ringel, I. Rowland, M. Saarela and K. Tuohy. 2005. Selected Topics in Probiotics and Prebiotics: Meeting Report for The 2004 International Scientific Association for Probiotics and Prebiotics. Current Issues in Intestinal Microbiology. 6:55-68.



  • Mills, D. A., E. Johannsen, and L. Cocolin. 2002. Yeast diversity and persistence in botrytis-affected wine fermentations. Applied and Environmental Microbiology 68:4884-4893.
  • Klaenhammer, T, E. Altermann, F. Arigoni, A. Bolotin, F. Breidt, J. Broadbent, R. Cano, S. Chaillou, J. Deutscher, M. Gasson, M. van de Guchte, J. Guzzo, T. Hawkins, P. Hols, R. Hutkins, M. Kleerebezem, J. Kok, O. Kuipers, M. Lubbers, E. Maguin, L. McKay, D. Mills, A. Nauta, R. Overbeek, H. Pel, D. Pridmore, M. Saier, D. van Sinderen, A. Sorokin, J. Steele, D. O'Sullivan, W. de Vos, B. Weimer, M. Zagorec, and R. Siezen. Discovering lactic acid bacteria by genomics. 2002. Antonie van Leeuwenhoek 82:29-58.
  • Weimer, B. and D. Mills. Enhancing foods with functional genomics. 2002. Food Technology 56:184-189.



Published work prior to UC Davis

  • Madsen, S. M., D. Mills, G. Djordjevic, H. Israelsen, and T. R. Klaenhammer. 2001. Analysis of genes involved in DNA replication and obligate lytic lifestyle of the virulent Lactococcus P335 type bacteriophage f31. Applied and Environmental Microbiology 67:1128-1139.
  • Mills, D. A., T. G. Phister, K. A. Baldwin, G. M. Dunny and L. L. McKay. 1998. Characterization of the lactococcal conjugative element pRS01 using IS946-mediated mutagenesis. Methods in Cell Science 20:71-78.
  • Cousineau, B., D. Smith, S. Lawrence-Cavanagh, J. E. Mueller, J. Yang, D. Mills, D. Manias, G. Dunny, A. M. Lambowitz, and M. Belfort. 1998. Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94:451-462.
  • Mills, D. A., T. G. Phister, G. M. Dunny, and L. L. McKay. 1998. An origin of transfer (oriT) on the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3. Applied and Environmental Microbiology, 64:1541-1544.
  • Mills, D. A., D. A. Manias, L. L. McKay, and G. M. Dunny. 1997. Homing of a group II intron from Lactococcus lactis subsp. lactis ML3. Journal of Bacteriology, 179:6107-6111.
  • Mills, D. A., L. L. McKay, and G. M. Dunny. 1996. Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci. Journal of Bacteriology 178:3531-3538.
  • Mills, D. A., C. K. Choi, G. M. Dunny, and L. L. McKay. 1995. Characterization of the conjugation system associated with the Lactococcus lactis spp. lactis plasmid pRS01. Developments in Biological Standardization 85:543-548.
  • Mills, D. A., C. K. Choi, G. M. Dunny, and L. L. McKay. 1994. Genetic analysis of regions of the Lactococcus lactis subsp. lactis plasmid pRS0 1 involved in conjugative transfer. Applied and Environmental Microbiology 60:4413-4420.
  • Mills, D. A., and M. C. Flickinger. 1993. Cloning sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes. Applied and Environmental Microbiology 59:2931-2936.
  • Alexandrescu, A. T., D. A. Mills, E. L. Ulrich, M. Chinami, and J. L. Markley. 1988. NMR assignment of the four histidines of staphylococcal nuclease in native and denatured states. Biochemistry 27:2158-2165.

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Zach Lewis Paper on Bifidobacterial Species QC profiled Nov 26, 2015
Frese & Mills interviewed by Proto Magazine on infant microbiome Nov 24, 2015
Wine microbiome work profiled by Nature Plants Nov 24, 2015
Liver Cancer-Gut Microbiome work profiled by Synthesis May 04, 2015
Bokulich interviewed on eLife brewery paper Apr 25, 2015
Zachery Lewis's paper in Microbiome Profiled by NPR and UC Davis Apr 11, 2015
Dr. Mills Elected Fellow in American Academy of Microbiology Feb 25, 2015
Milk Bioactives Group profiled by UC Davis Office of Research Dec 11, 2014
NIH Grant Success on Milk Bioactives!! Nov 26, 2014
UC Davis Milk Bioactives Group Profiled in Science Sep 26, 2014
Steve Frese honored by European Probiotics Association Sep 07, 2014
Nick Bokulich garners 2013-14 Kinsella Thesis award Sep 07, 2014
Bangladesh infant cohort paper profiled Jul 26, 2014
Milk Bioactives Program Profiled in Davis Enterprise Jul 26, 2014
Bokulich Sake Paper Profiled Jul 26, 2014
Gates project profiled Apr 03, 2014
Milk bioactives work profiled in Science News Dec 30, 2013
PNAS paper on wine microbial terroir profiled Dec 03, 2013
Bokulich garners Brewing award Oct 26, 2013
Premie probiotic paper profiled Oct 22, 2013
Bokulich beer microbiome work profiled Aug 29, 2013
Dr. Mills NIH talk online Aug 22, 2013
Dave Sela begins faculty position at University of Massachusetts-Amherst Aug 17, 2013
Chemical Engineering News article profiles milk glycan work Jul 08, 2013
Wine Microbial Terroir Work Profiled In Wines and Vines Article May 20, 2013
Mills lab alumni Daniel Garrido honored with award Apr 10, 2013
AJEV paper wins 2013 Best Enology Paper award Apr 09, 2013
Daniel Garrido begins faculty position at Pontifical Catholic University of Chile Mar 24, 2013
Nick Bokulich's Nature Methods paper profiled Dec 05, 2012
Join the American Gut project!! Nov 21, 2012