• Lukacik P, Lobley CM, Bumann M, Arena de Souza V, Owens RJ, O'Toole PW, Walsh MA. High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate. Acta Crystallogr F Struct Biol Commun. Acta Crystallogr F Struct Biol Commun. 2015; 71(Pt 10):1327-34.
  • Konieczna P, Schiavi E, Ziegler M, Groeger D, Healy S, Grant R, O'Mahony L. Human Dendritic Cell DC-SIGN and TLR-2 Mediate Complementary Immune Regulatory Activities in Response to Lactobacillus rhamnosus JB-1. PLoS One. 2015; 10(3):e0120261.
  • Lindsay KL, Brennan L, Kennelly MA, Maguire OC, Smith T, Curran S, Coffey M, Foley ME, Hatunic M, Shanahan F, McAuliffe FM. Impact of probiotics in women with gestational diabetes mellitus on metabolic health: a randomized controlled trial. Am J Obstet Gynecol. 2015; 212(4):496.e1-11.


  • Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA,Edwards RA. Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol Med. 2013; 8(1):23.
  • Charbonneau D, Gibb RD, Quigley EM.  Fecal excretion of Bifidobacterium infantis 35624 and changes in fecal microbiota after eight weeks of oral supplementation with encapsulated probiotic. Gut Microbes. 2013;4(3):201-211.
  • Clarke SF, Murphy EF, O'Sullivan O, Ross RP, O'Toole PW, Shanahan F, Cotter PD. Targeting the microbiota to address diet-induced obesity: a time dependent challenge. PLoS One. 2013;8(6):e65790.
  • Groeger D, O'Mahony L, Murphy EF, Bourke JF, Dinan TG, Kiely B, Shanahan F, Quigley EM. Bifidobacterium infantis 35624 modulates host inflammatory processes beyond the gut. Gut Microbes. 2013;4(4):325-39.
  • Herfel TM, Jacobi SK, Lin X, Jouni ZE, Chichlowski M, Stahl CH, Odle J. Dietary supplementation of Bifidobacterium longum strain AH1206 increases its cecal abundance and elevates intestinal interleukin-10 expression in the neonatal piglet. Food Chem Toxicol. 2013;60:116-22.
  • Konieczna P, Ferstl R, Ziegler M, Frei R, Nehrbass D, Lauener RP, Akdis CA, O'Mahony L. Immunomodulation by Bifidobacterium infantis 35624 in the murine lamina propria requires retinoic acid-dependent and independent mechanisms. PLoS One. 2013;8(5): e62617.
  • Mathur H, O'Connor PM, Hill C, Cotter PD, Ross RP. Analysis of anti-Clostridium difficile activity of thuricin CD, vancomycin, metronidazole, ramoplanin, and actagardine, both singly and in paired combinations. Antimicrob Agents Chemother. 2013;57(6):2882-6.
  • McClemens J, Kim JJ, Wang H, Mao YK, Collins M, Kunze W, Bienenstock J, Forsythe P, Khan WI. Lactobacillus rhamnosus ingestion promotes innate host defense in an enteric parasitic infection. Clin Vaccine Immunol. 2013;20(6):818-26.
  • Murphy EF, Clarke SF, Marques TM, Hill C, Stanton C, Ross RP, O'Doherty RM, Shanahan F, Cotter PD. Antimicrobials: Strategies for targeting obesity and metabolic health? Gut Microbes. 2013;4(1):48-53.
  • Murphy EF, Cotter PD, Hogan A, O'Sullivan O, Joyce A, Fouhy F, Clarke SF, Marques TM, O'Toole PW, Stanton C, Quigley EM, Daly C, Ross PR, O'Doherty RM, Shanahan F. Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity. Gut. 2013;62(2):220-6.
  • Perez-Burgos A, Wang B, Mao YK, Mistry B, McVey Neufeld KA, Bienenstock J, Kunze W. Psychoactive bacteria Lactobacillus rhamnosus (JB-1) elicits rapid frequency facilitation in vagal afferents. Am J Physiol Gastrointest Liver Physiol. 2013;304(2):G211-20.
  • Quigley EM, Stanton C, Murphy EF. The gut microbiota and the liver. Pathophysiological and clinical implications. J Hepatol. 2013;58(5):1020-7.
  • Scully P, Macsharry J, O'Mahony D, Lyons A, O'Brien F, Murphy S, Shanahan F, O'Mahony L. Bifidobacterium infantis suppression of Peyer's patch MIP-1α and MIP-1β secretion during Salmonella infection correlates with increased local CD4+CD25+ T cell numbers. Cell Immunol. 2013;281(2):134-140.
  • Smelt MJ, de Haan BJ, Bron PA, van Swam I, Meijerink M, Wells JM, Faas MM, de Vos P. Probiotics can generate FoxP3 T-cell responses in the small intestine and simultaneously inducing CD4 and CD8 T cell activation in the large intestine. PLoS One. 2013;8(7):e68952.
  • Wu RY, Pasyk M, Wang B, Forsythe P, Bienenstock J, Mao YK, Sharma P, Stanisz AM, Kunze WA. Spatiotemporal maps reveal regional differences in the effects on gut motility for Lactobacillus reuteri and rhamnosus strains. Neurogastroenterol Motil. 2013;25(3):e205-14.


  • Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A. 2011;108(38):16050-5.
  • Frech TM, Khanna D, Maranian P, Frech EJ, Sawitzke AD, Murtaugh MA.  Probiotics for the treatment of systemic sclerosis-associated gastrointestinal bloating/distension. Clin Exp Rheumatol. 2011;29(2 Suppl 65):S22-5.
  • Gad M, Ravn P, Søborg DA, Lund-Jensen K, Ouwehand AC, Jensen SS.  Regulation of the IL-10/IL-12 axis in human dendritic cells with probiotic bacteria.  FEMS Immunol Med Microbiol. 2011;63(1):93-107. 
  • Guinane CM, Barrett E, Fitzgerald GF, van Sinderen D, Ross RP, Stanton C. Genome sequence of Bifidobacterium breve DPC 6330, a strain isolated from the human intestine. J Bacteriol. 2011;193(23):6799-800.
  • Johnson AC, Greenwood-Van Meerveld B, McRorie J.  Effects of Bifidobacterium infantis 35624 on Post-Inflammatory Visceral Hypersensitivity in the Rat.  Dig Dis Sci. 2011;56(11):3179-86.
  • Moslehi-Jenabian S, Gori K, Jespersen L. AI-2 signalling is induced by acidic shock in probiotic strains of Lactobacillus spp. Int J Food Microbiol. 2009;135(3):295-302.
  • Murphy K, O'Sullivan O, Rea MC, Cotter PD, Ross RP, Hill C. Genome mining for radical SAM protein determinants reveals multiple sactibiotic-like gene clusters. PLoS One. 2011;6(7):e20852.
  • O'Shea EF, O'Connor PM, Raftis EJ, O'Toole PW, Stanton C, Cotter PD, Ross RP, Hill C. Production of multiple bacteriocins from a single locus by gastrointestinal strains of Lactobacillus salivariusJ Bacteriol. 2011;193(24):6973-82.
  • O'Sullivan E, Barrett E, Grenham S, Fitzgerald P, Stanton C, Ross RP, Quigley EM, Cryan JF, Dinan TG. BDNF expression in the hippocampus of maternally separated rats: does Bifidobacterium breve 6330 alter BDNF levels? Benef Microbes. 2011;2(3):199-207.
  • Pruteanu M, Hyland NP, Clarke DJ, Kiely B, Shanahan F. Degradation of the extracellular matrix components by bacterial-derived metalloproteases: implications for inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17(5):1189-200.
  • Quigley E, Groeger D, O’Mahony L, Bourke J, Scully P, Dinan T, Shanahan F, Kiely B. Oral administration of the probiotic Bifidobacterium infantis 35624 to humans induces immunoregulatory responses in vivoAm J Gastroenterol. 2011;106(Suppl 2):S463-4.  Abstract 1228.
  • Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP. Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4639-44.
  • Schmulson M, Chang L. Review article: the treatment of functional abdominal bloating and distension. Aliment Pharmacol Ther. 2011;33(10):1071-86.
  • Sit CS, McKay RT, Hill C, Ross RP, Vederas JC. The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links. J Am Chem Soc. 2011;133(20):7680-3.


  • Abeln S, McCarthy N. Probiotic benefits demonstrated in a clinical setting translate to meaningful benefits in the real world:  post marketing experience with the probiotic strain Bifidobacterium infantis 35624. Am J Gastroentoerol 2009;104(Suppl 3):S496. Abstract 1327.
  • Brenner DM, Chey WD. Bifidobacterium infantis 35624: A novel probiotic for the treatment of IBS. Rev Gastroenterol Disord. 2009;9(1):7-15. Review.
  • Brenner DMMoeller MJChey WDSchoenfeld PS. The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review. Am J Gastroenterol. 2009;104(4):1033-49
  • Clayton EM, Rea MC, Shanahan F, Quigley EM, Kiely B, Hill C, Ross RP. The vexed relationship between Clostridium difficile and inflammatory bowel disease: an assessment of carriage in an outpatient setting among patients in remission. Am J Gastroenterol. 2009;104(5):1162-9.
  • Davies JM, Sheil B, Shanahan F. Bacterial signalling overrides cytokine signalling and modifies dendritic cell differentiation. Immunology. 2009;128(1 Suppl)
  • Fang F, Li Y, Bumann M, Raftis EJ, Casey PG, Cooney JC, Walsh MA, O'Toole PW. Allelic variation of bile salt hydrolase genes in Lactobacillus salivarius does not determine bile resistance levels. J Bacteriol. 2009;191(18):5743-57.
  • Kelley RL, Minikhiem D, Kiely B, O'Mahony L, O'Sullivan D, Boileau T, Park JS. Clinical benefits of probiotic canine-derived Bifidobacterium animalis strain AHC7 in dogs with acute idiopathic diarrhea. Vet Ther. 2009;10(3):121-30.
  • Moslehi-Jenabian S, Gori K, Jespersen L. AI-2 signalling is induced by acidic shock in probiotic strains of Lactobacillus spp. Int J Food Microbiol. 2009;135(3):295-302.
  • Murphy C, Murphy S, O'Brien F, O'Donoghue M, Boileau T, Sunvold G, Reinhart G, Kiely B, Shanahan F, O'Mahony L. Metabolic activity of probiotics-oxalate degradation. Vet Microbiol. 2009;136(1-2):100-7.
  • O’Mahony L, O’Mahony D, Lyons A, Groeger D, Drummond L, O’Brien F, Kiely B, Shanahan F. A secreted polysaccharide from Bifidobacterium infantis 35624 promotes development of Foxp3+ T regulatory cells in gnotobiotic mice in vivoGastroenterology. 2009;136(5 Suppl1):663.
  • O'Mahony D, Murphy KB, MacSharry J, Boileau T, Sunvold G, Reinhart G, Kiely B, Shanahan F, O'Mahony L. Portrait of a canine probiotic Bifidobacterium--from gut to gut. Vet Microbiol. 2009;139(1-2):106-12.
  • Ryan KA, O'Hara AM, van Pijkeren JP, Douillard FP, O'Toole PW. Lactobacillus salivarius modulates cytokine induction and virulence factor gene expression in Helicobacter pyloriJ Med Microbiol. 2009;58(Pt 8):996-1005.
  • Sibartie S, O'Hara AM, Ryan J, Fanning A, O'Mahony J, O'Neill S, Sheil B, O'Mahony L, Shanahan F. Modulation of pathogen-induced CCL20 secretion from HT-29 human intestinal epithelial cells by commensal bacteria. BMC Immunol. 2009;10:54.
  • Wall R, Ross RP, Shanahan F, O'Mahony L, O'Mahony C, Coakley M, Hart O, Lawlor P, Quigley EM, Kiely B, Fitzgerald GF, Stanton C. Metabolic activity of the enteric microbiota influences the fatty acid composition of murine and porcine liver and adipose tissues. Am J Clin Nutr. 2009;89(5):1393-401.
  • Wall R, Ross RP, Shanahan F, O'Mahony L, Kiely B, Quigley E, Dinan TG, Fitzgerald G, Stanton C. Impact of administered Bifidobacterium on murine host fatty acid composition. Lipids. 2010;45(5):429-36.


  • Corr SC, Li Y, Riedel CU, O'Toole PW, Hill C, Gahan CG. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci U S A. 2007 M;104(18):7617-21.
  • Li Y, Canchaya C, Fang F, Raftis E, Ryan KA, van Pijkeren JP, van Sinderen D, O'Toole PW. Distribution of megaplasmids in Lactobacillus salivarius and other lactobacilliJ Bacteriol. 2007;189(17):6128-39.
  • O'Mahony C, Scully P, O'Mahony D, Lyons A, O'Sullivan D, MacSharry J, Kiely B, Shanahan F, O'Mahony L. Commensal microbiota, including probiotics, promote T regulatory cells and attenuation of inflammatory responses to murine Salmonella infection. Gastroenterology. 2007;132(4 Suppl 2):401.
  • Rea MC, Clayton E, O'Connor PM, Shanahan F, Kiely B, Ross RP, Hill C. Antimicrobial activity of lacticin 3147 against clinical Clostridium difficile strains. J Med Microbiol. 2007;56(Pt 7):940-6.
  • Sheil B, MacSharry J, O'Mahony L, Shanahan F, Kiely B. Modulation of the commensal flora by probiotic feeding delays the onset and decreases the severity of disease in the collagen-induced arthritis (CIA) model in a strain-dependent manner. Gastroenterology. 2007;132(4 Suppl 2):A209.
  • Sheil B, Shanahan F, O'Mahony L. Probiotic effects on inflammatory bowel disease. J Nutr. 2007;137(3 Suppl 2):819S-24S.
  • Shilling D, Coffey C, Smith M, Kavanagh E, Kirwan W, Redmond H, Shanahan F, O’Mahony L . Bacterial stimulation combined with heat shock protein targeting induces potent dendritic cell anti-tumor responses in a murine model. Gastroenterology. 2005;128:A178 (Abstract S1250)
  • Symonds EL, O'Mahony C, O'Mahony D, O'Mahony L, Shanahan F. Probiotic prevention of digestive enzyme damage in a mouse model of SalmonellaGastroenterology. 2007;132(4 Suppl 2):A714-5.


  • Bairead E, O'Mahony L, MacSharry J, Scully P, Fanning A, Kiely B, O'Mahony S, Shanahan F, Quigley E. Alterations in immunological gene expression from colonic biopsies of female IBS patients following probiotic consumption. Gastroenterology, 2005, 128 (44).
  • Chang K, Fangyi L, Hendrix S, Altringer L, Charbonneau D, Poehner R, Carryl O, Trowbridge M, O'Mahony L, Quigley E, Shanahan F S. Modulation of cytokine profiles in healthy and IBS subjects following supplementation with the unique probiotic strain, Bifidobacterium infantis 35624 . P&G Health Sciences Institute Publication 2005. Gastroenterology, 2005;128, (4 Suppl 2):A661
  • Charbonneau D, Baria M, Poehner R, Mccauley-Myers D, Eads C, Furnish C, Donovan-Brand R. Impact of Bifidobacterium infantis 35624 on fecal flora from healthy and IBS subjects in a chemostat model. Gastroenterology. 2005;128(4 Suppl 2):A660-61.
  • Charbonneau DL, Altringer LA, Carryl OR, Chen K-S, Kidd KJ, Darcy T, Fawcett DH, Trowbridge M M, Jang C, Luo F, Poehner RD, Meller ST. Fecal flora effects following oral supplementation with Bifidobacteria infantis 35624 in healthy and IBS subjects. Can J Gastroenterol. 2005;19(Suppl SB):R1097.
  • Chen K-S, Luo F, Hendrix SW, Altringer LA, Charbonneau DL, Poehner RD, Carryl OR, Trowbridge MM, O'Mahony L, Shanahan F, Quigley E, Meller ST.Oral administration with a unique probiotic strain, Bifidobacterium infantis 35624, to IBS subjects normalizes their systemic immunological imbalance in cytokine profile toward healthy subjects. Can J Gastroenterol. 2005;19(Suppl SB):R.1112.
  • Kelly P, Maguire PB, Bennett M, Fitzgerald DJ, Edwards RJ, Thiede B, Treumann A, Collins JK, O'Sullivan GC, Shanahan F, Dunne C. Correlation of probiotic Lactobacillus salivarius growth phase with its cell wall-associated proteome. FEMS Microbiol Lett. 2005 ;252(1):153-9.
  • O'Mahony L, McCarthy J, Kelly P, Hurley G, Luo F, Chen K, O'Sullivan GC, Kiely B, Collins JK, Shanahan F, Quigley E. Lactobacillus and Bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology. 2005;128(3):541-51.
  • O'Mahony L, Sheil B, Murphy C, Duke K, Murphy S, Kiely B, Shanahan F. Bifidobacterial induced cytokine production in vitro as predictive biomarkers of in vivo performance in the lymphocyte transfer model of IBD. Gastroenterology. 2005;128(4 Suppl 2):A619.
  • Quigley EM, Whorwell PJ, Altringer L, Morel J, O'Mahony L, Shanahan F. Probiotic use results in normalization of bowel movement frequency in IBS. Results from a clinical trial with the novel probiotic Bifidobacteria infantis 35624. Am J of Gastroenterology, 2005;100( 9 Suppl S):S326
  • Quigley EM, Whorwell PJ, Altringer L, Morel J, O'Mahony L, Shanahan F. Who is the responder to probiotic therapy in IBS? Data from a controlled clinical trial with Bifidobacterium infantis 35624. Am J Gastroenterol. 2005;100(9 Suppl S):A325-326.
  • Sommerfield D, MacSharry J, O’Mahony D, O’Mahony L, Kiely B, Shanahan F, Quigley EM Effect of probiotic feeding on Salmonella translocation in a Mouse model. Gastroenterology. 2005;128:A120.(Abstract 770)




  • Allen AP, Hutch W, Borre YE, Kennedy PJ, Temko A, Boylan G, Murphy E, Cryan JF, Dinan TG, Clarke G. Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers. Transl Psychiatry. 2016; 6(11):e939
  • Schiavi E, Gleinser M, Molloy E, Groeger D, Frei R, Ferstl R, Rodriguez-Perez N, Ziegler M, Grant R, Moriarty TF, Plattner S, Healy S, O'Connell Motherway M, Akdis CA, Roper J, Altmann F, van Sinderen D, O'Mahony L. The surface associated exopolysaccharide of Bifidobacterium longum 35624 plays an essential role in dampening host pro-inflammatory responses and in repressing local TH17 responses. Appl Environ Microbiol. 2016 Oct 7. pii: AEM.02238-16.
  • 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. Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome. Cell Host Microbe. 2016; 20(4):515-526.
  • 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. Genome Analysis and Characterisation of the Exopolysaccharide Produced by Bifidobacterium longumsubsp. longum 35624™. PLoS One. 2016; 11(9):e0162983.
  • Hoy-Schulz YE, Jannat K, Roberts T, Zaidi SH, Unicomb L, Luby S, Parsonnet J. Safety and acceptability of Lactobacillus reuteri DSM 17938 and Bifidobacterium longum subspecies infantis 35624 in Bangladeshi infants: a phase I randomized clinical trial. BMC Complement Altern Med. 2016; 16:44.


  • Al-Nedawi K, Mian MF, Hossain N, Karimi K, Mao YK, Forsythe P, Min KK, Stanisz AM, Kunze WA, Bienenstock J. Gut commensal microvesicles reproduce parent bacterial signals to host immune and enteric nervous systems. FASEB J. 2015; 29(2):684-95.
  • Perez-Burgos A, Mao YK, Bienenstock J, Kunze WA. The gut-brain axis rewired: adding a functional vagal nicotinic "sensory synapse". FASEB J. 2014; 28(7):3064-74.
  • Lomasney KW, Cryan JF, Hyland NP. Converging effects of a Bifidobacterium and Lactobacillus probiotic strain on mouse intestinal physiology. Am J Physiol Gastrointest Liver Physiol. 2014; 307(2):G241-7.


  • Alemka A, Clyne M, Shanahan F, Tompkins T, Corcionivoschi N, Bourke B. Probiotic colonization of the adherent mucus layer of HT29MTXE12 cells attenuates Campylobacter jejuni virulence properties. Infect Immun. 2010;78(6):2812-22.
  • Barrett E, Fitzgerald P, Dinan TG, Cryan JF, Ross RP, Quigley EM, Shanahan F, Kiely B, Fitzgerald GF, O'Toole PW, Stanton C. Bifidobacterium breve with α-linolenic acid and linoleic acid alters fatty acid metabolism in the maternal separation model of irritable bowel syndrome. PLoS One. 2012;7(11):e48159.
  • Clarke SF, Murphy EF, Nilaweera K, Ross PR, Shanahan F, O'Toole PW, Cotter PD. The gut microbiota and its relationship to diet and obesity: new insights. Gut Microbes. 2012;3(3):186-202.
  • Forsythe P, Wang B, Khambati I, Kunze WA. Systemic effects of ingested Lactobacillus rhamnosus: inhibition of mast cell membrane potassium (IKCa) current and degranulation. PLoS One. 2012;7(7):e41234.
  • Hennessy AA, Barrett E, Paul Ross R, Fitzgerald GF, Devery R, Stanton C. The production of conjugated α-linolenic, γ-linolenic and stearidonic acids by strains of Bifidobacteria and Propionibacteria. Lipids. 2012;47(3):313-27.
  • Konieczna P, Akdis CA, Quigley EMM, Shanahan F, O’Mahony.  Portrait of an immunoregulatory BifidobacteriumGut Microbes 2012;3(3): 261-266.
  • Konieczna P, Groeger D, Ziegler M, Frei, R, Ferstl R, Shanahan F, Quigley EM, Kiely B, Akdis CA, O’Mahony L.  Bifidobacterium infantis 35624 administration induces Foxp3 T Regulatory cells in human peripheral blood: potential role for myeloid and plasmacytoid dendritic cells. Gut. 2012;61(3):354-66.
  • Lobley CM, Aller P, Douangamath A, Reddivari Y, Bumann M, Bird LE, Nettleship JE, Brandao-Neto J, Owens RJ, O'Toole PW, Walsh MA. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68(Pt 12):1427-33.
  • Miyauchi E, O'Callaghan J, Buttó LF, Hurley G, Melgar S, Tanabe S, Shanahan F, Nally K, O'Toole PW.Mechanism of protection of transepithelial barrier function by Lactobacillus salivarius: strain dependence and attenuation by bacteriocin production. Am J Physiol Gastrointest Liver Physiol. 2012;303(9):G1029-41.
  • Murphy EF, Quigley EM. The microbiota and bariatric surgery: it's a bug's life. Gastroenterology. 2012;142(2):399-401; discussion 401-2.
  • Neville BA, O'Toole PW. Probiotic properties of Lactobacillus salivarius and closely related Lactobacillus species. Future Microbiol. 2010;5(5):759-74.
  • O'Callaghan J, Buttó LF, MacSharry J, Nally K, O'Toole PW. Influence of adhesion and bacteriocin production by Lactobacillus salivarius on the intestinal epithelial cell transcriptional response. Appl Environ Microbiol. 2012;78(15):5196-203
  • O'Shea EF, O' Connor PM, Raftis EJ, O' Toole PW, Stanton C, Cotter PD, Ross RP, Hill C. Subspecies diversity in bacteriocin production by intestinal Lactobacillus salivarius strains. Gut Microbes. 2012;3(5):468-73.
  • Quigley E, Catanzaro D, Wycherley C, Tillisch K.  Tolerability and safety of the probiotic Bifidobacterium infantis 35624:  review of clinical and postmarketing data. Am J Gastroenterol. 2010;105(Suppl 1):S480-S481.  Abstract 1305.
  • 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. Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota. PLoS One. 2012;7(2):e31113.
  • Smelt MJ, de Haan BJ, Bron PA, van Swam I, Meijerink M, Wells JM, Faas MM, de Vos P. L. plantarum, L. salivarius, and L. lactis attenuate Th2 responses and increase Treg frequencies in healthy mice in a strain dependent manner. PLoS One. 2012;7(10):e47244.
  • Symonds EL, O’Mahony C, Lapthorne S, O’Mahony D, Mac Sharry J, O’Mahony L, Shanahan F.  Bifidobacterium infantis 35624 protects against Salmonella-induced reductions in digestive enzyme activity in mice by attenuation of the host inflammatory response.  Clin Transl Gastroenterol. 2012;3:e15.
  • Wall R, Marques T, O’Sullivan O, Ross R, Shanahan F, Quigley E, Dinan T, Kiely B, Fitzgerald G, Cotter P, Fouhy F, and Stanton C. Contrasting effects of Bifidobacterium breve NCIMB 702258 and Bifidobacterium breve DPC 6330 on the composition of brain fatty acids and gut microbiota. Am J Clin Nutr 2012;95:1278–87.


  • Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan JF, Dinan TG. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience. 2010 170(4):1179-88.
  • Horsham  M, Saxby H, Blake J, Isaacs NW, Mitchell TJ, Riboldi-Tunnicliffe A. Expression, purification, crystallization and preliminary X-ray crystallographic data from TktA, a transketolase from the lactic acid bacterium Lactobacillus salivariusActa Crystallogr Sect F Struct Biol Cryst Commun. 2010;66(Pt 8):899-901.
  • Kelley RL, Park JS, O'Mahony L, Minikhiem D, Fix A. Safety and tolerance of dietary supplementation with a canine-derived probiotic (Bifidobacterium animalis strain AHC7) fed to growing dogs. Vet Ther. 2010;11(3):E1-14.
  • Lyons A, O'Mahony D, O'Brien F, MacSharry J, Sheil B, Ceddia M, Russell WM, Forsythe P, Bienenstock J, Kiely B, Shanahan F, O'Mahony L. Bacterial strain-specific induction of Foxp3+ T regulatory cells is protective in murine allergy models. Clin Exp Allergy. 2010;40(5):811-9.
  • McKernan DP, Fitzgerald P, Dinan TG, Cryan JF. The probiotic Bifidobacterium infantis 35624 displays visceral antinociceptive effects in the rat. Neurogastroenterol Motil. 2010;22(9):1029-35.
  • O'Mahony D, Murphy S, Boileau T, Park J, O'Brien F, Groeger D, Konieczna P, Ziegler M, Scully P, Shanahan F, Kiely B, O'Mahony L. Bifidobacterium animalis AHC7 protects against pathogen-induced NF-κB activation in vivoBMC Immunol. 2010;11:63.
  • Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F, Clarke SF, O'Toole PW, Quigley EM, Stanton C, Ross PR, O'Doherty RM, Shanahan F. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut. 2010;59(12):1635-42.
  • Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP. Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4639-44.
  • Rea MC, Sit CS, Clayton E, O'Connor PM, Whittal RM, Zheng J, Vederas JC, Ross RP, Hill C. Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficileProc Natl Acad Sci U S A. 2010;107(20):9352-7.
  • Wall R, Ross RP, Shanahan F, O'Mahony L, Kiely B, Quigley E, Dinan TG, Fitzgerald G, Stanton C. Impact of administered Bifidobacterium on murine host fatty acid composition. Lipids. 2010;45(5):429-36.
  • Wang B, Mao YK, Diorio C, Pasyk M, Wu RY, Bienenstock J, Kunze WA. Luminal administration ex vivo of a live Lactobacillus species moderates mouse jejunal motility within minutes. FASEB J. 2010;24(10):4078-88.
  • Williams MD, Ha CY, Ciorba MA. Probiotics as therapy in gastroenterology: a study of physician opinions and recommendations. J Clin Gastroenterol. 2010;44(9):631-6.


  • Desbonnet L, Garrett L, Clarke G, Bienenstock J, Dinan TG. The probiotic Bifidobacteria infantis: an assessment of potential antidepressant properties in the rat. Journal of Psychiatric Research. 2008;43(2):164-74.
  • Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP, Collins JK, van Sinderen D, O'Toole PW. Characterization of endogenous plasmids from Lactobacillus salivarius UCC118. Appl Environ Microbiol. 2008;74(10):3216-28.
  • Feighery LM, Smith P, O'Mahony L, Fallon PG, Brayden DJ. Effects of Lactobacillus salivarius 433118 on intestinal inflammation, immunity status and in vitro colon function in two mouse models of inflammatory bowel disease. Dig Dis Sci. 2008;53(9):2495-506.
  • Macsharry J, O'Mahony L, Fanning A, Bairead E, Sherlock G, Tiesman J, Fulmer A, Kiely B, Dinan TG, Shanahan F, Quigley EM. Mucosal cytokine imbalance in irritable bowel syndrome. Scand J Gastroenterol. 2008;43(12):1467-76.
  • O'Mahony C, Scully P, O'Mahony D, Murphy S, O'Brien F, Lyons A, Sherlock G, MacSharry J, Kiely B, Shanahan F, O'Mahony L. Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-kappaB activation. PLoS Pathog. 2008;4(8):e1000112.
  • O'Mahony C, Scully P, O'Mahony D, Murphy S, O'Brien F, Lyons A, Kiely B, Shanahan F, O'Mahony, L. In vivo imaging of a probiotic-mediated regulatory T cell response following adoptive transfer. Gastroenterology. 2008;134(4 Suppl 1):A254.
  • van der Kleij HO'Mahony CShanahan FO'Mahony LBienenstock J. Protective effects of Lactobacillus reuteri and Bifidobacterium infantis in murine models for colitis do not involve the vagus nerve. Am J Physiol Regul Integr Comp Physiol. 2008;295(4):R1131-7.


  • Charbonneau D, Poehner R, Donovan-Brand R, Xu J, Fawcett D. Development of strain-specific molecular method for the identification of Bifidobacteria infantis 35624. Gastroenterology. 2006;130(4 Suppl 2):A314.
  • Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Tárraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK, Higgins D, Shanahan F, Fitzgerald GF, van Sinderen D, O'Toole PW. Multireplicon genome architecture of Lactobacillus salivariusProc Natl Acad Sci U S A. 2006 Ap;103(17):6718-23.
  • Gilman J, Cashman KD. The effect of probiotic bacteria on transepithelial calcium transport and calcium uptake in human intestinal-like Caco-2 cells. Curr Issues Intest Microbiol. 2006;7(1):1-5.
  • Li Y, Raftis E, Canchaya C, Fitzgerald GF, van Sinderen D, O'Toole PW. Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and Lactobacillus salivarius subspsalicinius do not merit separate subspecies status. Int J Syst Evol Microbiol. 2006;56(Pt 10):2397-403.
  • O'Hara AM, O'Regan P, Fanning A, O'Mahony C, MacSharry J, Lyons A, Bienenstock J, O'Mahony L, Shanahan F. Functional modulation of human intestinal epithelial cell responses by Bifidobacterium infantis and Lactobacillus salivarius. Immunology. 2006;118(2):202-15.
  • O'Mahony L, O'Callaghan L, McCarthy J, Shilling D, Scully P, Sibartie S, Kavanagh E, Kirwan WO, Redmond HP, Collins JK, Shanahan F. Differential cytokine response from dendritic cells to commensal and pathogenic bacteria in different lymphoid compartments in humans. Am J Physiol Gastrointest Liver Physiol. 2006;290(4):G839-45.
  • Quigley EM, Whorwell PJ, Shanahan F, Vansinderen D, Xu J, Altringer L, O'Mahony L, Guarner F, Progid Investigators. Safety and tolerability of the probiotic organism Bifidobacterium infantis 35624: Clinical experience and molecular basis. Gastroenterology. 2006;130(4 Suppl 2):A493.
  • Shanahan F, Guarner F, Von Wright A, Vilpponen-Salmela T, O'Donoghue D, Kiely B, Progid Investigators. A one year, randomised, double-blind, placebo controlled trial of a Lactobacillus or a Bidifobacterium probiotic for maintenance of steroid-induced remission of ulcerative colitis. Gastroenterology. 2006;130( 4 Suppl 2):A44.
  • Sheehan VM, Sleator RD, Fitzgerald GF, Hill C. Heterologous expression of BetL, a betaine uptake system, enhances the stress tolerance of Lactobacillus salivarius UCC118. Appl Environ Microbiol. 2006;72(3):2170-7.
  • Sheil B, MacSharry J, O'Callaghan L, O'Riordan A, Waters A, Morgan J, Collins JK, O'Mahony L, Shanahan F. Consumption of the probiotic Bifidobacterium infantis 35624 influences subsequent immune responses to in vitro challenge of isolated murine Peyer's patch cells with bacterial stimuli. Gastroenterology. 2006;130(4 Suppl 2):A371.
  • Sheil B, MacSharry J, O'Callaghan L, O'Riordan A, Waters A, Morgan J, Collins JK, O'Mahony L, Shanahan F. Role of interleukin (IL-10) in probiotic-mediated immune modulation: an assessment in wild-type and IL-10 knock-out mice. Clin Exp Immunol. 2006;144(2):273-80.
  • 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. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118. Appl Environ Microbiol. 2006;72(6):4143-53.
  • 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. Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseriLactobacillus salivarius, and Lactobacillus casei. Appl Environ Microbiol. 2006;72(5):3130-46.
  • Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D, O'Mahony L, Kiely B, Shanahan F, Quigley EM. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome. Am J Gastroenterol. 2006;101(7):1581-90.


  • Dunne C, Kelly P, O’Halloran S, Soden D, Bennett M, Von Wright A, Vilpponen- Salmela T, Kiely B, O’Mahony L, Collins JK, O’Sullivan GC, Shanahan D.  Mechanisms of adherence of a probiotic Lactobacillus strain during and after in vivo assessment in ulcerative colitis patients. Microb Ecol Health Dis, 16, 96-104.
  • Ma D, Forsythe P, Bienenstock J. Live Lactobacillus rhamnosus [corrected] is essential for the inhibitory effect on tumor necrosis factor alpha-induced interleukin-8 expression. Infect Immun. 2004 Sep;72(9):5308-14. Erratum in: Infect Immun. 2011;79(7):2961.
  • O’Callaghan L, Sheil B, MacSharry J, Collins J, O’Mahony L, Shanahan F. Cytokine responses in different lymphoid compartments in IL-10/ko mice fed Bifidobacterium infantisGastroenterology. 2004;126:A563 (Abstract W1075).
  • O’Mahony L, Shiel B, MacSharry, O’Callaghan L, Collins J, O’Sullivan G, Kiely B, Shanahan F. Mechanism of probiotic/commensal mediated protection against invasive Salmonella infection. Gastroenterology. 2004;126:A516 (Abstract T1809).
  • Sheil B, McCarthy J, O'Mahony L, Bennett MW, Ryan P, Fitzgibbon JJ, Kiely B, Collins JK, Shanahan F. Is the mucosal route of administration essential for probiotic function? Subcutaneous administration is associated with attenuation of murine colitis and arthritis. Gut. 2004;53(5):694-700.


  • Collins K, Dunne C, Murphy L, Morrissey D, O'Mahony L, O’Sullivan E, Fitzgerald G, Kiely B, O'Sullivan G, Daly C, Marteau P, Shanahan F. A randomised controlled trial of a probiotic Lactobacillus strain in healthy adults: assessment of its delivery, transit and in fluence on microbial flora and enteric immunity. Microbial Ecology in Health and Disease, 2002;14;81-89.
  • Flynn S, van Sinderen D, Thornton GM, Holo H, Nes IF, Collins JK. Characterization of the genetic locus responsible for the production of ABP-118, a novel bacteriocin produced by the probiotic bacterium Lactobacillus salivarius subsp. salivarius UCC118. Microbiology. 2002;148(Pt 4):973-84.
  • O’Callaghan L, O’Mahony L, O’Mahony K, Kavanaugh E, Kirwan W, Collins J, Shanahan F. Human cytokine production by mesenteric lymph node cells in response to probiotic and pathogenic bacteria. Gastroenterology. 2002;122:A151 (Abstract S1040).
  • O’Mahony L, Kenneally P, O’Donoghue M, Kiely B, Shanahan F, Collins J. Multi-organism comparison of probiotic performance in a murine model of Salmonella typhimurimum infection. Gastroenterology. 2002:122:T1337.


  • Gardiner GE, O'Sullivan E, Kelly J, Auty MA, Fitzgerald GF, Collins JK, Ross RP, Stanton C. Comparative survival rates of human-derived probiotic Lactobacillus paracasei and L. salivarius strains during heat treatment and spray drying. Appl Environ Microbiol. 2000;66(6):2605-12.
  • O’Mahony L, Dunne C, Feeney M, O’Halloran S, Kiely B, O’Sullivan GC, Shanahan FL, Collin JK. Probiotic human Bifidobacteria selection of a new strain and evaluation in vitro and in vivoGastroenterology. 2000;118(4 Suppl):A774.


  • Dunne C, O'Mahony L, Murphy L, Thornton G, Morrissey D, O'Halloran S, Feeney M, Flynn S, Fitzgerald G, Daly C, Kiely B, O'Sullivan GC, Shanahan F, Collins JK. In vitro selection criteria for probiotic bacteria of human origin: correlation with in vivo findings. Am J Clin Nutr. 2001;73(2 Suppl):386S-392S.
  • O'Mahony L, Feeney M, O'Halloran S, Murphy L, Kiely B, Fitzgibbon J, Lee G, O'Sullivan G, Shanahan F, Collins JK. Probiotic impact on microbial flora, inflammation and tumour development in IL-10 knockout mice. Aliment Pharmacol Ther. 2001;15(8):1219-25.
  • O’Mahony L, Zong Z, Sharma S, Aranda R, O’Sullivan G, Collins JK, Shanahan F. Probiotic bacteria and pathogenic bacteria elicit differential cytokine responses from dendritic cells. Gastroenterology. 2001;120:A315 (Abstract 1625).


  • Dunne C, Murphy L, Flynn S, O’Mahony L, O’Halloran S, Feeney M, Morrissey D, Thornton G, Fitzgerald G, Daly C, Kiely B, Quigley EM, O’Sullivan G, Shanahan F, Collins JK. Probiotics: from myth to reality. Demonstration of functionality in animal models of disease and in human clinical trials. Antonie Van Leeuwenhoek. 1999; 76(1-4):279-92. Review.
  • Mattila-Sandholm1 T, Blumb S, Collinsc JK, Crittendena R, de Vosd W, Dunnec C, Fondéne R, Grenovf G, Isolaurih E, Kiely B, Marteaui P, Morellij L, Ouwehandg A, Renierob R, Saarelaa M, Salmineng S, Saxelink M, Schiffrinb E, Shanahanc F, Vaughand E, A. von Wrightl. Probiotics: towards demonstrating efficacy. Trends in Food Science & Technology, 1999:10:393-399. 

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