Peer-Reviewed Publications (Journals and Book Chapters)

231Couture, G., S. E. Cheang, C. Suarez, Y. Chen, N. P. Bacalzo, J. Jiang, C.-Y. Weng, A. Stacy, J. J. Castillo, O. Delannoy-Bruno, D. M. Webber, M. J. Barratt, J. I. Gordon, D. A. Mills, J. B. German, N. K. Fukagawa, C. B. Lebrilla.  2024.  A multi-glycemic platform for analysis of food carbohydrates.   Nature Protocols. (In Press)
230Barnum, C. R.,  B. Paviani, G. Couture, C. Masarweh, Y. Chen, Y.-P. Huang, K. Markel, D. A. Mills, C. B. Lebrilla, D. Barile, M. Yang, P. M. Shih. 2024. Engineered plants provide a photosynthetic platform for the production of diverse human milk oligosaccharides.  Nature Foods (In Press)
229Park, J. S. Wickramasinghe, D. A. Mills, P Ji. Iron-Fortification and inulin supplementation in early-infancy: Evaluating the impact on iron metabolism and trace mineral status in a piglet model.   Current Developments in Nutrition.  (In Press)
228Xu, X., Q. Feng, T. Zhang, Y. Gao, Q. Cheng, W. Zhang, Q. Wu, K. Xu, Y. Li, N. Nguyen, D. Taft, D. A. Mills, D. Lemay, W. Zhu, S. Mao, A. Zhang, K. Xu, J. Liu.  2024. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life.  iMeta e169. doi.org/10.1002/imt2.169.
227Larke, J. A., B. E. Heiss, A. M. Ehrlich, D. H. Taft, H. E. Raybould, D. A. Mills, C. M. Slupsky. 2023. Milk oligosaccharide driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice.  Microbiome 11:194. doi.org/10.1186/s40168-023-01624-9.
226Hebib, V. M., D. H. Taft, B. Stoll, J. Liu, L. Call, G. Guthrie, N. M. Jensen, A. B. Hair, D. A. Mills, D. G. Burrin. 2023. Probiotics and human milk differentially influence the gut microbiome and NEC incidence in preterm pigs.  Nutrients 15:2585. PMC10255242. doi.org/10.3390/nu15112585.
225Mills, D. A., J. B. German, C. B. Lebrilla, and M. A. Underwood. 2023. Translating neonatal microbiome science into commercial innovation: Metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants.  Gut Microbes 15:2192458. PMC10075334. doi: 10.1080/19490976.2023.2192458
224Larke, J. A., K. Kuhn-Riordon, D. H. Taft, K. Sohn, S. Iqbal, M. A. Underwood, D. A. Mills, C. M. Slupsky. 2022.  Preterm infant fecal microbiota and metabolite profiles are modulated in a probiotic specific manner.  Journal Pediatric Gastroenterology and Nutrition. PMC9489674. doi:10.1097/MPG.0000000000003570
223Vongbhavit, K., L. Salinero, K. Kalanetra, C. Masarweh, A. Yu, D. Taft, D. A. Mills and M. Underwood. 2022. A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit.  Journal of Perinatology. PMC9616717. DOI: 10.1038/s41372-022-01452-z
222German, J. B., C. Lebrilla, D. A. Mills. 2022. Milk: A scientific model for diet and health research in the 21st century.  Frontiers in Nutrition. 2022 9:922907. PMC9226620 DOI: 10.3389/fnut.2022.922907.
221Oliver, A., Z. Xue, Y. Tang, B. Durbin-Johnson, Z. Alkan, D. Taft, J. Liu, I. Korf, K. Laugero, C. Stephensen, D. A. Mills, M. Kable and D. Lemay.  2022.  Association of diet and antimicrobial resistance in healthy US adults.  mBio 13:e0010122. PMC9239165. DOI: 10.1128/mbio.00101-22
220Vinjamuri, A., J. C. C. Davis, S. M. Totten, L. D. Wu, L. D. Klein, M. Martin, E. A. Quinn, B. Scelza, A. Breakey, M. Gurven, G. Jasienska, H. Kaplan, C. Valeggia, K. Hinde, J. T. Smilowitz, R. M. Bernstein, A. M. Zivkovic, M. J. Barratt, J. I. Gordon, M. A. Underwood, D. A. Mills, J. B. German, C. B. Lebrilla. 2022. Human milk oligosaccharide compositions illustrate global variations in early nutrition The Journal of Nutrition 152:1239-1253. PMC9071347 DOI: 10.1093/jn/nxac027.
219Castillo, J. J., G. Couture, N. P. Bacalzo, Y. Chen, E. L. Chin, S. E. Blecksmith,Y.  Y. Bouzid, Y. Vainberg, C. Masarweh, Q. Zhou, J. T. Smilowitz, J. B. German, D. A. Mills, D. G. Lemay and C. B. Lebrilla. 2022. The development of the Davis Food Glycopedia — A glycan encyclopedia of food. Nutrients 14: 1639  doi.org/10.3390/nu14081639.
218Taft, D. H., Z. T. Lewis, N. Nguyen, S. Ho, C. Masarweh, V. Dunne-Castagna, D. J. Tancredi, M. N. Huda, C. B. Stephensen, K. Hinde, E. von Mutius, P. V Kirjavainen, J.-C. Dalphin, R. Lauener, J. Riedler, J. T. Smilowitz, J. B. German, A. L. Morrow, D. A. Mills. 2022. Bifidobacterium species colonization in infancy: A global cross-sectional comparison by population history of breastfeeding. Nutrients 14: 1423. PMC9003546 DOI: 10.3390/nu14071423
217Illi S., M. Depner, P. I. Pfefferle, H. Renz, C. Roduit. D. H. Taft. K. M. Kalanetra, D. A. Mills, F. M. Farquharson, P. Louis, E. Schmausser-Hechfellner, A. Divaret-Chauveau, R. Lauener, A. M. Karvonen, J. Pekkanen, J. Riedler, M. Kabesch, B. Schaub , E. von Mutius and the PASTURE Study Group.  2022. Immune responsiveness to LPS determines risk of childhood wheeze and asthma in 17q21 risk allele carriers. American Journal of Respiratory and Critical Care Medicine 205: 641-650. doi.org/10.1164/rccm.202106-1458OC  PubMed: 34919021
216Shani, G., J. L. Hoeflinger, B. E. Heiss, C. F. Masarweh, J. A. Larke, N. M. Jensen, S. Wickramasinghe, J. C. Davis, E. Goonatilleke, A. El-Hawiet, L. Nguyen, J. S. Klassen, C. M. Slupsky, C. B. Lebrilla and D. A. Mills. Fucosylated human milk oligosaccharide foraging within the species Bifidobacterium pseudocatenulatum is driven by glycosyl hydrolase content and specificity. Applied and Environmental Microbiology 88:e0170721. PMC8788745. DOI:10.1128/AEM.01707-21
215Cernioglo, K., K. M. Kalanetra, A. Meier, Z. T. Lewis, M. A. Underwood, D. A. Mills, J. T. Smilowitz. 2021. Multi-strain probiotic supplementation with a product containing human-native S. salivarius K12 in healthy adults increases oral S. salivarius. Nutrients 13:4392. doi.org/10.3390/nu13124392
214Couture, G., T.-T. T. Vo, J. J. Castillo, D. A. Mills, J. B. German, E. Maverakis, and C. B. Lebrilla. 2021.  Glycomic mapping of the maize plant points to greater utilization of the entire plant.  ACS Food Sci. Technol. 1:2117–2126.
213Heiss, B. E., A. M. Ehrlich, M. X. Maldonado-Gomez, D. H. Taft, J. A. Larke, M. L. Goodson, C. M. Slupsky, D. J. Tancredi, H. E. Raybould and D. A. Mills. Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection.  Gut Microbes 13:1986666. PMC8555557 DOI: 10.1080/19490976.2021.1986666.  
212Ba, Z., Y Lee, H. Meng, P. Kris-Etherton, C. Rogers, Z. T. Lewis, D. A. Mills, E. Furumoto, M. Rolon, J. Fleming, and R. Roberts. 2021. Matrix effects on the delivery efficacy of Bifidobacterium animalis subsp. lactis BB-12® on the fecal microbiota, gut transit time, and short chain fatty acids in healthy young adults. mSphere 6:e0008421. PMC8386398. DOI: 10.1128/mSphere.00084-21
211Wang, H., J. Simpson, M. Kotra, Y. Zhu, S. Wickramsinghe, D. A. Mills, N. H. L. Chiu.  2021. Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin.  BMC Research Notes 14:1-6. PMC8058956. DOI: 10.1186/s13104-021-05563-2
210Griggs R. G., K. L. Steenwerth, D. A. Mills, D. Cantu and N. A. Bokulich. 2021.  Sources and assembly of microbial communities in vineyards as a functional component of winegrowing.  Frontiers in Microbiology 12:673810.  PMC8076609. DOI: 10.3389/fmicb.2021.673810
209Kumar, S., M. A. Khan, E. Beijer, J. Liu, K. K. Lowe, W. Young, D. A. Mills, C. D. Moon.  2021. Milk replacer allowances influence calf faecal bacterial community profiles and protein fermentation. Animal Microbiome 3:27. PMC8017768. DOI: 10.1186/s42523-021-00088-2
208Chin, N., D. Taft, G. Méndez-Lagares, H. Kieu, N. Narayan, S. Roberts, D. A. Mills, D. Hartigan-O'Connor, and V. Flaherman.  2021.  Transient effect of infant formula supplementation on the intestinal microbiota.  Nutrients 13:807.  PMC7998963.  DOI: 10.3390/nu13030807
207Ehrlich, A. M., A. R. Pacheco, B. M. Henrick, D. Taft, G. Xe; M. N. Huda, D. Mishchuk, M. L. Goodson, C. Slupsky, D. Barile, C. B. Lebrilla, C. B. Stephensen, D. A. Mills, H. Raybould. 2020. Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells. BMC Microbiology 20:357. PMC7681996.  DOI: 10.1186/s12866-020-02023-y
206Depner, M., K. M. Kalanetra, D. H. Taft, P. Kirjavainen, A. M. Karvonen, E. Schmausser-Hechfellner, C. Roduit, A. Divaret-Chauveau, J.-C. Dalphin, R. Lauener, J. Riedler, J. Kabesch, J. Pekkanen, D. A. Mills, E. von Mutius, M. J. Ege, on behalf of the PASTURE/EFRAIM study group*. 2020. Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma. Nature Medicine 26:1766-1775. PMID: 33139948. DOI: 10.1038/s41591-020-1095-x
205Zhu, Y. J. Liu, J. M. Lopez, and D. A. Mills. 2020. Inulin fermentation by lactobacilli and bifidobacteria from dairy calves. Applied and Environmental Microbiology AEM.01738-20 PMID: 33008824. DOI: 10.1128/AEM.01738-20.
204Liu, 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 750:141694.  PMID: 32871373. DOI: 10.1016/j.scitotenv.2020.141694. 
203Hasegawa, 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. PMC7477228  DOI: 10.1038/s41598-020-71592-9.
202Oliver, 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. PMC7448280  DOI: 10.1128/mBio.01851-20
201Amicucci, 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. PMC7414865  DOI: 10.1038/s41467-020-17778-1
200Welker, 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.  J. Microbiology Methods 175:105967.  PMID: 32512121  DOI: 10.1016/j.mimet.2020.105967
199Liu, 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. PMC7320593  DOI: 10.1186/s40168-020-00861-6.
198Treiber, 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. PMC7041091  DOI: 10.1186/s12859-020-3416-y.
197Westreich, 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.  The Journal of Nutritional Biochemistry 79:108340.  PMC7233280. DOI: 10.1016/j.jnutbio.2020.108340
196Weinborn, 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. PMC7034812. DOI: 10.1016/j.idairyj.2019.104583.
195Ozturk, 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. DOI: 10.1016/j.idairyj.2019.104581.
194Wedgwood 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.  PMC703599 DOI: 10.1038/s41390-019-0578-2
193Taft, D. H., S. Akre, N. Madrid, A. Knoesen, D. A. Mills, Z. T. Lewis. 2019. Resident microbes of lactation rooms and daycares. PeerJ 7:e8168. PMC6913265. DOI: 10.7717/peerj.8168
192Cremonini, E., E. Daveri, A. Mastaloudis, A. M. Adamo, D. A. Mills, K. Kalanetra, S. Hester, S. Wood, C. Fraga. 2019. Anthocyanins protect the gastrointestinal tract from high fat diet-induced alterations in redox signaling, barrier integrity and dysbiosis. Redox Biology 26:101269.  PMC6646927. DOI: 10.1016/j.redox.2019.101269
191Elgin 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. PMC6826024. DOI: 10.1242/dmm.040808
190Liu, 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. PMID: 3128997. DOI: 10.1007/s10295-019-02209-y
189Liu, 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. PMC6765000. DOI: 10.1038/s41467-019-12111-x.
188Taft, 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.  PMC6449222.  DOI: 10.1093/femsec/fiz039.
187Cowardin, 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.  2019. Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse model of infant undernutrition.  Proceedings of the National Academy of Sciences 116:11988-11996. PMC6575181  DOI: 10.1073/pnas.1821770116
186Huda, 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 increases Bifidobacterium abundance in early infancy.  J. Nutrition 149:1075-1088.
185Sanctuary, 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. PMC632656, DOI: 10.1371/journal.pone.0210064
184Huda, 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. PMC6361348 DOI: 10.1542/peds.2018-1489
183Lueschow, 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.  2019.  Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. PLOS One 14:e0210064.  PMC616699  DOI: 10.1371/journal.pone.0204967
182Taft, 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. PMC6158511 DOI: 10.1128/mSphere.00441-18
181Bever, 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. PMC591529  DOI: 10.1016/j.chemosphere.2018.03.186
180Jena 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. PMC5997954 DOI: 10.1016/j.dib.2018.05.127
179Westreich, S. T., M. L. Treiber, D. A. Mills, I. Korf, D. G. Lemay. 2018. SAMSA2: A standalone metatranscriptome analysis pipeline.  BMC Bioinformatics 19:175. PMC5963165 DOI: 10.1186/s12859-018-2189-z
178Jena 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.  PMC6015547 DOI: 10.1016/j.jnutbio.2018.04.007
177Oteiza, 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. PMID: 29317252 DOI: 10.1016/j.mam.2018.01.001
176Fricke, 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. Exposure to LPS-induced maternal inflammation induces direct placental injury without alteration in placental blood flow. Placenta 79: e12816.
175Cremonini, 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. 2018. Redox Biology 14:588-599.
174Kirmiz, 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.
173Garcia-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 31:539-46.
172Frese, 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. 2017. Persistence of supplemented Bifidobacterium longum subsp. infantis EVC001 in breastfed infants. mSphere 2: e00501-17.
171Mills, D. A. Probiotic nomenclature matters redux: confusion on Bifidobacterium longum subsp. infantis taxonomy persists. 2017. Current Medical Research and Opinion 33:2097.
170Kirmiz, N., R. C. Robinson, I. M. Shah, D. Barile and D. A. Mills.  2017.  Milk glycans and their interaction with the infant gut microbiota.  Annual Review in Food Science & Technology 9:429-450.
169Sheng, 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.
168Sinha, 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.  2017. The Microbiome Quality Control Project Baseline: Variation in microbial community amplicon sequencing.  Nature Biotechnology 35:1077-1086.
167Park, 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.
166Sheng, L., P. K. 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.  
165Jena, P. K., L. Sheng, H.-X. Liu, K. M Kalanetra, A. Mirsoian, W. J. Murphy, S. French, K. Krishnan, D. A. Mills, 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.
164Underwood, 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.
163Hamilton, 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.
162Smilowitz, 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.
161Lewis, 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.
160Davis, 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.
159Boudry, 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.
158Westreich, S. T., I. Korf, D. A. Mills, DG Lemay.  SAMSA: A comprehensive metatranscriptome analysis pipeline. 2016. BMC Bioinformatics 17:399.
157Garrido, 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. Scientific Reports. 6:35045.  
156Davis, 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.
155Salcedo 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.
154Garcia-Mazcorro, J., D. A. Mills, G. Noratto. 2016. Molecular exploration of fecal microbiome in quinoa-supplemented obese mice. FEMS Microbiology Ecology 92: fiw089.
153Jeong 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.
152Awasthi,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.
151Charbonneau 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.
150Bokulich, 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.
149Karav, S., A. Le Parc, J. M. L. N. de Moura Bell, S. A. Frese, 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.
148Walker, 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.
147Chao 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.
146Lewis, Z. T., J. Davis, J. T. Smilowitz, J B. German, C. B Lebrilla, D. A Mills. 2016.  The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 4:e1612.
145Charbonneau, 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.
144Bokulich, 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.  
143Dallas, 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.
142Garcia-Mazcorro , J. F., I. Ivanov, D. A. Mills, G. Noratto . 2016. Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice. PeerJ 4:e1702; DOI 10.7717/peerj.1702.
141Hutkins, 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.
140Lewis, Z. T., G. Shani, C. Masarweh, M. Popovic, S. A. Frese, D. A. Sela, M. A. Underwood and D. A. Mills. 2016. Validating bifidobacterial species and subspecies identity in commercial probiotic products.  Pediatrics Research 79: 445-452.
139Powell, 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.
138Sohn, 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.
137Pudlo, 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.
136Le 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.
135Karav, 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.
134Wickramasinghe, 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 Microbiology 15:172.
133Frese, SA, K, Parker, C. C. Calvert and D. A. Mlls. 2015.  Diet shapes the microbiome of pigs during nursing and weaning. Microbiome 3:28.
132Underwood, 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.
131Swadener, 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.
130Karav, 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-β-N-acetylglucosaminidase on concentrated bovine colostrum whey to release bioactive glycans.  Enzyme and Microbial Technology 77:46–53.
129Garrido, 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. Scientific Reports 5:13517.
128Frese, 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.
127Kim, 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.
126Frese, S. A. and D. A. Mills.  2015.  Birth of the infant gut microbiome: Moms deliver twice!  Cell Host and Microbe 17:543–544.
125Subramanian, 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.
124Porcellato, 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.
123Zarraonaindia, 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
122Bokulich, 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.
121Lewis, 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.
120Bokulich, 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.
119Madrid, N. M., D. J Killeen, A. Knoesen, D. A. Mills and R. B. Boulton. 2015. Wireless monitoring of the indoor air environment of a winery during harvest.  Proceedings: Healthy Buildings 2015 America, Boulder, CO, July 19-22.  (Peer Reviewed Proceedings)
118Bokulich, N. A., M. Swadener, K. Sakamoto, D. A. Mills and Linda F. Bisson. 2015. Sulfur dioxide treatment alters wine microbial diversity and fermentation progression in a dose-dependent fashion. American Journal of Enology and Viticulture. 66:73-79.
117De 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.
116Pacheco, 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.
115Underwood, 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.
114McInniss, 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.
113Choy, 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.
112Bokulich, 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.
111Huda, 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.
110Underwood, 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.
109Tsuei, J., T. Chau, D. A. Mills and Y.-J. Y. Wan. Bile acid dysregulation, gut dysbiosis, and GI cancer.  Experimental Biology and Medicine 239:1489-1504.   
108Ravel, 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.
107Ozcan, 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. Scientific Reports 4:4983
106Smilowitz, 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.
105Lee 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.
104Sela, 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.
103Underwood, 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.
102Bokulich, 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-E148.
101Peacock, K., L. R. Ruhaak, M. K. Tsui, D. A. Mills, and C. B. Lebrilla.  2013.  Structure-specific consumption of galacto-oligosaccharides by bifidobacterial species.  Journal of Agricultural and Food Chemistry 61:12612-12619.
100Ruiz-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.
99Underwood, 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.
98De 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.
97Bokulich, N. A. and D. A. Mills. 2013. House microbiome drives microbial landscapes of artisan cheesemaking plants.  Applied and Environmental Microbiology 79:5214-5223.
96Bokulich, 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.
95Zivkovic, 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.
94Bokulich, N. A., M. Ohta, P. M. Richardson and D. A. Mills.  2013. Monitoring seasonal changes in winery-resident microbiota.  PLoS One8:e66437.
93Ellis, 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.
92Bokulich, N. A. and D. A. Mills. 2013. Improved ITS primer selection enables quantitative, ultra-high-throughput fungal community profiling. 79:2519-2526.
91Garrido, D., D. C. Dallas and D. A. Mills.  2013. Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications.  Microbiology 159:649-664.
90Kim, J. H., H. J. An, D. 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.
89Lewis, 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.
88Ramsey, M. S. and D. A. Mills.   2013.  Winery Biofilms:  A source for contamination throughout the winery.  Practical Winery and Vineyard Journal.  Winter Issue.
87Garrido, 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.
86Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, J. G. Caporaso.  2012. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10:57-59.
85Ma, 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: e47416.
84Strum, 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.
83De 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.
82Garrido, 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.  
81Bokulich, 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.
80Chichlowski, 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.
79Garrido, 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.
78Bokulich, 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.
77Gordon, J. I., K. Dewey, D. A. Mills and R M. Medzhitov. 2012. The human gut microbiota and undernutrition.  Science Translational Medicine 4:137ps12.
76Bokulich, N., C. M. L. Joseph, G. Allen, A. Benson and D. A. Mills.  2012. Next-generation sequencing reveals significant bacterial diversity of botrytized wine.  PLoS One 7:e36357.
75Bokulich, 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.
74Garrido, D., D. Barile and D. A. Mills. 2012.   A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract 3:415S-421S.
73Bokulich, N. A., C. Bamforth, and D. A. Mills. 2012. Brewhouse-resident microbiota responsible for fermentation of American coolship ale. PLoS One 7:e35507.
72Bokulich, 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.
71Ruiz-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.
70Sela, 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.
69Marcobal 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.
68Liu 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).
67Sela, 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.  
66Garrido, D., J.-H. Kim, J. B. German, H. E. Raybould, C. B. Lebrilla, and D. A. Mills. 2011. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans. PLoS One 6:e175315.
65Zivkovic, A., J. B. German, C. B. Lebrilla and D. A. Mills.  2011. The human milk glycobiome and its impact on the infant microbiota.  Proceedings in the National Academy of Sciences 108:4653-4658.
64Chichlowski, 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.
63Turroni, 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.
62LoCascio, R. G., P. Desai, D. A. Sela, B. Weimer, and D. A. Mills. Broad conservation of milk utilization genes in Bifidobacterium longum subsp. infantis as revealed by comparative genomic hybridization. Applied and Environmental Microbiology 76:7373-7381.
61Kim, 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.
60Kim, 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.
59Sela, D. A. and D. A. Mills.  2010.  Nursing our microbiota: a molecular link between bifidobacteria and human milk oligosaccharides.  Trends in Microbiology 18:298-307.
58German, J. B., C. Lebrilla and D. A. Mills. 2010. Milk’s emerging health ingredients.  NutraSolutions, Prepared Foods May Issue.  
57Marcobal, A., M. Barboza, J. Froehlich, D. E. Block, J. B. German, C. B. Lebrilla and D. A. Mills.  2010. Consumption of human milk oligosaccahrides by gut-related microbes.  Journal of Agricultural and Food Chemistry 58:5334-40.
56Kim, 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.
55Barboza, 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.
54Ventura, 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.
53Oddone, 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.
52Oddone, 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.
51Oddone, 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.
50Kim, J.-H., S. Shoemaker, and D. A. Mills. 2009. Relaxed control of sugar utilization in Lactobacillus brevis. Microbiology 155: 1351-1359.
49Underwood, M. A., N. H. Salzman, S. H. Bennett, M. Barman, D. 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.
48Zhang, 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.
47LoCascio, R. G, M. R. Ninonuevo, S. Kronewitter, S. L. Freeman, J. B. German, C. L. Lebrilla and D. A. Mills. 2009. High throughput glycoprofiling of bifidobacterial consumption of milk oliogosaccharides. Microbial Biotechnology 2:333-342.
46Sela, D. A., J. Chapman, A. Adeuya, 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 ssp. infantis suggests adaptation for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences 105:18964-18969.
45Lee, J.-H., A. Slesarev, P. Richardson, S. Kozyavkin, D. Mills, 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.
44Marcobal, A., M. Underwood and D. A. Mills. 2008 Rapid determination of the bacterial composition of commercial probiotic products by terminal restriction fragment length polymorphism analysis. Journal of Pediatric Gastroenterology and Nutrition. 46:608–611.
43Marcobal, A. D. A. Sela, K. Makarova, Y. Wolf and D. A. Mills.  2008. Hypermutability in Oenococcus.  2007. Journal of Bacteriology. 190:564-570.  (Cover article).
42Seipert, R. R., M. Barboza, M. R. Ninonuevo, R. G. LoCascio, D. A. Mills, S. L. Freeman, J. B. German and C. L. Lebrilla.  2007. Analysis and quantitation of fructooligosaccharides using matrix-assisted laser desorption/ionization fourier transform ion cyclotron resonance mass spectrometry. Journal of Agricultural and Food Chemistry. 80:159-65.
41Ninonuevo, 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.  2007. Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry. Journal of Agricultural and Food Chemistry. 56:618-626..
40Ward, 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 and Nutrition 51:1398-1405.
39LoCascio, R. G, M. R. Ninonuevo, S. L. Freeman, 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.
38Kim, 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.
37Scharfen, 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.
36Sela, 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.
35Phister, T. G., H. Rawsthorne, L. Joseph and D. A. Mills. 2007. A quantitative real-time PCR assay for detection and enumeration of Hanseniaspora sp. from wine and juice. American Journal of Enology and Viticulture 58: 229-233.
34Ninonuevo, M. R., R. E. Ward, R. G. LoCascio, J. B. German, S. L. Freeman, M. Barboza, D. A. Mills, and C. B. Lebrilla. 2007. Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry.  Analytical Biochemistry. 361:15-23.
33Oddone, 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.
32Lan, 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. 2006. Biotechnology and Bioengineering. 95:1070-1080.
31Makarova, 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. 2006. Proceedings of the National Academy of Sciences. 103:15611-15616.
30Rawsthorne, 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.
29LoCascio, 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.  
28Ward, R. E., M. Niñonuevo, 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.
27Neeley, E., T. Phister, and D. A. Mills. 2005. A differential real-time PCR assay for enumeration of lactic acid bacteria in wine. Applied and Environmental Microbiology. 71:8954-8957.
26Mills, D. A., H. Rawsthorne, C. Parker, D. Tamir, and K. Makarova. 2005. Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking.  FEMS Microbiology Reviews. 29: 465-475.
25Sanders, 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
24Mills, D. A. 2004. The lactic acid bacteria genome project. Journal of Food Science, 69: FMS28-30.
23Phister, T. and D. A. Mills.  2003. Real-time PCR assay for detection and enumeration of Dekkera bruxellensis in wine. Applied and Environmental Microbiology. 69:7430-7434.
22Lopez, F. Ruiz-Larrea, L. Cocolin, E. Orr, T. Phister, M. Marshall, J. VanderGheynst and D. A. Mills. 2003. Design and evaluation of PCR primers for direct analysis of bacterial populations in wine.  Applied and Environmental Microbiology. 69:6801-6807
21Marshall, M. N., L. Cocolin, D. A. Mills and J. S. VanderGheynst.  2003. Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost.  Journal of Applied Microbiology.  95:934-948.
20Cocolin, L. and D. A. Mills. 2003. Wine yeast inhibition by sulfur dioxide: a comparison of culture-dependent and –independent methods. American Journal of Enology and Viticulture. 54:125-130
19Frazier, C. J. SanFillipo, A. Lambowitz and D. A. Mills. 2003. Genetic manipulation of Lactococcus lactis using targeted group II introns: generation of stable insertions without selection. Applied and Environmental Microbiology 69:1121-1128.
18Mills, D. A., E. Johannsen, and L. Cocolin. 2002. Yeast diversity and persistence in botrytis-affected wine fermentations. Applied and Environmental Microbiology 68:4884-4893
17Klaenhammer, 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. A. 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.
16Weimer, B. and D. Mills. Enhancing foods with functional genomics. 2002. Food Technology 56:184-189
15Mills, D. A. 2001. Mutagenesis in the post genomics era: Tools for generating insertional mutations in the Lactic Acid Bacteria. Current Opinion in Biotechnology 12:503-509.
14Cocolin, L., A. Heisy and D. A. Mills. 2001. Direct identification of the indigenous yeasts in commercial wine fermentations. American Journal of Enology and Viticulture. 52:49-53.
13Mills, D. A., K. Kelley, and M. Jones. 2001 Use of a digital camera to document student observations in a microbiology laboratory class. American Biology Teacher 63:119-123
12Guihabert, M. R., L. M. Hoffman, D. A. Mills and B. C. Kirkpatrick. 2001. Transposon mutagenesis of Xylella fastidiosa by electroporation of Tn5 synaptic complexes. Molecular Plant Microbe Interactions 14:701-706.
11Madsen, 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.
10Cocolin, L., L. F. Bisson, and D. A. Mills. 2000. Direct profiling of the yeast dynamics in wine fermentations. FEMS Microbiology Letters 189:81-87.
9Mills, 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.
8Cousineau, 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.
7Mills, 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.
6Mills, 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.
5Mills, 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.
4Mills, 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.
3Mills, 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.
2Mills, 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.
1Alexandrescu, 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.