Taminiau, Bernard ; Université de Liège - ULiège > Département de sciences des denrées alimentaires (DDA) > Microbiologie des denrées alimentaires
Delcenserie, Véronique ; Université de Liège - ULiège > Département de sciences des denrées alimentaires (DDA) > Gestion de la qualité dans la chaîne alimentaire
Ventura M, Turroni F, O'Connell Motherway M, MacSharry J, van Sinderen D. 2012. Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria. Trends Microbiol. 20:467-476. http://dx.doi.org/10.1016/j.tim.2012.07.002.
Bergey DH, Goodfellow M, Whitman WB, Parte AC. 2012. The actinobacteria, p 1. In Bergey's manual of systematic bacteriology, vol 5, 2nd ed. Springer, New York, NY.
Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M. 2012. Diversity of bifidobacteria within the infant gut microbiota. PLoS One 7:e36957. http://dx.doi.org/10.1371/journal.pone.0036957.
Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martin R, Gueimonde M, van Sinderen D, Margolles A, Ventura M. 2013. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One 8:e68739. http://dx.doi.org/10.1371/journal.pone.0068739.
Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, Cagnasso P, Bizzarri B, de'Angelis GL, Shanahan F, van Sinderen D, Ventura M. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75:1534-1545. http://dx.doi.org/10.1128/AEM.02216-08.
Chenoll E, Casinos B, Bataller E, Astals P, Echevarria J, Iglesias JR, Balbarie P, Ramon D, Genoves S. 2011. Novel probiotic Bifidobacterium bifidum CECT 7366 strain active against the pathogenic bacterium Helicobacter pylori. Appl. Environ. Microbiol. 77:1335-1343. http://dx.doi.org/10.1128/AEM.01820-10.
Shirasawa Y, Shibahara-Sone H, Iino T, Ishikawa F. 2010. Bifidobacterium bifidum BF-1 suppresses Helicobacter pylori-induced genes in human epithelial cells. J. Dairy Sci. 93:4526-4534. http://dx.doi.org/10.3168/jds.2010-3274.
Khailova L, Mount Patrick SK, Arganbright KM, Halpern MD, Kinouchi T, Dvorak B. 2010. Bifidobacterium bifidum reduces apoptosis in the intestinal epithelium in necrotizing enterocolitis. Am. J. Physiol. Gastrointest. Liver Physiol. 299:G1118-G1127. http://dx.doi.org/10.1152/ajpgi.00131.2010.
Guglielmetti S, Mora D, Gschwender M, Popp K. 2011. Randomised clinical trial: Bifidobacterium bifidum MIMBb75 significantly alleviates irritable bowel syndrome and improves quality of life-a double-blind, placebo-controlled study. Aliment. Pharmacol. Ther. 33:1123-1132. http://dx.doi.org/10.1111/j.1365-2036.2011.04633.x.
Malago JJ, Tooten PC, Koninkx JF. 2010. Anti-inflammatory properties of probiotic bacteria on Salmonella-induced IL-8 synthesis in enterocytelike Caco-2 cells. Benef. Microbes 1:121-130. http://dx.doi.org/10.3920/BM2009.0021.
Ventura M, Turroni F, Lugli GA, van Sinderen D. 2014. Bifidobacteria and humans: our special friends, from ecological to genomic perspectives. J. Sci. Food Agric. 94:163-168. http://dx.doi.org/10.1002/jsfa.6356.
Biavati B, Mattarelli P. 1991. Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle. Int. J. Syst. Bacteriol. 41:163-168. http://dx.doi.org/10.1099/00207713-41-1-163.
Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LM. 2012. Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas). Syst. Appl. Microbiol. 35:92-97. http://dx.doi.org/10.1016/j.syapm.2011.11.006.
Killer J, Kopecny J, Mrazek J, Koppova I, Havlik J, Benada O, Kott T. 2011. Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. Int. J. Syst. Evol. Microbiol. 61(Pt 6):1315-1321. http://dx.doi.org/10.1099/ijs.0.022525-0.
Ventura M, O'Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, O'Toole PW. 2009. Genome-scale analyses of healthpromoting bacteria: probiogenomics. Nat. Rev. Microbiol. 7:61-71. http://dx.doi.org/10.1038/nrmicro2047.
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S. 2004. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14:1147-1159. http://dx.doi.org/10.1101/gr.1917404.
Gish W, States DJ. 1993. Identification of protein coding regions by database similarity search. Nat. Genet. 3:266-272. http://dx.doi.org/10.1038/ng0393-266.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
Schmid R, Blaxter ML. 2008. annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics 9:180. http://dx.doi.org/10.1186/1471-2105-9-180.
Roberts RJ, Vincze T, Posfai J, Macelis D. 2010. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 38:D234-D236. http://dx.doi.org/10.1093/nar/gkp874.
Busch W, Saier MH, Jr. 2002. The transporter classification (TC) system, 2002. Crit. Rev. Biochem. Mol. Biol. 37:287-337. http://dx.doi.org/10.1080/10409230290771528.
Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28:416-418. http://dx.doi.org/10.1093/bioinformatics/btr655.
Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. http://dx.doi.org/10.1093/nar/30.7.1575.
Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066. http://dx.doi.org/10.1093/nar/gkf436.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404.
Segata N, Bornigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4:2304. http://dx.doi.org/10.1038/ncomms3304.
Ye Y, Wei B, Wen L, Rayner S. 2013. BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. Bioinformatics 29:3222-3224. http://dx.doi.org/10.1093/bioinformatics/btt553.
Podell S, Gaasterland T. 2007. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 8:R16. http://dx.doi.org/10.1186/gb-2007-8-2-r16.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R. 2006. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMCBioinformatics 7:142. http://dx.doi.org/10.1186/1471-2105-7-142.
Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52-W57. http://dx.doi.org/10.1093/nar/gkm360.
Ventura M, Turroni F, Lugli GA, van Sinderen D. 2014. Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. J. Sci. Food Agric. 94:163-168. http://dx.doi.org/10.1002/jsfa.6356.
Koskiniemi S, Sun S, Berg OG, Andersson DI. 2012. Selection-driven gene loss in bacteria. PLoS Genet. 8:e1002787. http://dx.doi.org/10.1371/journal.pgen.1002787.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, MetaHIT Consortium, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, et al. 2011. Enterotypes of the human gut microbiome. Nature 473:174-180. http://dx.doi.org/10.1038/nature09944.
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, MadoffLC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.“ Proc. Natl. Acad. Sci. U. S. A. 102:13950-13955. http://dx.doi.org/10.1073/pnas.0506758102.
Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, Smith RD, Adkins JN, Lipton MS. 2008. Comparative bacterial proteomics: analysis of the core genome concept. PLoS One 3:e1542. http://dx.doi.org/10.1371/journal.pone.0001542.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. http://dx.doi.org/10.1186/1471-2105-4-41.
Philippot L, Andersson SG, Battin TJ, Prosser JI, Schimel JP, Whitman WB, Hallin S. 2010. The ecological coherence of high bacterial taxonomic ranks. Nat. Rev. Microbiol. 8:523-529. http://dx.doi.org/10.1038/nrmicro2367.
Ventura M, Canchaya C, Del Casale A, Dellaglio F, Neviani E, Fitzgerald GF, van Sinderen D. 2006. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 56:2783-2792. http://dx.doi.org/10.1099/ijs.0.64233-0.
Bottacini F, Milani C, Turroni F, Sanchez B, Foroni E, Duranti S, Serafini F, Viappiani A, Strati F, Ferrarini A, Delledonne M, Henrissat B, Coutinho P, Fitzgerald GF, Margolles A, van Sinderen D, Ventura M. 2012. Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PLoS One 7:e44229. http://dx.doi.org/10.1371/journal.pone.0044229.
Mirkin BG, Fenner TI, Galperin MY, Koonin EV. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMCEvol. Biol. 3:2. http://dx.doi.org/10.1186/1471-2148-3-2.
Snipen L, Ussery DW. 2010. Standard operating procedure for computing pangenome trees. Stand. Genomic Sci. 2:135-141. http://dx.doi.org/10.4056/sigs.38923.
Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Diaz-Muniz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O'Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. U. S. A. 103:15611-15616. http://dx.doi.org/10.1073/pnas.0607117103.
Schleifer ME, Krusch KHU, Neve H. 1991. Revival of the species Streptococcus thermophilus (ex Orla-Jensen, 1919) nom. rev. Syst. Appl. Microbiol. 14:386-388. http://dx.doi.org/10.1016/S0723-2020(11)80314-0.
Pfeiffer T, Schuster S, Bonhoeffer S. 2001. Cooperation and competition in the evolution of ATP-producing pathways. Science 292:504-507. http://dx.doi.org/10.1126/science.1058079.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42:D490-D495. http://dx.doi.org/10.1093/nar/gkt1178.
Cho I, Blaser MJ. 2012. The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13:260-270. http://dx.doi.org/10.1038/nrg3182.
DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE. 2008. Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J. Bacteriol. 190:5455-5463. http://dx.doi.org/10.1128/JB.01701-07.
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712. http://dx.doi.org/10.1126/science.1138140.
Barrangou R. 2013. CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip. Rev. RNA 4:267-278. http://dx.doi.org/10.1002/wrna.1159.
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV. 2011. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9:467-477. http://dx.doi.org/10.1038/nrmicro2577.
Makarova KS, Koonin EV. 2007. Evolutionary genomics of lactic acid bacteria. J. Bacteriol. 189:1199-1208. http://dx.doi.org/10.1128/JB.01351-06.
Loquasto JR, Barrangou R, Dudley EG, Roberts RF. 2011. Short communication: the complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527T and comparative analysis of growth in milk with B. animalis subspecies lactisDSM10140T. J. Dairy Sci. 94:5864-5870. http://dx.doi.org/10.3168/jds.2011-4499.
Ventura M, Turroni F, Lima-Mendez G, Foroni E, Zomer A, Duranti S, Giubellini V, Bottacini F, Horvath P, Barrangou R, Sela DA, Mills DA, van Sinderen D. 2009. Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl. Environ. Microbiol. 75:6929-6936. http://dx.doi.org/10.1128/AEM.01112-09.
de Vries W, Stouthamer AH. 1969. Factors determining the degree of anaerobiosis of Bifidobacterium strains. Arch. Mikrobiol. 65:275-287. http://dx.doi.org/10.1007/BF00407109.
Scardovi V, Trovatelli LD. 1965. The fructose-6-phosphate shunt as a peculiar pattern of hexose degradation in the genus Bifidobacterium. Ann. Microbiol. 15:19-29.
Camilo E, Zimmerman J, Mason JB, Golner B, Russell R, Selhub J, Rosenberg IH. 1996. Folate synthesized by bacteria in the human upper small intestine is assimilated by the host. Gastroenterology 110:991-998. http://dx.doi.org/10.1053/gast.1996.v110.pm8613033.
Corbett AJ, Eckle SB, Birkinshaw RW, Liu L, Patel O, Mahony J, Chen Z, Reantragoon R, Meehan B, Cao H, Williamson NA, Strugnell RA, Van Sinderen D, Mak JY, Fairlie DP, Kjer-Nielsen L, Rossjohn J, McCluskey J. 2014. T-cell activation by transitory neo-antigens derived from distinct microbial pathways. Nature 509:361-365. http://dx.doi.org/10.1038/nature13160.
Heuston S, Begley M, Davey MS, Eberl M, Casey PG, Hill C, Gahan CG. 2012. HmgR, a key enzyme in the mevalonate pathway for isoprenoid biosynthesis, is essential for growth of Listeria monocytogenes EGDe. Microbiology 158:1684-1693. http://dx.doi.org/10.1099/mic.0.056069-0.
Eberl M, Hintz M, Reichenberg A, Kollas AK, Wiesner J, Jomaa H. 2003. Microbial isoprenoid biosynthesis and human γδ T cell activation. FEBS Lett. 544:4-10. http://dx.doi.org/10.1016/S0014-5793(03)00483-6.
Lin JT, Stewart V. 1998. Nitrate assimilation by bacteria. Adv. Microb. Physiol. 39:1-30, 379.
Kuraishi T, Binggeli O, Opota O, Buchon N, Lemaitre B. 2011. Genetic evidence for a protective role of the peritrophic matrix against intestinal bacterial infection in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 108:15966-15971. http://dx.doi.org/10.1073/pnas.1105994108.
