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Items: 49

1.

Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions.

Egan M, Bottacini F, O'Connell Motherway M, Casey PG, Morrissey R, Melgar S, Faurie JM, Chervaux C, Smokvina T, van Sinderen D.

Appl Microbiol Biotechnol. 2018 Dec;102(24):10645-10663. doi: 10.1007/s00253-018-9413-7. Epub 2018 Oct 10.

PMID:
30306201
2.

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts.

Mavrich TN, Casey E, Oliveira J, Bottacini F, James K, Franz CMAP, Lugli GA, Neve H, Ventura M, Hatfull GF, Mahony J, van Sinderen D.

Sci Rep. 2018 Aug 24;8(1):12772. doi: 10.1038/s41598-018-31181-3.

3.

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.

Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M.

Microbiome. 2018 Aug 20;6(1):145. doi: 10.1186/s40168-018-0527-z.

4.

Comparative genomics and genotype-phenotype associations in Bifidobacterium breve.

Bottacini F, Morrissey R, Esteban-Torres M, James K, van Breen J, Dikareva E, Egan M, Lambert J, van Limpt K, Knol J, O'Connell Motherway M, van Sinderen D.

Sci Rep. 2018 Jul 13;8(1):10633. doi: 10.1038/s41598-018-28919-4.

5.

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan.

Odamaki T, Bottacini F, Kato K, Mitsuyama E, Yoshida K, Horigome A, Xiao JZ, van Sinderen D.

Sci Rep. 2018 Jan 8;8(1):85. doi: 10.1038/s41598-017-18391-x.

6.

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.

Arboleya S, Bottacini F, O'Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, Stanton C.

BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.

7.

Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.

Bottacini F, Morrissey R, Roberts RJ, James K, van Breen J, Egan M, Lambert J, van Limpt K, Knol J, Motherway MO, van Sinderen D.

Nucleic Acids Res. 2018 Feb 28;46(4):1860-1877. doi: 10.1093/nar/gkx1289.

8.

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003.

Bottacini F, Zomer A, Milani C, Ferrario C, Lugli GA, Egan M, Ventura M, van Sinderen D.

BMC Genomics. 2017 Dec 28;18(1):991. doi: 10.1186/s12864-017-4387-x.

9.

Omics of bifidobacteria: research and insights into their health-promoting activities.

Bottacini F, van Sinderen D, Ventura M.

Biochem J. 2017 Dec 6;474(24):4137-4152. doi: 10.1042/BCJ20160756. Review.

PMID:
29212851
10.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M.

Microbiol Mol Biol Rev. 2017 Nov 8;81(4). pii: e00036-17. doi: 10.1128/MMBR.00036-17. Print 2017 Dec. Review.

11.

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003.

Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D.

Sci Rep. 2017 Jul 17;7(1):5648. doi: 10.1038/s41598-017-05795-y.

12.

Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation.

Lanigan N, Bottacini F, Casey PG, O'Connell Motherway M, van Sinderen D.

Front Microbiol. 2017 May 31;8:964. doi: 10.3389/fmicb.2017.00964. eCollection 2017.

13.

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.

Kelleher P, Bottacini F, Mahony J, Kilcawley KN, van Sinderen D.

BMC Genomics. 2017 Mar 29;18(1):267. doi: 10.1186/s12864-017-3650-5.

14.
15.

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.

Maldonado-Gómez MX, Martínez I, Bottacini F, O'Callaghan A, Ventura M, van Sinderen D, Hillmann B, Vangay P, Knights D, Hutkins RW, Walter J.

Cell Host Microbe. 2016 Oct 12;20(4):515-526. doi: 10.1016/j.chom.2016.09.001. Epub 2016 Sep 29.

16.

Genome Analysis and Characterisation of the Exopolysaccharide Produced by Bifidobacterium longum subsp. longum 35624™.

Altmann F, Kosma P, O'Callaghan A, Leahy S, Bottacini F, Molloy E, Plattner S, Schiavi E, Gleinser M, Groeger D, Grant R, Rodriguez Perez N, Healy S, Svehla E, Windwarder M, Hofinger A, O'Connell Motherway M, Akdis CA, Xu J, Roper J, van Sinderen D, O'Mahony L.

PLoS One. 2016 Sep 22;11(9):e0162983. doi: 10.1371/journal.pone.0162983. eCollection 2016.

17.

Glycoside hydrolase family 13 α-glucosidases encoded by Bifidobacterium breve UCC2003; A comparative analysis of function, structure and phylogeny.

Kelly ED, Bottacini F, O'Callaghan J, Motherway MO, O'Connell KJ, Stanton C, van Sinderen D.

Int J Food Microbiol. 2016 May 2;224:55-65. doi: 10.1016/j.ijfoodmicro.2016.02.014. Epub 2016 Feb 26.

PMID:
26967000
18.

Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages.

Murphy J, Bottacini F, Mahony J, Kelleher P, Neve H, Zomer A, Nauta A, van Sinderen D.

Sci Rep. 2016 Feb 19;6:21345. doi: 10.1038/srep21345.

19.

Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.

O'Callaghan A, Bottacini F, O'Connell Motherway M, van Sinderen D.

BMC Genomics. 2015 Oct 21;16:832. doi: 10.1186/s12864-015-1968-4.

20.

Discovery of a conjugative megaplasmid in Bifidobacterium breve.

Bottacini F, O'Connell Motherway M, Casey E, McDonnell B, Mahony J, Ventura M, van Sinderen D.

Appl Environ Microbiol. 2015 Jan;81(1):166-76. doi: 10.1128/AEM.02871-14. Epub 2014 Oct 17.

21.

Lactobacillus rossiae, a vitamin B12 producer, represents a metabolically versatile species within the Genus Lactobacillus.

De Angelis M, Bottacini F, Fosso B, Kelleher P, Calasso M, Di Cagno R, Ventura M, Picardi E, van Sinderen D, Gobbetti M.

PLoS One. 2014 Sep 29;9(9):e107232. doi: 10.1371/journal.pone.0107232. eCollection 2014.

22.

Bifidobacterium bifidum as an example of a specialized human gut commensal.

Turroni F, Duranti S, Bottacini F, Guglielmetti S, Van Sinderen D, Ventura M.

Front Microbiol. 2014 Aug 21;5:437. doi: 10.3389/fmicb.2014.00437. eCollection 2014. Review.

23.

Diversity, ecology and intestinal function of bifidobacteria.

Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M.

Microb Cell Fact. 2014 Aug 29;13 Suppl 1:S4. doi: 10.1186/1475-2859-13-S1-S4. Epub 2014 Aug 29. Review.

24.

Progress in lactic acid bacterial phage research.

Mahony J, Bottacini F, van Sinderen D, Fitzgerald GF.

Microb Cell Fact. 2014 Aug 29;13 Suppl 1:S1. doi: 10.1186/1475-2859-13-S1-S1. Epub 2014 Aug 29. Review.

25.

Genomic encyclopedia of type strains of the genus Bifidobacterium.

Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2014 Oct;80(20):6290-302. doi: 10.1128/AEM.02308-14. Epub 2014 Aug 1.

26.

Molecular characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages.

Casey E, Mahony J, O'Connell-Motherway M, Bottacini F, Cornelissen A, Neve H, Heller KJ, Noben JP, Dal Bello F, van Sinderen D.

Appl Environ Microbiol. 2014 Sep;80(18):5623-35. doi: 10.1128/AEM.01268-14. Epub 2014 Jul 7.

27.

Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003.

Christiaen SE, O'Connell Motherway M, Bottacini F, Lanigan N, Casey PG, Huys G, Nelis HJ, van Sinderen D, Coenye T.

PLoS One. 2014 May 28;9(5):e98111. doi: 10.1371/journal.pone.0098111. eCollection 2014.

28.

The Lactococcus lactis plasmidome: much learnt, yet still lots to discover.

Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D.

FEMS Microbiol Rev. 2014 Sep;38(5):1066-88. doi: 10.1111/1574-6976.12074. Epub 2014 Jun 23. Review.

29.

Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis.

O' Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JE, Smokvina T, van Sinderen D.

PLoS One. 2014 Apr 17;9(4):e94875. doi: 10.1371/journal.pone.0094875. eCollection 2014.

30.

Kefir fermented milk and kefiran promote growth of Bifidobacterium bifidum PRL2010 and modulate its gene expression.

Serafini F, Turroni F, Ruas-Madiedo P, Lugli GA, Milani C, Duranti S, Zamboni N, Bottacini F, van Sinderen D, Margolles A, Ventura M.

Int J Food Microbiol. 2014 May 16;178:50-9. doi: 10.1016/j.ijfoodmicro.2014.02.024. Epub 2014 Mar 11.

PMID:
24667318
31.

Comparative genomics of the Bifidobacterium breve taxon.

Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D.

BMC Genomics. 2014 Mar 1;15:170. doi: 10.1186/1471-2164-15-170.

32.

Draft Genome Sequence of Lactobacillus crispatus EM-LC1, an Isolate with Antimicrobial Activity Cultured from an Elderly Subject.

Power SE, Harris HM, Bottacini F, Ross RP, O'Toole PW, Fitzgerald GF.

Genome Announc. 2013 Dec 19;1(6). pii: e01070-13. doi: 10.1128/genomeA.01070-13.

33.

Complete Genome Sequence of Lactobacillus plantarum Strain 16, a Broad-Spectrum Antifungal-Producing Lactic Acid Bacterium.

Crowley S, Bottacini F, Mahony J, van Sinderen D.

Genome Announc. 2013 Aug 1;1(4). pii: e00533-13. doi: 10.1128/genomeA.00533-13.

34.

Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon.

Milani C, Duranti S, Lugli GA, Bottacini F, Strati F, Arioli S, Foroni E, Turroni F, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2013 Jul;79(14):4304-15. doi: 10.1128/AEM.00984-13. Epub 2013 May 3.

35.

Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.

Ainsworth S, Zomer A, de Jager V, Bottacini F, van Hijum SA, Mahony J, van Sinderen D.

Genome Announc. 2013 Jan;1(1). pii: e00119-12. doi: 10.1128/genomeA.00119-12. Epub 2013 Jan 31.

36.

Exploration of the genomic diversity and core genome of the Bifidobacterium adolescentis phylogenetic group by means of a polyphasic approach.

Duranti S, Turroni F, Milani C, Foroni E, Bottacini F, Dal Bello F, Ferrarini A, Delledonne M, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2013 Jan;79(1):336-46. doi: 10.1128/AEM.02467-12. Epub 2012 Oct 12.

37.

Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut.

Bottacini F, Milani C, Turroni F, Sánchez 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.

PLoS One. 2012;7(9):e44229. doi: 10.1371/journal.pone.0044229. Epub 2012 Sep 20.

38.

Genome sequence of Parascardovia denticolens IPLA 20019, isolated from human breast milk.

Gueimonde M, Bottacini F, van Sinderen D, Ventura M, Margolles A, Sánchez B.

J Bacteriol. 2012 Sep;194(17):4776-7. doi: 10.1128/JB.01035-12.

39.

Complete genome sequence of Bifidobacterium animalis subsp. lactis BLC1.

Bottacini F, Dal Bello F, Turroni F, Milani C, Duranti S, Foroni E, Viappiani A, Strati F, Mora D, van Sinderen D, Ventura M.

J Bacteriol. 2011 Nov;193(22):6387-8. doi: 10.1128/JB.06079-11.

40.

Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium.

Foroni E, Serafini F, Amidani D, Turroni F, He F, Bottacini F, O'Connell Motherway M, Viappiani A, Zhang Z, Rivetti C, van Sinderen D, Ventura M.

Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S16. doi: 10.1186/1475-2859-10-S1-S16. Epub 2011 Aug 30.

41.

Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis.

Turroni F, Foroni E, Serafini F, Viappiani A, Montanini B, Bottacini F, Ferrarini A, Bacchini PL, Rota C, Delledonne M, Ottonello S, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2011 Oct;77(20):7408-17. doi: 10.1128/AEM.05336-11. Epub 2011 Aug 19.

42.

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.

O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11217-22. doi: 10.1073/pnas.1105380108. Epub 2011 Jun 20.

43.

Insights into physiological and genetic mupirocin susceptibility in bifidobacteria.

Serafini F, Bottacini F, Viappiani A, Baruffini E, Turroni F, Foroni E, Lodi T, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2011 May;77(9):3141-6. doi: 10.1128/AEM.02540-10. Epub 2011 Mar 18.

44.

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.

Turroni F, Bottacini F, Foroni E, Mulder I, Kim JH, Zomer A, Sánchez B, Bidossi A, Ferrarini A, Giubellini V, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Fitzgerald GF, Mills D, Margolles A, Kelly D, van Sinderen D, Ventura M.

Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19514-9. doi: 10.1073/pnas.1011100107. Epub 2010 Oct 25.

45.

Comparative genomics of the genus Bifidobacterium.

Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, Giubellini V, Tettelin H, van Sinderen D, Ventura M.

Microbiology. 2010 Nov;156(Pt 11):3243-54. doi: 10.1099/mic.0.039545-0. Epub 2010 Jul 15.

PMID:
20634238
46.

Characterization of the serpin-encoding gene of Bifidobacterium breve 210B.

Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2010 May;76(10):3206-19. doi: 10.1128/AEM.02938-09. Epub 2010 Mar 26.

47.

Analyses of bifidobacterial prophage-like sequences.

Ventura M, Turroni F, Foroni E, Duranti S, Giubellini V, Bottacini F, van Sinderen D.

Antonie Van Leeuwenhoek. 2010 Jun;98(1):39-50. doi: 10.1007/s10482-010-9426-4. Epub 2010 Mar 15.

PMID:
20229290
48.

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

Ventura M, Turroni F, Zomer A, Foroni E, Giubellini V, Bottacini F, Canchaya C, Claesson MJ, He F, Mantzourani M, Mulas L, Ferrarini A, Gao B, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Gupta RS, Zhang Z, Beighton D, Fitzgerald GF, O'Toole PW, van Sinderen D.

PLoS Genet. 2009 Dec;5(12):e1000785. doi: 10.1371/journal.pgen.1000785. Epub 2009 Dec 24.

49.

Comparative analyses of prophage-like elements present in bifidobacterial genomes.

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.

Appl Environ Microbiol. 2009 Nov;75(21):6929-36. doi: 10.1128/AEM.01112-09. Epub 2009 Sep 4.

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