Tough nuts to crack

References

• Lee J-H, O’Sullivan DJ. Genomic insights into bifidobacteria. Microbiol Mol Biol Rev 2010; 74:378 - 416; http://dx.doi.org/10.1128/MMBR.00004-10; PMID: 20805404
   PubMed Web of Science ®Google Scholar
• Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature 2012; 486:222 - 7; PMID: 22699611
   PubMed Web of Science ®Google Scholar
• Leahy SC, Higgins DG, Fitzgerald GF, van Sinderen D. Getting better with bifidobacteria. J Appl Microbiol 2005; 98:1303 - 15; http://dx.doi.org/10.1111/j.1365-2672.2005.02600.x; PMID: 15916644
   PubMed Web of Science ®Google Scholar
• Picard C, Fioramonti J, Francois A, Robinson T, Neant F, Matuchansky C. Review article: bifidobacteria as probiotic agents -- physiological effects and clinical benefits. Aliment Pharmacol Ther 2005; 22:495 - 512; http://dx.doi.org/10.1111/j.1365-2036.2005.02615.x; PMID: 16167966
   PubMed Web of Science ®Google Scholar
• Sun Z, Baur A, Zhurina D, Yuan J, Riedel CU. Accessing the inaccessible: molecular tools for bifidobacteria. Appl Environ Microbiol 2012; 78:5035 - 42; http://dx.doi.org/10.1128/AEM.00551-12; PMID: 22582076
   PubMed Web of Science ®Google Scholar
• Wei X, Guo Y, Shao C, Sun Z, Zhurina D, Liu D, et al. Fructose uptake in Bifidobacterium longum NCC2705 is mediated by an ATP-binding cassette transporter. J Biol Chem 2012; 287:357 - 67; http://dx.doi.org/10.1074/jbc.M111.266213; PMID: 22102285
   PubMed Web of Science ®Google Scholar
• Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011; 469:543 - 7; http://dx.doi.org/10.1038/nature09646; PMID: 21270894
   PubMed Web of Science ®Google Scholar
• Nakamura T, Sasaki T, Fujimori M, Yazawa K, Kano Y, Amano J, et al. Cloned cytosine deaminase gene expression of Bifidobacterium longum and application to enzyme/pro-drug therapy of hypoxic solid tumors. Biosci Biotechnol Biochem 2002; 66:2362 - 6; http://dx.doi.org/10.1271/bbb.66.2362; PMID: 12506973
   PubMed Web of Science ®Google Scholar
• Sakaguchi K, He J, Tani S, Kano Y, Suzuki T. A targeted gene knockout method using a newly constructed temperature-sensitive plasmid mediated homologous recombination in Bifidobacterium longum. Appl Microbiol Biotechnol 2012; 95:499 - 509; http://dx.doi.org/10.1007/s00253-012-4090-4; PMID: 22639142
   PubMed Web of Science ®Google Scholar
• Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010; 38:Database issue D234 - 6; http://dx.doi.org/10.1093/nar/gkp874; PMID: 19846593
   PubMed Web of Science ®Google Scholar
• Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 2003; 31:1805 - 12; http://dx.doi.org/10.1093/nar/gkg274; PMID: 12654995
   PubMed Web of Science ®Google Scholar
• Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol 2010; 8:317 - 27; http://dx.doi.org/10.1038/nrmicro2315; PMID: 20348932
   PubMed Web of Science ®Google Scholar
• Chen Q, Fischer JR, Benoit VM, Dufour NP, Youderian P, Leong JM. In vitro CpG methylation increases the transformation efficiency of Borrelia burgdorferi strains harboring the endogenous linear plasmid lp56. J Bacteriol 2008; 190:7885 - 91; http://dx.doi.org/10.1128/JB.00324-08; PMID: 18849429
   PubMed Web of Science ®Google Scholar
• Groot MN, Nieboer F, Abee T. Enhanced transformation efficiency of recalcitrant Bacillus cereus and Bacillus weihenstephanensis isolates upon in vitro methylation of plasmid DNA. Appl Environ Microbiol 2008; 74:7817 - 20; http://dx.doi.org/10.1128/AEM.01932-08; PMID: 18952874
   PubMed Web of Science ®Google Scholar
• Monk IR, Shah IM, Xu M, Tan M-W, Foster TJ. (2012) Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis. MBio 3. Available: http://www.ncbi.nlm.nih.gov/pubmed/22434850.
   Google Scholar
• Zhang G, Wang W, Deng A, Sun Z, Zhang Y, Liang Y, et al. A mimicking-of-DNA-methylation-patterns pipeline for overcoming the restriction barrier of bacteria. PLoS Genet 2012; 8:e1002987; http://dx.doi.org/10.1371/journal.pgen.1002987; PMID: 23028379
   PubMedGoogle Scholar
• O’Connell Motherway M, O’Driscoll J, Fitzgerald GF, Van Sinderen D. Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003. Microb Biotechnol 2009; 2:321 - 32; http://dx.doi.org/10.1111/j.1751-7915.2008.00071.x; PMID: 21261927
   PubMedGoogle Scholar
• Yasui K, Kano Y, Tanaka K, Watanabe K, Shimizu-Kadota M, Yoshikawa H, et al. Improvement of bacterial transformation efficiency using plasmid artificial modification. Nucleic Acids Res 2009; 37:e3; http://dx.doi.org/10.1093/nar/gkn884; PMID: 19004868
   PubMedGoogle Scholar
• Pokusaeva K, O’Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D. Cellodextrin utilization by bifidobacterium breve UCC2003. Appl Environ Microbiol 2011; 77:1681 - 90; http://dx.doi.org/10.1128/AEM.01786-10; PMID: 21216899
   PubMed Web of Science ®Google Scholar
• O’Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, et al. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A 2011; 108:11217 - 22; http://dx.doi.org/10.1073/pnas.1105380108; PMID: 21690406
   PubMed Web of Science ®Google Scholar
• Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J, Goulding D, et al. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci U S A 2012; 109:2108 - 13; http://dx.doi.org/10.1073/pnas.1115621109; PMID: 22308390
   PubMed Web of Science ®Google Scholar
• Alvarez-Martin P, Fernández M, O’Connell-Motherway M, O’Connell KJ, Sauvageot N, Fitzgerald GF, et al. A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2012; 78:5258 - 69; http://dx.doi.org/10.1128/AEM.00804-12; PMID: 22635988
   PubMed Web of Science ®Google Scholar
• Alvarez-Martin P, O’Connell Motherway M, Turroni F, Foroni E, Ventura M, van Sinderen D. A two-component regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2012; 78:7032 - 41; http://dx.doi.org/10.1128/AEM.01776-12; PMID: 22843530
   PubMed Web of Science ®Google Scholar
• Riedel CU, Foata F, Goldstein DR, Blum S, Eikmanns BJ. Interaction of bifidobacteria with Caco-2 cells-adhesion and impact on expression profiles. Int J Food Microbiol 2006; 110:62 - 8; http://dx.doi.org/10.1016/j.ijfoodmicro.2006.01.040; PMID: 16713644
   PubMed Web of Science ®Google Scholar
• Preising J, Philippe D, Gleinser M, Wei H, Blum S, Eikmanns BJ, et al. Selection of bifidobacteria based on adhesion and anti-inflammatory capacity in vitro for amelioration of murine colitis. Appl Environ Microbiol 2010; 76:3048 - 51; http://dx.doi.org/10.1128/AEM.03127-09; PMID: 20228095
   PubMed Web of Science ®Google Scholar
• Gleinser M, Grimm V, Zhurina D, Yuan J, Riedel CU. Improved adhesive properties of recombinant bifidobacteria expressing the Bifidobacterium bifidum-specific lipoprotein BopA. Microb Cell Fact 2012; 11:80; http://dx.doi.org/10.1186/1475-2859-11-80; PMID: 22694891
   PubMed Web of Science ®Google Scholar
• Riedel C-U, Foata F, Philippe D, Adolfsson O, Eikmanns B-J, Blum S. Anti-inflammatory effects of bifidobacteria by inhibition of LPS-induced NF-kappaB activation. World J Gastroenterol 2006; 12:3729 - 35; PMID: 16773690
   PubMed Web of Science ®Google Scholar
• Philippe D, Heupel E, Blum-Sperisen S, Riedel CU. Treatment with Bifidobacterium bifidum 17 partially protects mice from Th1-driven inflammation in a chemically induced model of colitis. Int J Food Microbiol 2011; 149:45 - 9; http://dx.doi.org/10.1016/j.ijfoodmicro.2010.12.020; PMID: 21257218
   PubMed Web of Science ®Google Scholar
• Zhurina D, Zomer A, Gleinser M, Brancaccio VF, Auchter M, Waidmann MS, et al. Complete genome sequence of Bifidobacterium bifidum S17. J Bacteriol 2011; 193:301 - 2; http://dx.doi.org/10.1128/JB.01180-10; PMID: 21037011
   PubMed Web of Science ®Google Scholar
• Yu BJ, Kang KH, Lee JH, Sung BH, Kim MS, Kim SC. Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res 2008; 36:e84; http://dx.doi.org/10.1093/nar/gkn359; PMID: 18567910
   PubMed Web of Science ®Google Scholar
• Riedel CU, Casey PG, Mulcahy H, O’Gara F, Gahan CGM, Hill C. Construction of p16Slux, a novel vector for improved bioluminescent labeling of gram-negative bacteria. Appl Environ Microbiol 2007; 73:7092 - 5; http://dx.doi.org/10.1128/AEM.01394-07; PMID: 17766445
   PubMed Web of Science ®Google Scholar
• MacNeil DJ, Gewain KM, Ruby CL, Dezeny G, Gibbons PH, MacNeil T. Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector. Gene 1992; 111:61 - 8; http://dx.doi.org/10.1016/0378-1119(92)90603-M; PMID: 1547955
   PubMed Web of Science ®Google Scholar
• Klijn A, Moine D, Delley M, Mercenier A, Arigoni F, Pridmore RD. Construction of a reporter vector for the analysis of Bifidobacterium longum promoters. Appl Environ Microbiol 2006; 72:7401 - 5; http://dx.doi.org/10.1128/AEM.01611-06; PMID: 16997985
   PubMed Web of Science ®Google Scholar
• MacConaill LE, Fitzgerald GF, Van Sinderen D. Investigation of protein export in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2003; 69:6994 - 7001; http://dx.doi.org/10.1128/AEM.69.12.6994-7001.2003; PMID: 14660341
   PubMed Web of Science ®Google Scholar
• O’Connell Motherway M, Fitzgerald GF, Neirynck S, Ryan S, Steidler L, van Sinderen D. Characterization of ApuB, an extracellular type II amylopullulanase from Bifidobacterium breve UCC2003. Appl Environ Microbiol 2008; 74:6271 - 9; http://dx.doi.org/10.1128/AEM.01169-08; PMID: 18689518
   PubMed Web of Science ®Google Scholar
• Law J, Buist G, Haandrikman A, Kok J, Venema G, Leenhouts K. A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes. J Bacteriol 1995; 177:7011 - 8; PMID: 8522504
   PubMed Web of Science ®Google Scholar
• Monk IR, Gahan CGM, Hill C. Tools for functional postgenomic analysis of listeria monocytogenes. Appl Environ Microbiol 2008; 74:3921 - 34; http://dx.doi.org/10.1128/AEM.00314-08; PMID: 18441118
   PubMed Web of Science ®Google Scholar
• Turnbough CL Jr., Switzer RL. Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 2008; 72:266 - 300; http://dx.doi.org/10.1128/MMBR.00001-08; PMID: 18535147
   PubMed Web of Science ®Google Scholar
• Weidenmaier C, Peschel A. Teichoic acids and related cell-wall glycopolymers in Gram-positive physiology and host interactions. Nat Rev Microbiol 2008; 6:276 - 87; http://dx.doi.org/10.1038/nrmicro1861; PMID: 18327271
   PubMed Web of Science ®Google Scholar
• Op den Camp HJ, Veerkamp JH, Oosterhof A, Van Halbeek H. Structure of the lipoteichoic acids from Bifidobacterium bifidum spp. pennsylvanicum. Biochim Biophys Acta 1984; 795:301 - 13; http://dx.doi.org/10.1016/0005-2760(84)90080-8; PMID: 6477947
   PubMed Web of Science ®Google Scholar
• Fischer W. ‘Lipoteichoic acid’ of Bifidobacterium bifidum subspecies pennsylvanicum DSM 20239. A lipoglycan with monoglycerophosphate side chains. Eur J Biochem 1987; 165:639 - 46; http://dx.doi.org/10.1111/j.1432-1033.1987.tb11488.x; PMID: 3595606
   PubMedGoogle Scholar
• Janusz MJ, Esser RE, Schwab JH. In vivo degradation of bacterial cell wall by the muralytic enzyme mutanolysin. Infect Immun 1986; 52:459 - 67; PMID: 3516873
   PubMed Web of Science ®Google Scholar
• Stimpson SA, Lerch RA, Cleland DR, Yarnall DP, Clark RL, Cromartie WJ, et al. Effect of acetylation on arthropathic activity of group A streptococcal peptidoglycan-polysaccharide fragments. Infect Immun 1987; 55:16 - 23; PMID: 3539800
   PubMed Web of Science ®Google Scholar