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Host Microbiota Regulates Central Nervous System Serotonin Receptor 2C Editing in Rodents.

van de Wouw M, Stilling RM, Peterson VL, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF, Schellekens H.

ACS Chem Neurosci. 2019 Sep 18;10(9):3953-3960. doi: 10.1021/acschemneuro.9b00414. Epub 2019 Aug 19.


Microbiome analysis as a platform R&D tool for parasitic nematode disease management.

Hogan G, Walker S, Turnbull F, Curiao T, Morrison AA, Flores Y, Andrews L, Claesson MJ, Tangney M, Bartley DJ.

ISME J. 2019 Nov;13(11):2664-2680. doi: 10.1038/s41396-019-0462-4. Epub 2019 Jun 25.


Differential gene expression in the mesocorticolimbic system of innately high- and low-impulsive rats.

Moloney GM, van Oeffelen WEPA, Ryan FJ, van de Wouw M, Cowan C, Claesson MJ, Schellekens H, Dinan TG, Cryan JF.

Behav Brain Res. 2019 May 17;364:193-204. doi: 10.1016/j.bbr.2019.01.022. Epub 2019 Feb 6.


Making Sense of … the Microbiome in Psychiatry.

Bastiaanssen TFS, Cowan CSM, Claesson MJ, Dinan TG, Cryan JF.

Int J Neuropsychopharmacol. 2019 Jan 1;22(1):37-52. doi: 10.1093/ijnp/pyy067.


Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice.

Stilling RM, Moloney GM, Ryan FJ, Hoban AE, Bastiaanssen TF, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF.

Elife. 2018 May 29;7. pii: e33070. doi: 10.7554/eLife.33070.


Species classifier choice is a key consideration when analysing low-complexity food microbiome data.

Walsh AM, Crispie F, O'Sullivan O, Finnegan L, Claesson MJ, Cotter PD.

Microbiome. 2018 Mar 20;6(1):50. doi: 10.1186/s40168-018-0437-0.


Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn's Disease and Ulcerative Colitis.

Laserna-Mendieta EJ, Clooney AG, Carretero-Gomez JF, Moran C, Sheehan D, Nolan JA, Hill C, Gahan CGM, Joyce SA, Shanahan F, Claesson MJ.

J Crohns Colitis. 2018 Jan 24;12(2):204-216. doi: 10.1093/ecco-jcc/jjx137.


Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal.

Harris HMB, Bourin MJB, Claesson MJ, O'Toole PW.

Microb Genom. 2017 Jun 13;3(8):e000115. doi: 10.1099/mgen.0.000115. eCollection 2017 Aug.


A clinician's guide to microbiome analysis.

Claesson MJ, Clooney AG, O'Toole PW.

Nat Rev Gastroenterol Hepatol. 2017 Oct;14(10):585-595. doi: 10.1038/nrgastro.2017.97. Epub 2017 Aug 9. Review.


Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

Walsh AM, Crispie F, Daari K, O'Sullivan O, Martin JC, Arthur CT, Claesson MJ, Scott KP, Cotter PD.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e01144-17. doi: 10.1128/AEM.01144-17. Print 2017 Aug 15.


Correction for Walsh et al., Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PD.

mSystems. 2017 Feb 21;2(1). pii: e00003-17. doi: 10.1128/mSystems.00003-17. eCollection 2017 Jan-Feb.


Translating Omics to Food Microbiology.

Walsh AM, Crispie F, Claesson MJ, Cotter PD.

Annu Rev Food Sci Technol. 2017 Feb 28;8:113-134. doi: 10.1146/annurev-food-030216-025729. Epub 2017 Jan 11. Review.


Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PD.

mSystems. 2016 Oct 4;1(5). pii: e00052-16. eCollection 2016 Sep-Oct. Erratum in: mSystems. 2017 Feb 21;2(1):.


16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform.

Fouhy F, Clooney AG, Stanton C, Claesson MJ, Cotter PD.

BMC Microbiol. 2016 Jun 24;16(1):123. doi: 10.1186/s12866-016-0738-z.


Regulation of prefrontal cortex myelination by the microbiota.

Hoban AE, Stilling RM, Ryan FJ, Shanahan F, Dinan TG, Claesson MJ, Clarke G, Cryan JF.

Transl Psychiatry. 2016 Apr 5;6:e774. doi: 10.1038/tp.2016.42.


Tumour-associated and non-tumour-associated microbiota in colorectal cancer.

Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F, O'Toole PW.

Gut. 2017 Apr;66(4):633-643. doi: 10.1136/gutjnl-2015-309595. Epub 2016 Mar 18.


A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors.

Clooney AG, Bernstein CN, Leslie WD, Vagianos K, Sargent M, Laserna-Mendieta EJ, Claesson MJ, Targownik LE.

Aliment Pharmacol Ther. 2016 May;43(9):974-84. doi: 10.1111/apt.13568. Epub 2016 Feb 29.


Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis.

Clooney AG, Fouhy F, Sleator RD, O' Driscoll A, Stanton C, Cotter PD, Claesson MJ.

PLoS One. 2016 Feb 5;11(2):e0148028. doi: 10.1371/journal.pone.0148028. eCollection 2016.


SPINGO: a rapid species-classifier for microbial amplicon sequences.

Allard G, Ryan FJ, Jeffery IB, Claesson MJ.

BMC Bioinformatics. 2015 Oct 8;16:324. doi: 10.1186/s12859-015-0747-1.


Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.

Stilling RM, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JF.

Brain Behav Immun. 2015 Nov;50:209-220. doi: 10.1016/j.bbi.2015.07.009. Epub 2015 Jul 14.


BlastXtract2: Improving early exploration of (meta) genomes.

de Weerd H, van der Veen BE, Claesson MJ.

Bioinformation. 2015 Apr 30;11(4):173-5. doi: 10.6026/97320630011173. eCollection 2015.


Metaphor: finding bi-directional best hit homology relationships in (meta)genomic datasets.

van der Veen BE, Harris HM, O'Toole PW, Claesson MJ.

Genomics. 2014 Dec;104(6 Pt B):459-63. doi: 10.1016/j.ygeno.2014.10.008. Epub 2014 Oct 27.


Unusual genome complexity in Lactobacillus salivarius JCM1046.

Raftis EJ, Forde BM, Claesson MJ, O'Toole PW.

BMC Genomics. 2014 Sep 8;15:771. doi: 10.1186/1471-2164-15-771.


Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats.

O'Mahony SM, Felice VD, Nally K, Savignac HM, Claesson MJ, Scully P, Woznicki J, Hyland NP, Shanahan F, Quigley EM, Marchesi JR, O'Toole PW, Dinan TG, Cryan JF.

Neuroscience. 2014 Sep 26;277:885-901. doi: 10.1016/j.neuroscience.2014.07.054. Epub 2014 Aug 1.


Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.

Neville BA, Sheridan PO, Harris HM, Coughlan S, Flint HJ, Duncan SH, Jeffery IB, Claesson MJ, Ross RP, Scott KP, O'Toole PW.

PLoS One. 2013 Jul 23;8(7):e68919. doi: 10.1371/journal.pone.0068919. Print 2013.


The core faecal bacterial microbiome of Irish Thoroughbred racehorses.

O' Donnell MM, Harris HM, Jeffery IB, Claesson MJ, Younge B, O' Toole PW, Ross RP.

Lett Appl Microbiol. 2013 Dec;57(6):492-501. doi: 10.1111/lam.12137. Epub 2013 Aug 19.


The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.

Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HM, Jeffery IB, Claesson MJ, O'Toole PW, Peyret P, Brugère JF.

PLoS One. 2013 May 17;8(5):e62544. doi: 10.1371/journal.pone.0062544. Print 2013.


Categorization of the gut microbiota: enterotypes or gradients?

Jeffery IB, Claesson MJ, O'Toole PW, Shanahan F.

Nat Rev Microbiol. 2012 Sep;10(9):591-2. No abstract available.


Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy.

O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C, Ross RP; ELDERMET Consortium.

J Antimicrob Chemother. 2013 Jan;68(1):214-21. doi: 10.1093/jac/dks348. Epub 2012 Sep 4.


Characterization of pro-inflammatory flagellin proteins produced by Lactobacillus ruminis and related motile Lactobacilli.

Neville BA, Forde BM, Claesson MJ, Darby T, Coghlan A, Nally K, Ross RP, O'Toole PW.

PLoS One. 2012;7(7):e40592. doi: 10.1371/journal.pone.0040592. Epub 2012 Jul 10.


Gut microbiota composition correlates with diet and health in the elderly.

Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O'Sullivan O, Fitzgerald GF, Deane J, O'Connor M, Harnedy N, O'Connor K, O'Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O'Toole PW.

Nature. 2012 Aug 9;488(7410):178-84. doi: 10.1038/nature11319.


Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein.

Collins J, van Pijkeren JP, Svensson L, Claesson MJ, Sturme M, Li Y, Cooney JC, van Sinderen D, Walker AW, Parkhill J, Shannon O, O'Toole PW.

Mol Microbiol. 2012 Sep;85(5):862-77. doi: 10.1111/j.1365-2958.2012.08148.x. Epub 2012 Jul 11.


Diversity of bifidobacteria within the infant gut microbiota.

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.

PLoS One. 2012;7(5):e36957. doi: 10.1371/journal.pone.0036957. Epub 2012 May 11.


Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota.

Riboulet-Bisson E, Sturme MH, Jeffery IB, O'Donnell MM, Neville BA, Forde BM, Claesson MJ, Harris H, Gardiner GE, Casey PG, Lawlor PG, O'Toole PW, Ross RP.

PLoS One. 2012;7(2):e31113. doi: 10.1371/journal.pone.0031113. Epub 2012 Feb 17.


An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota.

Jeffery IB, O'Toole PW, Öhman L, Claesson MJ, Deane J, Quigley EM, Simrén M.

Gut. 2012 Jul;61(7):997-1006. doi: 10.1136/gutjnl-2011-301501. Epub 2011 Dec 16.


Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts.

Forde BM, Neville BA, O'Donnell MM, Riboulet-Bisson E, Claesson MJ, Coghlan A, Ross RP, O'Toole PW.

Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S13. doi: 10.1186/1475-2859-10-S1-S13. Epub 2011 Aug 30.


Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects.

O'Sullivan Ó, Coakley M, Lakshminarayanan B, Claesson MJ, Stanton C, O'Toole PW, Ross RP; ELDERMET consortium (

J Appl Microbiol. 2011 Aug;111(2):467-73. doi: 10.1111/j.1365-2672.2011.05067.x. Epub 2011 Jul 1.


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.


Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities.

Claesson MJ, O'Toole PW.

Gut Microbes. 2010 Jul;1(4):277-278. Epub 2010 Mar 24.


Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.

Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW.

Nucleic Acids Res. 2010 Dec;38(22):e200. doi: 10.1093/nar/gkq873. Epub 2010 Sep 29.


Composition, variability, and temporal stability of the intestinal microbiota of the elderly.

Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4586-91. doi: 10.1073/pnas.1000097107. Epub 2010 Jun 22.


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.


Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW.

PLoS One. 2009 Aug 20;4(8):e6669. doi: 10.1371/journal.pone.0006669.


Lactobacillus phylogenomics--towards a reclassification of the genus.

Claesson MJ, van Sinderen D, O'Toole PW.

Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2945-54. doi: 10.1099/ijs.0.65848-0.


Genome-scale analyses of health-promoting bacteria: probiogenomics.

Ventura M, O'Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, O'Toole PW.

Nat Rev Microbiol. 2009 Jan;7(1):61-71. doi: 10.1038/nrmicro2047. Epub 2008 Nov 24. Review.


Characterization of endogenous plasmids from Lactobacillus salivarius UCC118.

Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP, Collins JK, van Sinderen D, O'Toole PW.

Appl Environ Microbiol. 2008 May;74(10):3216-28. doi: 10.1128/AEM.02631-07. Epub 2008 Apr 4.


The genus Lactobacillus--a genomic basis for understanding its diversity.

Claesson MJ, van Sinderen D, O'Toole PW.

FEMS Microbiol Lett. 2007 Apr;269(1):22-8. Review.


Diversity of the genus Lactobacillus revealed by comparative genomics of five species.

Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O'Toole PW.

Microbiology. 2006 Nov;152(Pt 11):3185-96.


Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118.

van Pijkeren JP, Canchaya C, Ryan KA, Li Y, Claesson MJ, Sheil B, Steidler L, O'Mahony L, Fitzgerald GF, van Sinderen D, O'Toole PW.

Appl Environ Microbiol. 2006 Jun;72(6):4143-53.


Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei.

Ventura M, Canchaya C, Bernini V, Altermann E, Barrangou R, McGrath S, Claesson MJ, Li Y, Leahy S, Walker CD, Zink R, Neviani E, Steele J, Broadbent J, Klaenhammer TR, Fitzgerald GF, O'toole PW, van Sinderen D.

Appl Environ Microbiol. 2006 May;72(5):3130-46.

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