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Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults.

McCann A, Jeffery IB, Ouliass B, Ferland G, Fu X, Booth SL, Tran TTT, O'Toole PW, O'Connor EM.

Am J Clin Nutr. 2019 Dec 1;110(6):1404-1415. doi: 10.1093/ajcn/nqz220.


Gut microbiota alterations associated with reduced bone mineral density in older adults.

Das M, Cronin O, Keohane DM, Cormac EM, Nugent H, Nugent M, Molloy C, O'Toole PW, Shanahan F, Molloy MG, Jeffery IB.

Rheumatology (Oxford). 2019 Dec 1;58(12):2295-2304. doi: 10.1093/rheumatology/kez302.


Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids.

Sheridan PO, Martin JC, Minton NP, Flint HJ, O'Toole PW, Scott KP.

Anaerobe. 2019 Oct;59:131-140. doi: 10.1016/j.anaerobe.2019.06.008. Epub 2019 Jun 19.


Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir.

Slattery C, Cotter PD, O'Toole PW.

Nutrients. 2019 Jun 1;11(6). pii: E1252. doi: 10.3390/nu11061252. Review.


Schistosoma mansoni Worm Infection Regulates the Intestinal Microbiota and Susceptibility to Colitis.

Floudas A, Aviello G, Schwartz C, Jeffery IB, O'Toole PW, Fallon PG.

Infect Immun. 2019 Jul 23;87(8). pii: e00275-19. doi: 10.1128/IAI.00275-19. Print 2019 Aug.


International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis.

Scott AJ, Alexander JL, Merrifield CA, Cunningham D, Jobin C, Brown R, Alverdy J, O'Keefe SJ, Gaskins HR, Teare J, Yu J, Hughes DJ, Verstraelen H, Burton J, O'Toole PW, Rosenberg DW, Marchesi JR, Kinross JM.

Gut. 2019 Sep;68(9):1624-1632. doi: 10.1136/gutjnl-2019-318556. Epub 2019 May 15.


APOE genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer's disease pathophysiology.

Tran TTT, Corsini S, Kellingray L, Hegarty C, Le Gall G, Narbad A, Müller M, Tejera N, O'Toole PW, Minihane AM, Vauzour D.

FASEB J. 2019 Jul;33(7):8221-8231. doi: 10.1096/fj.201900071R. Epub 2019 Apr 8.


Perinatal factors affect the gut microbiota up to four years after birth.

Fouhy F, Watkins C, Hill CJ, O'Shea CA, Nagle B, Dempsey EM, O'Toole PW, Ross RP, Ryan CA, Stanton C.

Nat Commun. 2019 Apr 3;10(1):1517. doi: 10.1038/s41467-019-09252-4.


Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity.

Tran TTT, Cousin FJ, Lynch DB, Menon R, Brulc J, Brown JR, O'Herlihy E, Butto LF, Power K, Jeffery IB, O'Connor EM, O'Toole PW.

Microbiome. 2019 Mar 13;7(1):39. doi: 10.1186/s40168-019-0654-1.


The Gut Microbiota in Causation, Detection, and Treatment of Cancer.

Murphy CL, OʼToole PW, Shanahan F.

Am J Gastroenterol. 2019 Jul;114(7):1036-1042. doi: 10.14309/ajg.0000000000000075.


Potentially modifiable determinants of malnutrition in older adults: A systematic review.

O'Keeffe M, Kelly M, O'Herlihy E, O'Toole PW, Kearney PM, Timmons S, O'Shea E, Stanton C, Hickson M, Rolland Y, Sulmont Rossé C, Issanchou S, Maitre I, Stelmach-Mardas M, Nagel G, Flechtner-Mors M, Wolters M, Hebestreit A, De Groot LCPGM, van de Rest O, Teh R, Peyron MA, Dardevet D, Papet I, Schindler K, Streicher M, Torbahn G, Kiesswetter E, Visser M, Volkert D, O'Connor EM; MaNuEL consortium.

Clin Nutr. 2019 Dec;38(6):2477-2498. doi: 10.1016/j.clnu.2018.12.007. Epub 2018 Dec 11. Review.


Retention of Microbiota Diversity by Lactose-Free Milk in a Mouse Model of Elderly Gut Microbiota.

Ntemiri A, Ribière C, Stanton C, Ross RP, O'Connor EM, O'Toole PW.

J Agric Food Chem. 2019 Feb 20;67(7):2098-2112. doi: 10.1021/acs.jafc.8b06414. Epub 2019 Feb 7.


Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children.

Hurley E, Barrett MPJ, Kinirons M, Whelton H, Ryan CA, Stanton C, Harris HMB, O'Toole PW.

BMC Oral Health. 2019 Jan 14;19(1):13. doi: 10.1186/s12903-018-0693-1.


Draft Genome Sequence of Lactobacillus fermentum Lf2, an Exopolysaccharide-Producing Strain Isolated from Argentine Cheese.

Harris HMB, Ale EC, Reinheimer JA, Binetti AG, O'Toole PW.

Microbiol Resour Announc. 2018 Nov 8;7(18). pii: e01072-18. doi: 10.1128/MRA.01072-18. eCollection 2018 Nov.


Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives.

Ribière C, Hegarty C, Stephenson H, Whelan P, O'Toole PW.

Microb Ecol. 2019 Jul;78(1):195-205. doi: 10.1007/s00248-018-1287-9. Epub 2018 Nov 22.


Vitamin K status and inflammation are associated with cognition in older Irish adults.

Kiely A, Ferland G, Ouliass B, O'Toole PW, Purtill H, O'Connor EM.

Nutr Neurosci. 2018 Nov 19:1-9. doi: 10.1080/1028415X.2018.1536411. [Epub ahead of print]


Prevalence of malnutrition using harmonized definitions in older adults from different settings - A MaNuEL study.

Wolters M, Volkert D, Streicher M, Kiesswetter E, Torbahn G, O'Connor EM, O'Keeffe M, Kelly M, O'Herlihy E, O'Toole PW, Timmons S, O'Shea E, Kearney P, van Zwienen-Pot J, Visser M, Maitre I, Van Wymelbeke V, Sulmont-Rossé C, Nagel G, Flechtner-Mors M, Goisser S, Teh R, Hebestreit A; MaNuEL consortium.

Clin Nutr. 2019 Oct;38(5):2389-2398. doi: 10.1016/j.clnu.2018.10.020. Epub 2018 Nov 3.


Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp.

Campedelli I, Mathur H, Salvetti E, Clarke S, Rea MC, Torriani S, Ross RP, Hill C, O'Toole PW.

Appl Environ Microbiol. 2018 Dec 13;85(1). pii: e01738-18. doi: 10.1128/AEM.01738-18. Print 2019 Jan 1.


Erratum for Salvetti et al., "Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification".

Salvetti E, Harris HMB, Felis GE, O'Toole PW.

Appl Environ Microbiol. 2018 Oct 1;84(20). pii: e02052-18. doi: 10.1128/AEM.02052-18. Print 2018 Oct 15. No abstract available.


The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency.

Matthews C, Crispie F, Lewis E, Reid M, O'Toole PW, Cotter PD.

Gut Microbes. 2019;10(2):115-132. doi: 10.1080/19490976.2018.1505176. Epub 2018 Sep 12. Review.


Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection.

Brown JR, Flemer B, Joyce SA, Zulquernain A, Sheehan D, Shanahan F, O'Toole PW.

BMC Gastroenterol. 2018 Aug 28;18(1):131. doi: 10.1186/s12876-018-0860-5.


Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.

Doyle CJ, O'Toole PW, Cotter PD.

Front Microbiol. 2018 Jul 5;9:1507. doi: 10.3389/fmicb.2018.01507. eCollection 2018.


Dose-interval study of a dual probiotic in preterm infants.

Watkins C, Murphy K, Dempsey EM, O'Shea CA, Murphy BP, O'Toole PW, Ross RP, Stanton C, Ryan CA.

Arch Dis Child Fetal Neonatal Ed. 2019 Mar;104(2):F159-F164. doi: 10.1136/archdischild-2017-313468. Epub 2018 Jun 20.


Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification.

Salvetti E, Harris HMB, Felis GE, O'Toole PW.

Appl Environ Microbiol. 2018 Aug 17;84(17). pii: e00993-18. doi: 10.1128/AEM.00993-18. Print 2018 Sep 1. Erratum in: Appl Environ Microbiol. 2018 Oct 1;84(20):.


Archaea: Microbial Candidates in Next-generation Probiotics Development.

Brugère JF, Ben Hania W, Arnal ME, Ribière C, Ballet N, Vandeckerkove P, Ollivier B, O'Toole PW.

J Clin Gastroenterol. 2018 Nov/Dec;52 Suppl 1, Proceedings from the 9th Probiotics, Prebiotics and New Foods, Nutraceuticals and Botanicals for Nutrition & Human and Microbiota Health Meeting, held in Rome, Italy from September 10 to 12, 2017:S71-S73. doi: 10.1097/MCG.0000000000001043.


The viability of probiotics in water, breast milk, and infant formula.

Watkins C, Murphy K, Dempsey EM, Murphy BP, O'Toole PW, Paul Ross R, Stanton C, Anthony Ryan C.

Eur J Pediatr. 2018 Jun;177(6):867-870. doi: 10.1007/s00431-018-3133-y. Epub 2018 Apr 2.


Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.


Tumour-associated and non-tumour-associated microbiota: Addendum.

Flemer B, Herlihy M, O'Riordain M, Shanahan F, O'Toole PW.

Gut Microbes. 2018 Jul 4;9(4):369-373. doi: 10.1080/19490976.2018.1435246. Epub 2018 Apr 13.


Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.


A long and abundant non-coding RNA in Lactobacillus salivarius.

Cousin FJ, Lynch DB, Chuat V, Bourin MJB, Casey PG, Dalmasso M, Harris HMB, McCann A, O'Toole PW.

Microb Genom. 2017 Jul 17;3(9):e000126. doi: 10.1099/mgen.0.000126. eCollection 2017 Sep.


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.


The oral microbiota in colorectal cancer is distinctive and predictive.

Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O'Riordain M, Shanahan F, O'Toole PW.

Gut. 2018 Aug;67(8):1454-1463. doi: 10.1136/gutjnl-2017-314814. Epub 2017 Oct 7.


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.


Microbiome-health interactions in older people.

O'Toole PW, Jeffery IB.

Cell Mol Life Sci. 2018 Jan;75(1):119-128. doi: 10.1007/s00018-017-2673-z. Epub 2017 Oct 6. Review.


Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P.

Nat Biotechnol. 2017 Nov;35(11):1069-1076. doi: 10.1038/nbt.3960. Epub 2017 Oct 2.


Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals.

O' Donnell MM, Harris HMB, Ross RP, O'Toole PW.

Microbiologyopen. 2017 Oct;6(5). doi: 10.1002/mbo3.509. Epub 2017 Aug 22.


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.


Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments.

Doyle CJ, O'Toole PW, Cotter PD.

Environ Microbiol. 2017 Nov;19(11):4382-4391. doi: 10.1111/1462-2920.13859. Epub 2017 Sep 14. Review.


The contribution of microbial biotechnology to sustainable development goals: microbiome therapies.

O'Toole PW, Paoli M.

Microb Biotechnol. 2017 Sep;10(5):1066-1069. doi: 10.1111/1751-7915.12752. Epub 2017 Jul 11.


Feeding the microbiota: transducer of nutrient signals for the host.

Shanahan F, van Sinderen D, O'Toole PW, Stanton C.

Gut. 2017 Sep;66(9):1709-1717. doi: 10.1136/gutjnl-2017-313872. Epub 2017 Jun 29. Review.


The Genomic Basis of Lactobacilli as Health-Promoting Organisms.

Salvetti E, O'Toole PW.

Microbiol Spectr. 2017 Jun;5(3). doi: 10.1128/microbiolspec.BAD-0011-2016. Review.


Fecal microbiota variation across the lifespan of the healthy laboratory rat.

Flemer B, Gaci N, Borrel G, Sanderson IR, Chaudhary PP, Tottey W, O'Toole PW, Brugère JF.

Gut Microbes. 2017 Sep 3;8(5):428-439. doi: 10.1080/19490976.2017.1334033. Epub 2017 Jun 6.


Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.

Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugère JF, O'Toole PW.

ISME J. 2017 Sep;11(9):2059-2074. doi: 10.1038/ismej.2017.72. Epub 2017 Jun 6.


High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions.

Doyle CJ, Gleeson D, O'Toole PW, Cotter PD.

Int J Food Microbiol. 2017 Aug 16;255:1-6. doi: 10.1016/j.ijfoodmicro.2017.05.019. Epub 2017 May 22.


Next-generation probiotics: the spectrum from probiotics to live biotherapeutics.

O'Toole PW, Marchesi JR, Hill C.

Nat Microbiol. 2017 Apr 25;2:17057. doi: 10.1038/nmicrobiol.2017.57.


Forgotten fungi-the gut mycobiome in human health and disease.

Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD.

FEMS Microbiol Rev. 2017 Jul 1;41(4):479-511. doi: 10.1093/femsre/fuw047. Review.


Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes.

O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H.

Microb Genom. 2016 Feb 9;2(2):e000043. doi: 10.1099/mgen.0.000043. eCollection 2016 Feb.


Erratum to: Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort.

Hill CJ, Lynch DB, Murphy K, Ulaszewska M, Jeffery IB, O'Shea CA, Watkins C, Dempsey E, Mattivi F, Tuohy K, Ross RP, Ryan CA, O'Toole PW, Stanton C.

Microbiome. 2017 Feb 14;5(1):21. doi: 10.1186/s40168-017-0240-3. No abstract available.


Glycomacropeptide Sustains Microbiota Diversity and Promotes Specific Taxa in an Artificial Colon Model of Elderly Gut Microbiota.

Ntemiri A, Chonchúir FN, O'Callaghan TF, Stanton C, Ross RP, O'Toole PW.

J Agric Food Chem. 2017 Mar 1;65(8):1836-1846. doi: 10.1021/acs.jafc.6b05434. Epub 2017 Feb 17.


From Culture to High-Throughput Sequencing and Beyond: A Layperson's Guide to the "Omics" and Diagnostic Potential of the Microbiome.

O'Toole PW, Flemer B.

Gastroenterol Clin North Am. 2017 Mar;46(1):9-17. doi: 10.1016/j.gtc.2016.09.003. Review.


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