Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem. 2008;13(8):1205–18.
Article
CAS
PubMed
Google Scholar
Zimmermann MB, Hurrell RF. Nutritional iron deficiency. Lancet. 2007;370(9586):511–20.
Article
CAS
PubMed
Google Scholar
Zimmermann MB, Chassard C, Rohner F, N’Goran EK, Nindjin C, Dostal A, Utzinger J, Ghattas H, Lacroix C, Hurrell RF. The effects of iron fortification on the gut microbiota in African children: a randomized controlled trial in Cote d’Ivoire. Am J Clin Nutr. 2010;92(6):1406–15.
Article
CAS
PubMed
Google Scholar
Kortman GA, Raffatellu M, Swinkels DW, Tjalsma H. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective. FEMS Microbiol Rev. 2014;38:1202–34.
Article
CAS
PubMed
Google Scholar
Collins HL. Withholding iron as a cellular defence mechanism - friend or foe? Eur J Immunol. 2008;38(7):1803–6.
Article
CAS
PubMed
Google Scholar
Raffatellu M, George MD, Akiyama Y, Hornsby MJ, Nuccio SP, Paixao TA, Butler BP, Chu H, Santos RL, Berger T, et al. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell Host Microbe. 2009;5(5):476–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nairz M, Schroll A, Sonnweber T, Weiss G. The struggle for iron - a metal at the host-pathogen interface. Cell Microbiol. 2010;12(12):1691–702.
Article
CAS
PubMed
Google Scholar
Foligne B, Daniel C, Pot B. Probiotics from research to market: the possibilities, risks and challenges. Curr Opin Microbiol. 2013;16(3):284–92.
Article
PubMed
Google Scholar
Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307(5717):1915–20.
Article
PubMed
Google Scholar
Ventura M, Turroni F, van Sinderen D. Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut. Bioeng Bugs. 2012;3(2):73–9.
PubMed
PubMed Central
Google Scholar
Ventura M, Turroni F, Motherway MO, MacSharry J, van Sinderen D. Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria. Trends Microbiol. 2012;20(10):467–76.
Article
CAS
PubMed
Google Scholar
Vazquez-Gutierrez P, Lacroix C, Jaeggi T, Zeder C, Zimmerman M, Chassard C. Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron. BMC Microbiol. 2015;15(1):3.
Article
PubMed
PubMed Central
Google Scholar
Bailey JR, Probert CS, Cogan TA. Identification and characterisation of an iron-responsive candidate probiotic. PLoS One. 2011;6(10):e26507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kehl-Fie TE, Skaar EP. Nutritional immunity beyond iron: a role for manganese and zinc. Curr Opin Chem Biol. 2010;14(2):218–24.
Article
CAS
PubMed
Google Scholar
Liu JZ, Jellbauer S, Poe AJ, Ton V, Pesciaroli M, Kehl-Fie TE, Restrepo NA, Hosking MP, Edwards RA, Battistoni A, et al. Zinc sequestration by the neutrophil protein calprotectin enhances Salmonella growth in the inflamed gut. Cell Host Microbe. 2012;11(3):227–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diaz-Ochoa VE, Jellbauer S, Klaus S, Raffatellu M. Transition metal ions at the crossroads of mucosal immunity and microbial pathogenesis. Front Cell Infect Microbiol. 2014;4:2.
Article
PubMed
PubMed Central
Google Scholar
Sanchez B, Urdaci MC, Margolles A. Extracellular proteins secreted by probiotic bacteria as mediators of effects that promote mucosa-bacteria interactions. Microbiology. 2010;156(Pt 11):3232–42.
Article
CAS
PubMed
Google Scholar
Christie-Oleza JA, Pina-Villalonga JM, Bosch R, Nogales B, Armengaud J. Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics. 2012;11(2):M111–013110.
Article
PubMed
Google Scholar
Armengaud J. Microbiology and proteomics, getting the best of both worlds! Environ Microbiol. 2013;15(1):12–23.
Article
CAS
PubMed
Google Scholar
Gil C, Monteoliva L. Trends in microbial proteomics. J Proteomics. 2014;97:1–2.
Article
CAS
PubMed
Google Scholar
Yang XY, Lu J, Sun X, He QY. Application of subproteomics in the characterization of Gram-positive bacteria. J Proteomics. 2012;75(10):2803–10.
Article
CAS
PubMed
Google Scholar
Armengaud J, Christie-Oleza JA, Clair G, Malard V, Duport C. Exoproteomics: exploring the world around biological systems. Expert Rev Proteomics. 2012;9(5):561–75.
Article
CAS
PubMed
Google Scholar
Turroni F, Serafini F, Foroni E, Duranti S, O’Connell Motherway M, Taverniti V, Mangifesta M, Milani C, Viappiani A, Roversi T, et al. Role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proc Natl Acad Sci U S A. 2013;110(27):11151–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turroni F, Serafini F, Mangifesta M, Arioli S, Mora D, van Sinderen D, Ventura M. Expression of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in response to environmental gut conditions. FEMS Microbiol Lett. 2014;357(1):23–33.
Article
CAS
PubMed
Google Scholar
Ventura M, Turroni F, Lugli GA, van Sinderen D. Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. J Sci Food Agric. 2014;94(2):163–8.
Article
CAS
PubMed
Google Scholar
Joyce AR, Palsson BO. The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol. 2006;7(3):198–210.
Article
CAS
PubMed
Google Scholar
Lee IC, Tomita S, Kleerebezem M, Bron PA. The quest for probiotic effector molecules--unraveling strain specificity at the molecular level. Pharmacol Res. 2013;69(1):61–74.
Article
CAS
PubMed
Google Scholar
Seraphin B, Hettich R. Microbial proteomics: the quiet revolution. Curr Opin Microbiol. 2012;15(3):348–50.
Article
PubMed
Google Scholar
Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L. Proteomics boosts translational and clinical microbiology. J Proteomics. 2014;97:69–87.
Article
PubMed
Google Scholar
Renuse S, Chaerkady R, Pandey A. Proteogenomics. Proteomics. 2011;11(4):620–30.
Article
CAS
PubMed
Google Scholar
Vazquez-Gutierrez P, Lacroix C, Chassard C, Klumpp J, Jans C, Stevens MJ. Complete and Assembled Genome Sequence of Bifidobacterium kashiwanohense PV20-2, Isolated from the Feces of an Anemic Kenyan Infant. Genome Announc. 2015;3(1):e01467–14.
PubMed
PubMed Central
Google Scholar
Vazquez-Gutierrez P, Lacroix C, Chassard C, Klumpp J, Stevens MJ, Jans C. Bifidobacterium pseudolongum Strain PV8-2, Isolated from a Stool Sample of an Anemic Kenyan Infant. Genome Announc. 2015;3(1):e01469–14.
PubMed
PubMed Central
Google Scholar
Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32(Web Server issue):W327–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dertz EA, Xu J, Stintzi A, Raymond KN. Bacillibactin-mediated iron transport in Bacillus subtilis. J Am Chem Soc. 2006;128(1):22–3.
Article
CAS
PubMed
Google Scholar
Merriman TR, Merriman ME, Lamont IL. Nucleotide sequence of pvdD, a pyoverdine biosynthetic gene from Pseudomonas aeruginosa: PvdD has similarity to peptide synthetases. J Bacteriol. 1995;177(1):252–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turroni F, van Sinderen D, Ventura M. Bifidobacteria: from ecology to genomics. Front Biosci. 2009;14:4673–84.
Article
CAS
Google Scholar
Crociani F, Alessandrini A, Mucci MM, Biavati B. Degradation of complex carbohydrates by Bifidobacterium spp. Int J Food Microbiol. 1994;24(1–2):199–210.
Article
CAS
PubMed
Google Scholar
O’Connell Motherway M, Fitzgerald GF, van Sinderen D. Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003. Microb Biotechnol. 2011;4(3):403–16.
Article
PubMed
PubMed Central
Google Scholar
van den Broek LA, Hinz SW, Beldman G, Vincken JP, Voragen AG. Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebiotics. Mol Nutr Food Res. 2008;52(1):146–63.
Article
PubMed
Google Scholar
Jaeggi T, Kortman GA, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, et al. Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut. 2015;64(5):731–42.
Article
CAS
PubMed
Google Scholar
Haug MC, Tanner SA, Lacroix C, Stevens MJ, Meile L. Monitoring horizontal antibiotic resistance gene transfer in a colonic fermentation model. FEMS Microbiol Ecol. 2011;78(2):210–9.
Article
CAS
PubMed
Google Scholar
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011;480(7376):241–4.
Article
CAS
PubMed
Google Scholar
Baltrus DA. Exploring the costs of horizontal gene transfer. Trends Ecol Evol. 2013;28(8):489–95.
Article
PubMed
Google Scholar
Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, Giubellini V, Tettelin H, van Sinderen D, Ventura M. Comparative genomics of the genus Bifidobacterium. Microbiology. 2010;156(Pt 11):3243–54.
Article
CAS
PubMed
Google Scholar
Schaible UE, Kaufmann SH. Iron and microbial infection. Nat Rev Microbiol. 2004;2(12):946–53.
Article
CAS
PubMed
Google Scholar
Leal Jr SM, Roy S, Vareechon C, Carrion S, Clark H, Lopez-Berges MS, Di Pietro A, Schrettl M, Beckmann N, Redl B, et al. Targeting iron acquisition blocks infection with the fungal pathogens Aspergillus fumigatus and Fusarium oxysporum. PLoS Pathog. 2013;9(7):e1003436.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haase H, Rink L. Multiple impacts of zinc on immune function. Metallomics. 2014;6:1175–80.
Article
CAS
PubMed
Google Scholar
Johnson EE, Wessling-Resnick M. Iron metabolism and the innate immune response to infection. Microbes Infect. 2012;14(3):207–16.
Article
CAS
PubMed
Google Scholar
Cerasi M, Ammendola S, Battistoni A. Competition for zinc binding in the host-pathogen interaction. Front Cell Infect Microbiol. 2013;3:108.
Article
PubMed
PubMed Central
Google Scholar
Marco ML, Pavan S, Kleerebezem M. Towards understanding molecular modes of probiotic action. Curr Opin Biotechnol. 2006;17(2):204–10.
Article
CAS
PubMed
Google Scholar
Waldron KJ, Rutherford JC, Ford D, Robinson NJ. Metalloproteins and metal sensing. Nature. 2009;460(7257):823–30.
Article
CAS
PubMed
Google Scholar
Monack DM. The battle in the gut. Immunity. 2014;40(2):173–5.
Article
CAS
PubMed
Google Scholar
Raffatellu M, Baumler AJ. Salmonella’s iron armor for battling the host and its microbiota. Gut Microbes. 2010;1(1):70–2.
Article
PubMed
PubMed Central
Google Scholar
Cassat JE, Skaar EP. Iron in infection and immunity. Cell Host Microbe. 2013;13(5):509–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stastna M, Van Eyk JE. Secreted proteins as a fundamental source for biomarker discovery. Proteomics. 2012;12(4–5):722–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohmer L, Hocquet D, Miller SI. Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol. 2011;19(7):341–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weinberg ED. Iron availability and infection. Biochim Biophys Acta. 2009;1790(7):600–5.
Article
CAS
PubMed
Google Scholar
Vazquez-Gutierrez P, de Wouters T, Werder J, Chassard C, Lacroix C. High iron sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro. Front Microbiol. 2016;7:1480.
Article
PubMed
PubMed Central
Google Scholar
Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole 2nd FL, Jenney Jr FE, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ, et al. Microbial metalloproteomes are largely uncharacterized. Nature. 2010;466(7307):779–82.
Article
CAS
PubMed
Google Scholar
Ho TD, Davis BM, Ritchie JM, Waldor MK. Type 2 secretion promotes enterohemorrhagic Escherichia coli adherence and intestinal colonization. Infect Immun. 2008;76(5):1858–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gabbianelli R, Scotti R, Ammendola S, Petrarca P, Nicolini L, Battistoni A. Role of ZnuABC and ZinT in Escherichia coli O157:H7 zinc acquisition and interaction with epithelial cells. BMC Microbiol. 2011;11:36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Granato D, Bergonzelli GE, Pridmore RD, Marvin L, Rouvet M, Corthesy-Theulaz IE. Cell surface-associated elongation factor Tu mediates the attachment of Lactobacillus johnsonii NCC533 (La1) to human intestinal cells and mucins. Infect Immun. 2004;72(4):2160–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Xiang X, Lu Q, Zhang L, Ma F, Wang L. Adhesions of extracellular surface-layer associated proteins in Lactobacillus M5-L and Q8-L. J Dairy Sci. 2016;99(2):1011–8.
Article
CAS
PubMed
Google Scholar
Vazquez Gutierrez P. Screening and characterization of bifidobacteria with high iron binding properties. Zurich: ETH Zurich; 2014.
Google Scholar
Kinoshita H, Uchida H, Kawai Y, Kawasaki T, Wakahara N, Matsuo H, Watanabe M, Kitazawa H, Ohnuma S, Miura K, et al. Cell surface Lactobacillus plantarum LA 318 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) adheres to human colonic mucin. J Appl Microbiol. 2008;104(6):1667–74.
Article
CAS
PubMed
Google Scholar
Ramiah K, van Reenen CA, Dicks LM. Surface-bound proteins of Lactobacillus plantarum 423 that contribute to adhesion of Caco-2 cells and their role in competitive exclusion and displacement of Clostridium sporogenes and Enterococcus faecalis. Res Microbiol. 2008;159(6):470–5.
Article
CAS
PubMed
Google Scholar
Sanchez B, Schmitter JM, Urdaci MC. Identification of novel proteins secreted by Lactobacillus plantarum that bind to mucin and fibronectin. J Mol Microbiol Biotechnol. 2009;17(3):158–62.
Article
CAS
PubMed
Google Scholar
Katakura Y, Sano R, Hashimoto T, Ninomiya K, Shioya S. Lactic acid bacteria display on the cell surface cytosolic proteins that recognize yeast mannan. Appl Microbiol Biotechnol. 2010;86(1):319–26.
Article
CAS
PubMed
Google Scholar
Guglielmetti S, Tamagnini I, Mora D, Minuzzo M, Scarafoni A, Arioli S, Hellman J, Karp M, Parini C. Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells. Appl Environ Microbiol. 2008;74(15):4695–702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sengupta N, Alam SI, Kumar B, Kumar RB, Gautam V, Kumar S, Singh L. Comparative proteomic analysis of extracellular proteins of Clostridium perfringens type A and type C strains. Infect Immun. 2010;78(9):3957–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Butler E, Alsterfjord M, Olofsson TC, Karlsson C, Malmstrom J, Vasquez A. Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress. BMC Microbiol. 2013;13:235.
Article
PubMed
PubMed Central
Google Scholar
Hoppler M, Egli I, Petry N, Gille D, Zeder C, Walczyk T, Blair MW, Hurrell RF. Iron speciation in beans (Phaseolus vulgaris) biofortified by common breeding. J Food Sci. 2014;79(9):C1629–34.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, et al. Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Appl Environ Microbiol. 2014;80(20):6383–94.
Article
PubMed
PubMed Central
Google Scholar
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics. 2005;21(16):3422–3.
Article
CAS
PubMed
Google Scholar
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S. Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel. 2004;17(4):349–56.
Article
CAS
PubMed
Google Scholar
Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res. 2008;7(12):5082–93.
Article
CAS
PubMed
Google Scholar
Schagger H. Tricine-SDS-PAGE. Nat Protoc. 2006;1(1):16–22.
Article
PubMed
Google Scholar
Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2006;1(6):2856–60.
Article
CAS
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Article
PubMed
PubMed Central
Google Scholar
Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003;75(17):4646–58.
Article
CAS
PubMed
Google Scholar