Mills Laboratory > Research > Interaction between foods, microbes and the intestine

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Interaction between foods, microbes and the intestine

We are interested in how food substrates influence the growth of beneficial microbes in the gastrointestinal tract

babypicMilk glycans and intestinal microbiota

We are currently working as part of a large collaborative effort termed the Milk Bioactives Program.  During breast-feeding, Bifidobacterium sp. are often enriched in the infant gastrointestinal tract. It has been proposed that milk glycans are responsible for this enrichment. With our collaborators in the Milk Bioactives Program and the Functional Glycobiology Program we are investigating how milk glycans (free glycans, glycoproteins, glycolipids) impact the intestinal microbiota of the nursing infant as well as exploring the fundamental mechanistic basis for this interaction.  In a parallel effort we have examined other animal milks as potential sources for large quantities of these bioactive glycans that could serve as a means to protect the intestine from various chronic and pathogenic challenges observed in various populations.

 

Some general questions we are interested in:

  • How do different bacteria that consume milk glycans carry out that process?
  • Are glycan-consuming bacteria more predominant in infants who are breast-fed?
  • What are the genes involved in milk glycan consumption in bifidobacteria and how are they regulated?
  • How does growth on milk glycans impact bacterial-host interactions?
  • Does the genotype of the mother and the type of milk glycans delivered impact the infant microbiota?
  • Are other animal milk glycans mimic human milk glycan activities?

 

Publications in this area (see a full list of Mills Lab pubs here)

  • 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 (In Press).
  • 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 (In Press).
  • 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. (In Press).
  • Shani, G. I., Z. T. Lewis, A. M. Robinson and David A. Mills. 2017. In Biavati, B. W. H. Holzapfel, P. Mattarelli and B. J. B. Wood Eds. Interactions between bifidobacteria, milk oligosaccharides and neonate hosts.  Elsevier, New York, New York (In Press).
  • Lewis, Z. T. and D. A. Mills.  Differential establishment of bifidobacteria in the breastfed infant gut.   2017.  In Isolauri, E., P. Sherman, and A. Walker, Eds.  Microbiota.  Karger, New York.
  • 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 (In Press).
  • 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 (In Press).
  • 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 (In Press).
  • 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.
  • 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-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 4:e1612.
  • Lewis, Z. T., G. Shani, C. Masarweh, M. Popovic, S. A. Frese, D. A. Sela, M. A. Underwood and D. A. Mills. 2015. Validating bifidobacterial species and subspecies identity in commercial probiotic products.  Pediatrics Research79: 445-452.
  • 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. PeerJ4: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.
  • 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.
  • 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.
  • Lewis, Z. T., G. Shani, C. Masarweh, M. Popovic, S. A. Frese, D. A. Sela, M. A. Underwood and D. A. Mills. 2015. Validating bifidobacterial species and subspecies identity in commercial probiotic products.  Pediatrics Research 79: 445-452.
  • Wickramasinghe, S, A. R. Pacheco, D. G. Lemay, and D. A. Mills. Bifidobacteria grown in human milk oligosaccharides down regulate the expression of inflammation-related genes in Caco-2 cells.  BMC Microbiology15:172.
  • Karav, S., J. M. L. N. de Moura Bell, A. Le Parc, Y. Liu, D. A. Mills, D. E. Block and D. Barile. 2015.  Characterizing the release of bioactive N-glycans from dairy products by a novel endo-β-N-acetylglucosaminidase. Biotechnology Progress 31:1331-1339.
  • Le Parc, A., S. Karav, J. M. L. N. de Moura Bell, A. Le Parc, Y. Liu, D. A. Mills, D. E. Block and D. Barile. 2015. A novel endo-β-N-acetylglucosaminidase releases specific N-glycans depending on different reaction conditions. Biotechnology Progress 31:1323-1330.
  • 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.
  • 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.
  • Garrido, D. S. Ruiz-Moyano, D. G. Lemay, D. A. Sela, J B. German and D. A Mills. 2015. Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria. Nature Scientific Reports 5:13517.
  • 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.
  • Frese, S. A. and D. A. Mills.  2015.  Birth of the infant gut microbiome: Moms deliver twice!  Cell Host and Microbe 17:543–544.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Underwood, M., J. Arriola, C. Gerber, A. Kaveti, K. Kalanetra, A. Kananurak, C. Bevins, D. A. Mills, and B. Dvorak. 2014. Bifidobacterium longumsubsp. 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.
  • 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.
  • 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.
  • 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 Reports4:4983.
  • 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.
  • 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.
  • 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.
  • 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.
  • Peacock, K., R. L. Ruhaak, M. K. Tsui, D. A. Mills, C. B. Lebrilla. Isomer-specific consumption of galactooligosaccharides by bifidobacterial species. 2014. Journal of Agricultural and Food Chemistry 61:12612-12619.
  • 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.
  • 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 ofBifidobacterium 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.
  • 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.
  • 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.
  • Ellis, C. L., N. A. Bokulich, K. M. Kalanetra, M. Mirmiran, J. Elumalai, L. Haapanen, T. Schegg, J. C. Rutledge, G. Raff, D. A. Mills, M. A. Underwood. 2013.  Probiotic administration in congenital heart disease: A pilot study.  Journal of Perinatology 33:691-697.
  • 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.
  • Kim, J.-H., H. J. An, D. A. Garrido, J. B. German, C. B. Lebrilla and D. A. Mills.  2013. Proteomic analysis ofBifidobacterium 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.
  • 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.  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.  Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm. Journal of Proteome Research11:4662-4672
  • Strum, J., J-H Kim, S. Wu, M. L. De Leoz, K. Peacock, R. Grimm, J. B. German, D. A. Mills, C. B. Lebrilla. Rapid identification and accurate quantitation of biological oligosaccharide mixtures.  Analytical Biochemistry 84:7793-7801.
  • 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
    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.
  • Gordon, J. I., K. Dewey, D. A. Mills and R M. Medzhitov. 2012.   The human gut microbiota and undernutrition.  Science Translational Medicine 4:137ps12.
  • Garrido, D., S. Ruiz-Moyano and D. A. Mills. 2012.   Release and utilization of N-acetyl-D-glucosamine from human milk oligosaccharides by Bifidobacterium longumsubsp. infantis.  Anaerobe 18:430-435.
  • 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.
  • Ruiz-Moyano, S., N. Tao, M. Underwood and D. A. Mills.  2012.  Rapid discrimination of Bifidobacterium animalis subspecies by matrix-assisted desorption ionization time of flight (MALDI-TOF) mass spectrometry.  Food Microbiology 30:432-437.
  • Sela, D. A., D. Garrido, L. Lerno, S. Wu, K. Tan, H-J. Eom, A. Joachimiak, C. B. Lebrilla and D. A. Mills. 2012. Bifidobacterium longum subsp. infantis ATCC15697 α-fucosidases are active on fucosylated human milk oligosaccharides.  Applied and Environmental Microbiology 78:795-803.
  • Marcobal A., M. Barboza, E. D. Sonnenburg, N. Pudlo, E. C. Martens, P. Desai, C. B. Lebrilla, B. C. Weimer, D. A. Mills, J. B. German and J. L. Sonnenburg.  2011. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways.  Cell Host and Microbe 10: 507-514.
  • 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.
  • Garrido, 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.
  • Zivkovic, 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.
  • 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.
  • Turroni, F. F. Bottacini, E. Foroni, I. Mulder, J.-H. Kim, A. Zomer, B.S. Garcia, A. Bidossi, A. Ferrarini, V. Giubellini, M. Delledonne, B. Henrissat, P. Coutinho, M. Oggioni, G. F. Fitzgerald, D. A. Mills, A. Margolles, D. Kelly, D. van Sinderen and M. Ventura.  2010.  Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host derived glycan foraging.  Proceedings of the National Academy of Sciences 45:19514-19519.
  • LoCascio, R. G., P. Desai, D. A. Sela, B. Weimer, and D. A. Mills. Comparative genomic hybridization of Bifidobacterium longum strains reveals broad conservation of milk utilization genes in subsp. infantis. Applied and Environmental Microbiology 76:7373-7381.
  • Sela, 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.
  • German, J. B., C. Lebrilla and D. A. Mills. 2010. Milk’s emerging health ingredients.  NutraSolutions, Prepared Foods May Issue.
  • Marcobal, 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.
  • 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.  Horizon Scientific 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.
  • Underwood, 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.
  • LoCascio, 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.
  • Sela, 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. 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.
  • 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., 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.
  • Marcobal, 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.
  • Seipert, 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.
  • 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.  2007. Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry. Journal of Agricultural and Food Chemistry. 56:618-626..
  • 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 and Nutrition 51:1398-1405.
  • LoCascio, 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.
  • Ninonuevo, M. R., R. E. Ward, R. G. LoCascio, J. B. German, S. L. Freeman, M. Barboza, D. A. Mills, and C. B. Lebrilla. 2006. Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry.  Analytical Biochemistry. 361:15-23.
  • Ward, 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.
  • 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.

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