• Liu, J., F. Yu, D. R. Call, D. A. Mills, A. Zhang, Z. Zhao. 2020. On-farm soil resistome is modified after treating dairy calves with the antibiotic florfenicol.  Science of the Total Environment (In Press).
  • Hasegawa, Y., S.-Y. Chen, L. Sheng, P. Kumar Jena, K. M. Kalanetra, D. A. Mills, Y.-J. Wan and C. M. Slupsky. 2020. Long-term effects of western diet consumption in male and female mice.  Scientific Reports. 10:14686.
  • Oliver, A., B. LaMere, C. Weihe, S. Wandro, K. L. Lindsay, P. D. Wadhwa, D. A. Mills, D. Pride, O. Fiehn, T. Northen, M. de Raad, H. Li, J. B. H. Martiny, S. Lynch, K. Whiteson. 2020.  Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy.  mBio 11:e01851-20.         
  • Amicucci, M. J., E. Nandita, A. G. Galermo, J. Castillo, S. Chen, D. Park, J. Smilowitz, J. B. German, D. A. Mills, C. B. Lebrilla. 2020.  A nonenzymatic method for cleaving polysaccharides to yield oligosaccharides for structural analysis. Nature Communications 11:3963.
  • Welker, D. L., B. L. Crowley, J. B. Evans, M. H. Welker, J. R. Broadbent, R. F. Roberts, and D. A. Mills. 2020.  Transformation of Lactiplantibacillus plantarum and Apilactobacillus kunkeei is influenced by recipient cell growth temperature, vector replicon, and DNA methylation.  Journal of Microbiology Methods 175:105967.

  • Liu, J., Y. Zhu, M. Jay-Russell, D. G. Lemay and D. A. Mills.  2020.  Reservoirs of antimicrobial resistance genes in retail raw milk.  Microbiome 8:99.
  • Dunne-Castagna V., D. A. Mills, B. Lönnerdal. 2020. Effects of Milk Secretory Immunoglobin A on the Commensal Microbiota. Ogra PL, Walker WA, Lönnerdal B (eds): Milk, Mucosal Immunity and the Microbiome: Impact on the Neonate. Nestlé Nutr Inst Workshop Ser, Nestec Ltd. Vevey/S. Karger AG Basel, vol 94. doi: 10.1159/000505335
  • Treiber, M.L., D. H. Taft, I. Korf, D. A. Mills, and D. G. Lemay. 2020. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinformatics 21:74.
  • Westreich, S. T., J. Salcedo, B. Durbin-Johnson, J. T. Smilowitz, I. Korf, D. A. Mills, D. Barile, D. G Lemay. 2020. Fecal metatranscriptomics and glycomics suggests that bovine milk oligosaccharides are fully utilized by healthy adults.  Journal Nutritional Biochemistry 79:108340.
  • Ozturk, G., I. M. Shah, D. A. Mills, J. B. German and J. M. L. N. de Moura Bell. 2020. The antimicrobial activity of bovine milk xanthine oxidase. International Dairy Journal 102:104581. 
  • Weinborn V., Y. Li, I. M. Shah, H. Yu, D. C. Dallas, J. B. German, D. A. Mills, X. Chen, D. Barile. 2020. Production of functional mimics of human milk oligosaccharides by enzymatic glycosylation of bovine milk oligosaccharides.  International Dairy Journal 102:104583.
  • Wedgwood S, C. Warford, S. R. Agvatisiri, P. N. Thai, N. Chiamvimonvat, K. M. Kalanetra, S. Lakshminrusimha, R. H. Steinhorn, D. A. Mills and M. A. Underwood. 2020.  The developing gut-lung axis: post-natal growth restriction, intestinal dysbiosis and pulmonary hypertension in a rodent model. Pediatric Research 87:472–479.


  • Cremoninia, E. E. Daveri, A. Mastaloudis, A. M. Adamo, D. A. Mills, K. Kalanetra, S. N. Hester, S. M. Wood, C. G. Fragaah, P. I. Oteiza.  2019.  Anthocyanins protect the gastrointestinal tract from high fat diet-induced alterations in redox signaling, barrier integrity and dysbiosis.  Redox Biology 26:101269.
  • Taft, D. H., S. Akre, N. Madrid, A. Knoesen, D. A. Mills and Z. T. Lewis. 2019. Resident microbes of lactation rooms and daycares. PeerJ 7:e8168.
  • Liu, S., C. Skory, X. Liang, D. A. Mills, and N. Qureshi.  2019. Increased ethanol tolerance associated with the pntAB locus of Oenococcus oeni and Lactobacillus buchneri.  Journal of Industrial Microbiology and Biotechnology 46:1547-1556.
  • Elgin T.G., E. M. Fricke, H. Gong, J. Reese, D. A. Mills, K. M. Kalantera, M. A. Underwood and S. J. McElroy. 2019. Fetal exposure to maternal inflammation interrupts murine intestinal development and increases susceptibility to neonatal intestinal injury. Disease Models & Mechanisms. 12:dmm040808.
  • Liu, J., D. H. Taft, M. X. Maldonado-Gomez, D. Johnson, M. L. Treiber, D. G. Lemay, E. J. DePeters and D. A. Mills. 2019. The fecal resistome of dairy cattle is associated with diet during nursing. Nature Communications 10:4406.
  • Cowardin, C. A., P. P. Ahern, V. L. Kung, M. C. Hibberd, J. Cheng, J. L. Guruge, V. Sundaresan, R. D. Head, D. Barile, D. A. Mills, M. J. Barratt, S. Huqg, T. Ahmed, and J. I. Gordon.  Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse model of infant undernutrition.  Proceedings of the National Academy of Science 116:11988-11996.
  • Taft, D. H., L. K. Salinero, K. Vongbhavit, K. M. Kalanetra, C. Masarweh, A. Yu, M. A. Underwood, D. A. Mills.  2019. Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes.  FEMS Microbial Ecology 95:fiz039.
  • Huda, N. M., S. M. Ahmad, K. M. Kalanetra, D. H. Taft, M. J. Alam,A. Khanam, R. Raqib, M. A. Underwood, D. A. Mills, C. B. Stephensen. 2019. Neonatal vitamin A supplementation and vitamin A status are associated with gut microbiome composition in Bangladeshi infants in early infancy and at two years of age.  J. Nutrition 149:1075-1088.
  • Huda, M. N., S. M. Ahmad, J. Alam, A. Khanam, K. M. Kalanetra, D. H. Taft, R. Raqib, M. A. Underwood, D. A. Mills, C. B. Stephensen. 2019.  Bifidobacterium abundance in early infancy and vaccine response at two years of age.  Pediatrics 143:e20181489.
  • Sanctuary, M. R., J. N. Kain, S. Chen, K. Kananetra, D. G. Lemay, D. R. Rose, H. T. Yang, D. J. Tancredi, J. B. German, C. M. Slupsky, P. Ashwood, D. A. Mills, J. T. Smilowitz, K. Angkustisiri.  2019. Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.  PLOS One 14:e0210064.


  • Lueschow, S. R., J. Stumphy, H. Gong, S. L. Kern, T. G Elgin, M. A. Underwood, K. M. Kalanetra, D. A. Mills, M. H. Wong, D. K. Meyerholz, M. Good, and S. J. McElroy.  2018.  Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. PLOS One 13:e0204967.
  • Taft, D. H.,  J. Liu, M. X. Maldonado-Gomez, S. Akre, M. N. Huda, S.M. Ahmad, C. B. Stephensen and D. A. Mills. 2018. Bifidobacterial dominance of the gut in early life and acquisition of antimicrobial resistance. mSphere e00441-18.
  • Bever, C. S.,  A. A. Rand, M. Nording, D. Taft, K. M. Kalanetra, D. A. Mills, M. A Breck, J. T. Smilowitz, J B. German, B. D. Hammock.  Effects of triclosan in breast milk on the infant fecal microbiome. Chemosphere 203:467-473.
  • Jena P. K. L. Sheng, N. Nagar, C. Wu., D. Barile, D. A. Mills, Y-J Wan. 2018. The effect of synbiotic Bifidobacterium infantis and milk oligosaccharides on shaping gut microbiota community structure and NASH treatment.  Data in Brief 19:1025-1029.
  • Westreich, S. T., M. L. Treiber, D. A. Mills, I. Korf, D. G. Lemay. 2018. SAMSA2: A standalone metatranscriptome analysis pipeline.  BMC Bioinformatics 19:175.
  • Jena P. K., C. Wu, D. A. Mills, N. Nagar, D. Barile, L. Sheng,  Y.J. Wan. 2018. Synbiotics Bifidobacterium infantis and milk oligosaccharides are effective in reversing cancer-prone non-alcoholic steatohepatitis using Western diet-fed FXR knockout mouse models. J. Nutritional Biochemistry 57:246-254.
  • Oteiza, P. I., C.G. Fragaa, D.A. Mills, D.H. Taft. 2018. Flavonoids and the gastrointestinal tract: Local and systemic effects.  Molecular Aspects of Medicine 61:41-49.
  • Fricke, E. M., T. G. Elgin, H. Gong, J. Reese, K. Gibson-Corley, R. Weiss, K. Zimmerman, N. C. Bowdler, K. M. Kalantara, D. A. Mills, M. A. Underwood, S. J. McElroy. 2018. Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. Placenta 79:e12816.
  • Cremonini, E., Z. Wang, A. Bettaie, A. M. Adamo, E. Daveri, D. A. Mills, K. Kalanetra,  F. G. Hajb, P. I. Oteiza. 2018. Epicatechin protecs the intestinal barrier from high fat diet-induced permeabilization: Implications for steatosis and insulin resistance. Redox Biology 14:588-599.
  • Kirmiz, N., R. C. Robinson, I. M. Shah, D. Barile and D. A. Mills.  2018.  Milk glycans and their interaction with the infant gut microbiota.  Annual Review in Food Science & Technology 9:429-450.
  • Garcia-Mazcorro, J. F., D. A. Mills, K. Murphy, G. Noratto.  2018.  Effect of barley supplementation on the fecal microbiota, caecal biochemistry and key biomarkers of obesity and inflammation in obese db/db mice.  European Journal of Nutrition.
  • Shani, G. I., Z. T. Lewis, A. M. Robinson and D. A. Mills. 2017. In, The Bifidobacteria and Related Organisms, Biavati, B. W. H. Holzapfel, P. Mattarelli and B. J. B. Wood Eds. Interactions between bifidobacteria, milk oligosaccharides and neonate hosts. p165-175. Elsevier, New York, New York.


  • Frese, S., A. Hutton, L. Contreras, C. Shaw, M. Palumbo, G. Casaburi, G. Xu, J. Davis, C. Lebrilla, B. Henrick, S. Freeman, D. Barile, J. B. German, D. A. Mills, J. Smilowitz, M. Underwood. Persistence of supplemented Bifidobacterium longum subsp. infantis EVC001 in breastfed infants. mSphere 2: e00501-17.
  • Sheng, L., P. K. Jena, Y. Hu, H.-X. Liu, N. Nagar, K. M. Kalanetra, S. W. French, D. A. Mills, Y.-J. Wan. 2017. Hepatic inflammation caused by dysregulated bile acid synthesis is reversible by butyrate supplementation.  Journal of Pathology. 243:431-441.
  • Mills, D. A. Probiotic nomenclature matters redux: confusion on Bifidobacterium longum subsp. infantis taxonomy persists. 2017. Current Medical Research and Opinion 33:2097.
  • Sinha, R., G. A.-Ali, E. Vogtmann, A. A. Fodor, B. Ren, A. Amir, E. Schwager, J. Crabtree, S. Ma, The Microbiome Quality Control Project Consortium (inc. D. A. Mills), C. C. Abnet, R. Knight, O. White, Curtis Huttenhower.  The Microbiome Quality Control Project Baseline: Variation in microbial community amplicon sequencing.  Nature Biotechnology 35:1077-1086.
  • Park, C., G. Xu, M. Barboza, I. M. Shah, H. Raybould, D. A. Mills and C. B. Lebrilla. 2017. Enterocyte glycosylation is responsive to changes in extracellular conditions: Implications for membrane functions.  Glycobiology 27:847-860.
  • Jena, P. K., L. Sheng, H. X. Liu, K. M. Kalanetra, A. Mirsoian, W. J. Murphy, S. W. French, V. V. Krishnan, D. A. Mills, Y.-J. Y. Wan.  2017.  Western diet-induced dysbiosis in FXR knockout mice causes persistent hepatic inflammation post antibiotic treatment. American Journal of Pathology 187:1800-1813.
  • Sheng, L., P. Jena, H.-X. Liu, K. Kalanetra, F. Gonzalez, S. French, V. Krishnan, D. Mills, and Y.-J. Wan. 2017. Gender differences in bile acids and microbiota in relationship with gender dissimilarity in steatosis induced by diet and FXR inactivation.  Scientific Reports 7:1748.
  • Underwood, M. A., J. C. C. Davis, K. M. Kalanetra, S. Gehlot, S. Patole, D. J. Tancredi, D. A. Mills, C. B. Lebrilla, and K. Simmer. 2017. Digestion of human milk oligosaccharides by Bifidobacterium breve in the premature infant.  Journal of Pediatric Gastroenterology & Nutrition 4:449-455.
  • Hamilton, M. K., C. Ronveaux, B. M. Rust, J. W. Newman, M. Hawley, D. Barile, D. A. Mills and H. E. Raybould. Prebiotic milk oligosaccharides prevent development of obese phenotype, impairment of gut permeability and microbial dysbiosis in high-fat fed mice. 2017. American Journal of Physiology - Gastrointestinal and Liver Physiology 312:G474-G487.
  • Lewis, Z. T. and D. A. Mills.  Differential establishment of bifidobacteria in the breastfed infant gut.   2017. Nestle Nutrition Institute Workshop Series. 88:149-159.
  • Boudry, G.,  M K. Hamilton, M. Chichlowski, S. Wickramasinghe, D. Barile, K. M Kalanetra, D. A. Mills and H. E Raybould. 2016. Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice.  Journal of Dairy Science 100:2471-2481.
  • Lewis, Z. T., K. Sidamonidze, V. Tsaturyan, D. Tsereteli, N. Khachidze, A. Pepoyan, E. Zhgenti, L. Tevzadze, A. Manvelyan, M. Balayan, P. Imnadze, T. Torok, D. G. Lemay,  D. A. Mills. 2017.  The fecal microbial community of breast-fed infants from Armenia and Georgia. Scientific Reports 7: 40932.
  • Davis, J., Z. Lewis, S. Krishnan, R. Bernstein, S. Moore, A. M. Prentice, D. A. Mills, C. B. Lebrilla, and A. Zivkovic. 2017.  Growth and morbidity of Gambian infants are influenced by maternal milk oligosaccharides and infant gut microbiota. Scientific Reports 7:40466.
  • Smilowitz, J. T., D. G. Lemay, K. M. Kalanetra, E. L. Chin, A. M. Zivkovic, M. A. Breck, J. B. German, D. A. Mills, C. Slupsky and D. Barile. 2017.  Tolerability and safety for the intake of bovine milk oligosaccharides extracted from cheese whey in healthy human adults.  Journal of Nutritional Science. 6:e6.


  • Westreich, S. T., I. Korf, D. A. Mills, DG Lemay.  2016. SAMSA: A comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics 17:399.

  • Garrido, D., S. Ruiz-Moyano, N. Kirmiz, J. C. C. Davis, S. Totten, D. G. Lemay, J. A. Ugalde, J. B. German, C. B. Lebrilla, and D. A. Mills.  2016.  A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596. Nature Scientific Reports. 6:35045.
  • Davis, J. C.C.,  S. M. Totten, J. O. Huang, S. Nagshbandi, N. Kirmiz, D. A. Garrido, Z. T. Lewis, L. D. Wu, J. T. Smilowitz, J. B. German, D. A. Mills and C. B. Lebrilla.  2016.  Identification of oligosaccharides in feces of breast-fed infants and their correlation with the gut microbial community.  Molecular and Cellular Proteomics 15:2987-3002.
  • Salcedo Domiguez, J., S. Frese, D. A. Mills and D. Barile.  Characterization of porcine milk oligosaccharides during early lactation and their relation to the fecal microbiome.  Journal of Dairy Science 99:7733-7743.
  • Garcia-Mazcorro, J., D. A. Mills, G. Noratto. 2016. Molecular exploration of fecal microbiome in quinoa-supplemented obese mice. FEMS Microbiology Ecology 92: fiw089.
  • Awasthi,S., R. Wilken, F. Patel, J. B. German, D. A. Mills, C. B. Lebrilla, K. Kim, S. L. Freeman, J. T. Smilowitz, A. W. Armstrong and E. Maverakis.  2016. Dietary supplementation with Bifidobacterium longum subsp. infantis (B. infantis) in healthy breastfed infants: study protocol for a randomised controlled trial. Trials 17: 340.
  • Charbonneau M. R., L. V. Blanton, D. B. DiGiulio, D. A. Relmam, Lebrilla CB, D. A. Mills and J. I. Gordon, 2016. A microbial perspective of human developmental biology. Nature 535:48-55.
  • Bokulich, N. A., C. Masarweh, T. S. Collins, G. Allen, H. Heymann, S. E. Ebeler and D. A. Mills. 2016. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio 7:e00631-16.
  • Powell, W.T., R. A. Borghese, K. M. Kalanetra, M. Mirmiran, D. A Mills, and M. A. Underwood. 2016. Probiotic administration in infants with gastroschisis. Journal of Pediatric Gastroenterology and Nutrition. 62:852-857.
  • Kirmiz, N, and D. A. Mills. 2016. 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.
  • Jeong KH, B. Israr, S. P. Shoemaker, D. A. Mills, J. Kim. 2016.  Impact of lactic acid and hydrogen ion on the simultaneous fermentation of glucose and xylose by the carbon catabolite derepressed Lactobacillus brevis ATCC 14869.  Journal of Microbiology and Biotechnology 26:1182-1189.
  • Walker, G. A., A. Hjelmeland, N. A. Bokulich, D. A. Mills, S. E. Ebeler and L. F. Bisson. 2016.  Impact of the [GAR+] prion on fermentation progression and bacterial population composition with Saccharomyces cerevisiae strain UCD932.  American Journal of Enology and Viticulture. 67:296-307.
  • Karav, S., A. Le Parc, J. M. L. N. de Moura Bell, S. A. Frese1, N. Kirmiz, D. E. Block, D. Barile, and D. A. Mills. 2016. Oligosaccharides released from milk glycoproteins are selective growth substrates for infant-associated bifidobacteria.  Applied and Environmental Microbiology 82:3622-3630.
  • 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. 2016. Sialylated milk oligosaccharides promote growth in gnotobiotic mice and piglets harboring a stunted Malawian infant gut microbiota. Cell 164: 1–13.
  • Chao Z., Y. Wu, H. Yu, I. M. Shah, Y. Li, J. Zeng, B. Liu, D. A. Mills and X. Chen.  2016. One-pot multienzyme (OPME) synthesis of human blood group H antigens and a human milk oligosaccharide (HMOS) with highly active Thermosynechococcus elongatus α1–2-fucosyltransferase. Chemical Communications 52: 3899-3902.
  • Lewis, Z. T., J. Davis, J. T. Smilowitz, J B. German, C. B Lebrilla, D. A Mills. 2016.  The impact of freeze-dryingPeds Res Cover Zachinfant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 4:e1612.
  • Pediatric Research Book CoverLewis, 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 79: 445-452.
  • Bokulich, N. A., Z. T. Lewis, K. L Boundy-Mills, D. A. Mills.  2016.  A new perspective on microbial landscapes within food production. Current Opinion in Biotechnology. 37:182–189.
  • Sohn, K. K. Kalanetra, D. A. Mills and M. A. Underwood. 2016. Buccal administration of human colostrum: impact on the oral microbiota of premature infants. Journal of Perinatology 36:106–111.
  • Garcia-Mazcorro​, J. F., I. Ivanov, D. A. Mills, G. Noratto​.  Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice. PeerJ 4:e1702; DOI 10.7717/peerj.1702.
  • 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.


  • 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 78:670-677.
  • 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 Progress31:1323-1330.
  • 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 Reports5:13517.
  • 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.Peds Res Cover Underwood L. Waterhouse.  2014. Phenolic metabolites and substantial microbiome changes in pig feces by ingesting grape seed proanthocyanidins.  Food & Function 5: 2298-2308.
  • Pediatric Research Book CoverUnderwood, 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.
  • Ramsey, M. S., and D. A. Mills. Beer and Wine. 2014.  In, S. Doores, M.L. Tortorello, and B. Wilcke Eds, Compendium of Methods for the Microbiological Examination of Foods 5th Edition American Public Health Association, Washington DC. DOI: 10.2105/MBEF.0222.069.
  • Tsuei, J., T. Chau, D. A. Mills and Y.-J. Y. Wan. 2014. Bile acid dysregulation, gut dysbiosis, and GI cancer.  Experimental Biology and Medicine 239:1489-1504.
  • Bokulich, N. A., M. Ohta, M. Lee and D. A. Mills. 2014. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Applied and Environmental Microbiology 80:5522-5529.
  • 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.
  • Lewis, Z. and D. A. Mills.  2014.  Oligosaccharides as functional foods. In: D. R. Heldman, D. Hoover, M. B. Wheeler and A. B. Damania Eds.  Encyclopedia of Biotechnology in Agriculture and Foods.  DOI: 10.1081/E-EBAF-120045504.
  • 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.
  • Bokulich, N. A., J. H. Thorngate, P. M. Richardson and D. A. Mills. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.  Proceedings of the National Academy of Sciences 111:E139-148.


  • 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 Perinatology33:691-697.
  • 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.
  • Bokulich, N. A., C. W. Bamforth and D. A. Mills. 2012. A review of molecular methods for microbial community profiling of beer and wine.  Journal of the American Society for Brewing Chemists 70:150-162.
  • 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.


  • Journal of Bacteriology CoverMarcobal 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 Bacteriology193:4019-4020. (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.
  • Supplement to PNAS coverGarrido, 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. BottaTrends in Microbiology covercini, 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.
  • German, 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 brevis.  Microbiology 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.
  • Journal of 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 OenococcusJournal 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 lactisBiotechnology 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.