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Identification of Dual Receptor Binding Protein Systems in Lactococcal 936 Group Phages.

Hayes S, Duhoo Y, Neve H, Murphy J, Noben JP, Franz CMAP, Cambillau C, Mahony J, Nauta A, van Sinderen D.

Viruses. 2018 Nov 27;10(12). pii: E668. doi: 10.3390/v10120668.


Characterisation of a Hydroxycinnamic Acid Esterase From the Bifidobacterium longum subsp. longum Taxon.

Kelly SM, O'Callaghan J, Kinsella M, van Sinderen D.

Front Microbiol. 2018 Nov 9;9:2690. doi: 10.3389/fmicb.2018.02690. eCollection 2018.


Health benefits conferred by the human gut microbiota during infancy.

Ventura M, Milani C, Lugli GA, van Sinderen D.

Microb Biotechnol. 2018 Nov 8. doi: 10.1111/1751-7915.13334. [Epub ahead of print]


A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation.

O'Connell Motherway M, Houston A, O'Callaghan G, Reunanen J, O'Brien F, O'Driscoll T, Casey PG, de Vos WM, van Sinderen D, Shanahan F.

Mol Microbiol. 2018 Oct 23. doi: 10.1111/mmi.14155. [Epub ahead of print]


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.


Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer.

Mangifesta M, Mancabelli L, Milani C, Gaiani F, de'Angelis N, de'Angelis GL, van Sinderen D, Ventura M, Turroni F.

Sci Rep. 2018 Sep 18;8(1):13974. doi: 10.1038/s41598-018-32413-2.


Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria.

Hayes S, Vincentelli R, Mahony J, Nauta A, Ramond L, Lugli GA, Ventura M, van Sinderen D, Cambillau C.

Mol Microbiol. 2018 Dec;110(5):777-795. doi: 10.1111/mmi.14124. Epub 2018 Oct 30.


Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury.

Duranti S, Vivo V, Zini I, Milani C, Mangifesta M, Anzalone R, Mancabelli L, Viappiani A, Cantoni AM, Barocelli E, van Sinderen D, Bertoni S, Turroni F.

PLoS One. 2018 Aug 30;13(8):e0202670. doi: 10.1371/journal.pone.0202670. eCollection 2018.


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.


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.


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.


Carbohydrate Syntrophy enhances the establishment of Bifidobacterium breve UCC2003 in the neonatal gut.

O'Connell Motherway M, O'Brien F, O'Driscoll T, Casey PG, Shanahan F, van Sinderen D.

Sci Rep. 2018 Jul 13;8(1):10627. doi: 10.1038/s41598-018-29034-0.


Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut.

Lugli GA, Mancino W, Milani C, Duranti S, Turroni F, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2018 Jun 8. pii: AEM.00796-18. doi: 10.1128/AEM.00796-18. [Epub ahead of print]


Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.

Arzamasov AA, van Sinderen D, Rodionov DA.

Front Microbiol. 2018 Apr 24;9:776. doi: 10.3389/fmicb.2018.00776. eCollection 2018.


Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach.

Milani C, Duranti S, Mangifesta M, Lugli GA, Turroni F, Mancabelli L, Viappiani A, Anzalone R, Alessandri G, Ossiprandi MC, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2018 Jul 2;84(14). pii: e00706-18. doi: 10.1128/AEM.00706-18. Print 2018 Jul 15.


Exopolysaccharide from Bifidobacterium longum subsp. longum 35624™ modulates murine allergic airway responses.

Schiavi E, Plattner S, Rodriguez-Perez N, Barcik W, Frei R, Ferstl R, Kurnik-Lucka M, Groeger D, Grant R, Roper J, Altmann F, van Sinderen D, Akdis CA, O'Mahony L.

Benef Microbes. 2018 Sep 18;9(5):761-773. doi: 10.3920/BM2017.0180. Epub 2018 May 4.


Extraction of the same novel homoglycan mixture from two different strains of Bifidobacterium animalis and three strains of Bifidobacterium breve.

Alhudhud M, Sadiq S, Ngo HN, Hidalgo-Cantabrana C, Ruas-Madiedo P, van Sinderen D, Humphreys PN, Laws AP.

Benef Microbes. 2018 Jun 15;9(4):663-674. doi: 10.3920/BM2017.0145. Epub 2018 Apr 26.


Determination of the cell wall polysaccharide and teichoic acid structures from Lactococcus lactis IL1403.

Vinogradov E, Sadovskaya I, Courtin P, Kulakauskas S, Grard T, Mahony J, van Sinderen D, Chapot-Chartier MP.

Carbohydr Res. 2018 Jun 15;462:39-44. doi: 10.1016/j.carres.2018.04.002. Epub 2018 Apr 12.


In Vitro Characteristics of Phages to Guide 'Real Life' Phage Therapy Suitability.

Casey E, van Sinderen D, Mahony J.

Viruses. 2018 Mar 30;10(4). pii: E163. doi: 10.3390/v10040163. Review.


Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9.

Vinogradov E, Sadovskaya I, Grard T, Murphy J, Mahony J, Chapot-Chartier MP, van Sinderen D.

Carbohydr Res. 2018 May 22;461:25-31. doi: 10.1016/j.carres.2018.03.011. Epub 2018 Mar 17.


Assessing the functionality and genetic diversity of lactococcal prophages.

Kelleher P, Mahony J, Schweinlin K, Neve H, Franz CM, van Sinderen D.

Int J Food Microbiol. 2018 May 2;272:29-40. doi: 10.1016/j.ijfoodmicro.2018.02.024. Epub 2018 Mar 1.


A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant.

Lavelle K, Murphy J, Fitzgerald B, Lugli GA, Zomer A, Neve H, Ventura M, Franz CM, Cambillau C, van Sinderen D, Mahony J.

Appl Environ Microbiol. 2018 Mar 9. pii: AEM.02855-17. doi: 10.1128/AEM.02855-17. [Epub ahead of print]


Bifidobacterium breve UCC2003 employs multiple transcriptional regulators to control metabolism of particular human milk oligosaccharides.

James K, Motherway MO, Penno C, O'Brien RL, van Sinderen D.

Appl Environ Microbiol. 2018 Mar 2. pii: AEM.02774-17. doi: 10.1128/AEM.02774-17. [Epub ahead of print]


Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin?

Mahony J, Lugli GA, van Sinderen D, Ventura M.

Appl Microbiol Biotechnol. 2018 Mar;102(5):2091-2099. doi: 10.1007/s00253-018-8795-x. Epub 2018 Feb 2. Review.


Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov.

Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M.

Syst Appl Microbiol. 2018 May;41(3):173-183. doi: 10.1016/j.syapm.2018.01.002. Epub 2018 Jan 31.


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.


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.


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.


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.


Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach.

Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M, Turroni F, Viappiani A, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2018 Jan 31;84(4). pii: e02249-17. doi: 10.1128/AEM.02249-17. Print 2018 Feb 15.


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.


Generation of Bacteriophage-Insensitive Mutants of Streptococcus thermophilus via an Antisense RNA CRISPR-Cas Silencing Approach.

McDonnell B, Mahony J, Hanemaaijer L, Kouwen TRHM, van Sinderen D.

Appl Environ Microbiol. 2018 Jan 31;84(4). pii: e01733-17. doi: 10.1128/AEM.01733-17. Print 2018 Feb 15.


Identification of DNA Base Modifications by Means of Pacific Biosciences RS Sequencing Technology.

Kelleher P, Murphy J, Mahony J, van Sinderen D.

Methods Mol Biol. 2018;1681:127-137. doi: 10.1007/978-1-4939-7343-9_10.


Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.

Mancabelli L, Milani C, Lugli GA, Turroni F, Cocconi D, van Sinderen D, Ventura M.

FEMS Microbiol Ecol. 2017 Dec 1;93(12). doi: 10.1093/femsec/fix153.


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.


Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures.

Oliveira J, Mahony J, Hanemaaijer L, Kouwen TRHM, van Sinderen D.

J Dairy Sci. 2018 Jan;101(1):96-105. doi: 10.3168/jds.2017-13403. Epub 2017 Nov 2.


Glycan Utilization and Cross-Feeding Activities by Bifidobacteria.

Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M.

Trends Microbiol. 2018 Apr;26(4):339-350. doi: 10.1016/j.tim.2017.10.001. Epub 2017 Oct 28. Review.


Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production.

Borrero J, Kelly E, O'Connor PM, Kelleher P, Scully C, Cotter PD, Mahony J, van Sinderen D.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01801-17. doi: 10.1128/AEM.01801-17. Print 2018 Jan 1.


Selected aspects of the human gut microbiota.

Ventura M, O'Toole PW, de Vos WM, van Sinderen D.

Cell Mol Life Sci. 2018 Jan;75(1):81-82. doi: 10.1007/s00018-017-2669-8. Epub 2017 Oct 6.


Bifidobacteria and the infant gut: an example of co-evolution and natural selection.

Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M.

Cell Mol Life Sci. 2018 Jan;75(1):103-118. doi: 10.1007/s00018-017-2672-0. Epub 2017 Oct 5. Review.


Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF.

Nucleic Acids Res. 2017 Sep 29;45(17):10156-10167. doi: 10.1093/nar/gkx690.


Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage.

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF.

Nucleic Acids Res. 2017 Sep 29;45(17):10143-10155. doi: 10.1093/nar/gkx689.


Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.

Ferrario C, Alessandri G, Mancabelli L, Gering E, Mangifesta M, Milani C, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, Hiyashi R, Mackie R, van Sinderen D, Ventura M.

Environ Microbiol. 2017 Nov;19(11):4771-4783. doi: 10.1111/1462-2920.13943. Epub 2017 Oct 13.


Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus.

McDonnell B, Mahony J, Hanemaaijer L, Neve H, Noben JP, Lugli GA, Ventura M, Kouwen TR, van Sinderen D.

Front Microbiol. 2017 Sep 12;8:1754. doi: 10.3389/fmicb.2017.01754. eCollection 2017.


How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers.

Ferrario C, Statello R, Carnevali L, Mancabelli L, Milani C, Mangifesta M, Duranti S, Lugli GA, Jimenez B, Lodge S, Viappiani A, Alessandri G, Dall'Asta M, Del Rio D, Sgoifo A, van Sinderen D, Ventura M, Turroni F.

Front Microbiol. 2017 Sep 12;8:1749. doi: 10.3389/fmicb.2017.01749. eCollection 2017.


Another Brick in the Wall: a Rhamnan Polysaccharide Trapped inside Peptidoglycan of Lactococcus lactis.

Sadovskaya I, Vinogradov E, Courtin P, Armalyte J, Meyrand M, Giaouris E, Palussière S, Furlan S, Péchoux C, Ainsworth S, Mahony J, van Sinderen D, Kulakauskas S, Guérardel Y, Chapot-Chartier MP.

MBio. 2017 Sep 12;8(5). pii: e01303-17. doi: 10.1128/mBio.01303-17.


Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses.

Mancabelli L, Milani C, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ticinesi A, Nouvenne A, Meschi T, van Sinderen D, Ventura M.

Sci Rep. 2017 Aug 29;7(1):9879. doi: 10.1038/s41598-017-10663-w.


Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life.

Milani C, Mangifesta M, Mancabelli L, Lugli GA, James K, Duranti S, Turroni F, Ferrario C, Ossiprandi MC, van Sinderen D, Ventura M.

ISME J. 2017 Dec;11(12):2834-2847. doi: 10.1038/ismej.2017.138. Epub 2017 Aug 22.


Host recognition by lactic acid bacterial phages.

Mahony J, Cambillau C, van Sinderen D.

FEMS Microbiol Rev. 2017 Aug 1;41(Supp_1):S16-S26. doi: 10.1093/femsre/fux019. Review.


Detecting Lactococcus lactis Prophages by Mitomycin C-Mediated Induction Coupled to Flow Cytometry Analysis.

Oliveira J, Mahony J, Hanemaaijer L, Kouwen TRHM, Neve H, MacSharry J, van Sinderen D.

Front Microbiol. 2017 Jul 19;8:1343. doi: 10.3389/fmicb.2017.01343. eCollection 2017.

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