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The environmental stress sensitivities of pathogenic Candida species, including Candida auris, and implications for their spread in the hospital setting.

Heaney H, Laing J, Paterson L, Walker AW, Gow NAR, Johnson EM, MacCallum DM, Brown AJP.

Med Mycol. 2020 Jan 7. pii: myz127. doi: 10.1093/mmy/myz127. [Epub ahead of print]


Food additives: Assessing the impact of exposure to permitted emulsifiers on bowel and metabolic health - introducing the FADiets study.

Partridge D, Lloyd KA, Rhodes JM, Walker AW, Johnstone AM, Campbell BJ.

Nutr Bull. 2019 Dec;44(4):329-349. doi: 10.1111/nbu.12408. Epub 2019 Nov 25.


Colitis susceptibility in mice with reactive oxygen species deficiency is mediated by mucus barrier and immune defense defects.

Aviello G, Singh AK, O'Neill S, Conroy E, Gallagher W, D'Agostino G, Walker AW, Bourke B, Scholz D, Knaus UG.

Mucosal Immunol. 2019 Nov;12(6):1316-1326. doi: 10.1038/s41385-019-0205-x. Epub 2019 Sep 25.


Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle.

Lima J, Auffret MD, Stewart RD, Dewhurst RJ, Duthie CA, Snelling TJ, Walker AW, Freeman TC, Watson M, Roehe R.

Front Genet. 2019 Aug 8;10:701. doi: 10.3389/fgene.2019.00701. eCollection 2019.


Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery.

Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M.

Nat Biotechnol. 2019 Aug;37(8):953-961. doi: 10.1038/s41587-019-0202-3. Epub 2019 Aug 2.


A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses.

Walker AW.

mSystems. 2019 Jun 25;4(4). pii: e00362-19. doi: 10.1128/mSystems.00362-19.


Do Adolescent Women's Contraceptive Preferences Predict Method Use and Satisfaction? A Survey of Northern California Family Planning Clients.

Walker AW, Stern L, Cipres D, Rodriguez A, Alvarez J, Seidman D.

J Adolesc Health. 2019 May;64(5):640-647. doi: 10.1016/j.jadohealth.2018.10.291. Epub 2019 Jan 4.


Studying the microbiome and its complexities: an interview with Alan Walker.

Walker AW.

BMC Biol. 2018 Nov 1;16(1):134. doi: 10.1186/s12915-018-0599-z.


Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N.

Dalby MJ, Aviello G, Ross AW, Walker AW, Barrett P, Morgan PJ.

Sci Rep. 2018 Oct 23;8(1):15648. doi: 10.1038/s41598-018-33928-4.


Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition.

Drew JE, Reichardt N, Williams LM, Mayer CD, Walker AW, Farquharson AJ, Kastora S, Farquharson F, Milligan G, Morrison DJ, Preston T, Flint HJ, Louis P.

Sci Rep. 2018 Oct 22;8(1):15566. doi: 10.1038/s41598-018-34081-8.


Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D, Garcia-Campayo V, Parkhill J, Flint HJ, Duncan SH.

FEMS Microbiol Ecol. 2019 Jan 1;95(1). doi: 10.1093/femsec/fiy201.


Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.

Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TJ, Dewhurst RJ, Walker AW, Roehe R, Watson M.

Nat Commun. 2018 Feb 28;9(1):870. doi: 10.1038/s41467-018-03317-6.


The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

Kennedy NA, Lamb CA, Berry SH, Walker AW, Mansfield J, Parkes M, Simpkins R, Tremelling M, Nutland S; UK IBD Genetics Consortium, Parkhill J, Probert C, Hold GL, Lees CW.

Inflamm Bowel Dis. 2018 Feb 15;24(3):583-592. doi: 10.1093/ibd/izx061.


Gut microbiota trajectory in early life may predict development of celiac disease.

Olivares M, Walker AW, Capilla A, Benítez-Páez A, Palau F, Parkhill J, Castillejo G, Sanz Y.

Microbiome. 2018 Feb 20;6(1):36. doi: 10.1186/s40168-018-0415-6.


Corrigendum: Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Dec 8;35(12):1211. doi: 10.1038/nbt1217-1211b.


Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii.

Mukhopadhya I, Moraïs S, Laverde-Gomez J, Sheridan PO, Walker AW, Kelly W, Klieve AV, Ouwerkerk D, Duncan SH, Louis P, Koropatkin N, Cockburn D, Kibler R, Cooper PJ, Sandoval C, Crost E, Juge N, Bayer EA, Flint HJ.

Environ Microbiol. 2018 Jan;20(1):324-336. doi: 10.1111/1462-2920.14000. Epub 2017 Dec 7.


Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice.

Dalby MJ, Ross AW, Walker AW, Morgan PJ.

Cell Rep. 2017 Nov 7;21(6):1521-1533. doi: 10.1016/j.celrep.2017.10.056.


Shotgun metagenomics, from sampling to analysis.

Quince C, Walker AW, Simpson JT, Loman NJ, Segata N.

Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935. Review. Erratum in: Nat Biotechnol. 2017 Dec 8;35(12 ):1211.


Procedure to decouple reflectance and down-shifting effects in luminescent down-shifting enhanced photovoltaics.

Gabr AM, Walker AW, Wilkins MM, Kleiman R, Hinzer K.

Opt Express. 2017 Jun 12;25(12):A530-A538. doi: 10.1364/OE.25.00A530.


TPL-2 restricts Ccl24-dependent immunity to Heligmosomoides polygyrus.

Kannan Y, Entwistle LJ, Pelly VS, Perez-Lloret J, Walker AW, Ley SC, Wilson MS.

PLoS Pathog. 2017 Jul 31;13(7):e1006536. doi: 10.1371/journal.ppat.1006536. eCollection 2017 Jul.


A non-endoscopic device to sample the oesophageal microbiota: a case-control study.

Elliott DRF, Walker AW, O'Donovan M, Parkhill J, Fitzgerald RC.

Lancet Gastroenterol Hepatol. 2017 Jan;2(1):32-42. doi: 10.1016/S2468-1253(16)30086-3. Epub 2016 Nov 12. Erratum in: Lancet Gastroenterol Hepatol. 2017 Jan;2(1):e1. Lancet Gastroenterol Hepatol. 2017 Nov;2(11):e7.


Bacterial microbiota of the upper respiratory tract and childhood asthma.

Depner M, Ege MJ, Cox MJ, Dwyer S, Walker AW, Birzele LT, Genuneit J, Horak E, Braun-Fahrländer C, Danielewicz H, Maier RM, Moffatt MF, Cookson WO, Heederik D, von Mutius E, Legatzki A.

J Allergy Clin Immunol. 2017 Mar;139(3):826-834.e13. doi: 10.1016/j.jaci.2016.05.050. Epub 2016 Jul 27.


Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC.

BMC Genomics. 2016 Jun 8;17:440. doi: 10.1186/s12864-016-2777-0.


Studying the Human Microbiota.

Walker AW.

Adv Exp Med Biol. 2016;902:5-32. doi: 10.1007/978-3-319-31248-4_2. Review.


Editorial: further evidence that proton pump inhibitors may impact on the gut microbiota.

Walker AW, Flint HJ.

Aliment Pharmacol Ther. 2016 May;43(10):1104-5. doi: 10.1111/apt.13596. No abstract available.


Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis.

Sheridan PO, Duncan SH, Walker AW, Scott KP, Louis P, Flint HJ.

Int J Syst Evol Microbiol. 2016 May;66(5):2106. doi: 10.1099/ijsem.0.000969. Epub 2016 Feb 24. No abstract available.


Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.

Torondel B, Ensink JH, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C.

Microb Biotechnol. 2016 Mar;9(2):209-23. doi: 10.1111/1751-7915.12334. Epub 2016 Feb 15.


Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon.

Bernardo D, Durant L, Mann ER, Bassity E, Montalvillo E, Man R, Vora R, Reddi D, Bayiroglu F, Fernández-Salazar L, English NR, Peake ST, Landy J, Lee GH, Malietzis G, Siaw YH, Murugananthan AU, Hendy P, Sánchez-Recio E, Phillips RK, Garrote JA, Scott P, Parkhill J, Paulsen M, Hart AL, Al-Hassi HO, Arranz E, Walker AW, Carding SR, Knight SC.

Cell Mol Gastroenterol Hepatol. 2015 Sep 3;2(1):22-39.e5. eCollection 2016 Jan.


Modulation of the human gut microbiota by dietary fibres occurs at the species level.

Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ.

BMC Biol. 2016 Jan 11;14:3. doi: 10.1186/s12915-015-0224-3.


The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.

Karkey A, Jombart T, Walker AW, Thompson CN, Torres A, Dongol S, Tran Vu Thieu N, Pham Thanh D, Tran Thi Ngoc D, Voong Vinh P, Singer AC, Parkhill J, Thwaites G, Basnyat B, Ferguson N, Baker S.

PLoS Negl Trop Dis. 2016 Jan 6;10(1):e0004346. doi: 10.1371/journal.pntd.0004346. eCollection 2016 Jan.


Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW, Flint HJ.

Environ Microbiol. 2016 Jul;18(7):2214-25. doi: 10.1111/1462-2920.13158. Epub 2016 Jan 21.


Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE, Daniels TW, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.

ISME J. 2016 May;10(5):1081-91. doi: 10.1038/ismej.2015.198. Epub 2015 Nov 10.


The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation.

Zaiss MM, Rapin A, Lebon L, Dubey LK, Mosconi I, Sarter K, Piersigilli A, Menin L, Walker AW, Rougemont J, Paerewijck O, Geldhof P, McCoy KD, Macpherson AJ, Croese J, Giacomin PR, Loukas A, Junt T, Marsland BJ, Harris NL.

Immunity. 2015 Nov 17;43(5):998-1010. doi: 10.1016/j.immuni.2015.09.012. Epub 2015 Oct 27.


ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Koslicki D, Chatterjee S, Shahrivar D, Walker AW, Francis SC, Fraser LJ, Vehkaperä M, Lan Y, Corander J.

PLoS One. 2015 Oct 23;10(10):e0140644. doi: 10.1371/journal.pone.0140644. eCollection 2015.


Relaxin-3 receptor (Rxfp3) gene deletion reduces operant sucrose- but not alcohol-responding in mice.

Walker AW, Smith CM, Gundlach AL, Lawrence AJ.

Genes Brain Behav. 2015 Nov;14(8):625-34. doi: 10.1111/gbb.12239. Epub 2015 Oct 14.


Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis.

Landy J, Walker AW, Li JV, Al-Hassi HO, Ronde E, English NR, Mann ER, Bernardo D, McLaughlin SD, Parkhill J, Ciclitira PJ, Clark SK, Knight SC, Hart AL.

Sci Rep. 2015 Aug 12;5:12955. doi: 10.1038/srep12955.


16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP.

Microbiome. 2015 Jun 22;3:26. doi: 10.1186/s40168-015-0087-4. eCollection 2015.


Reduced protein turnover mediates functional deficits in transgenic mice expressing the 25 kDa C-terminal fragment of TDP-43.

Caccamo A, Shaw DM, Guarino F, Messina A, Walker AW, Oddo S.

Hum Mol Genet. 2015 Aug 15;24(16):4625-35. doi: 10.1093/hmg/ddv193. Epub 2015 May 22.


Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation.

Powell N, Lo JW, Biancheri P, Vossenkämper A, Pantazi E, Walker AW, Stolarczyk E, Ammoscato F, Goldberg R, Scott P, Canavan JB, Perucha E, Garrido-Mesa N, Irving PM, Sanderson JD, Hayee B, Howard JK, Parkhill J, MacDonald TT, Lord GM.

Gastroenterology. 2015 Aug;149(2):456-67.e15. doi: 10.1053/j.gastro.2015.04.017. Epub 2015 Apr 25.


Relaxin-3 receptor (RXFP3) signalling mediates stress-related alcohol preference in mice.

Walker AW, Smith CM, Chua BE, Krstew EV, Zhang C, Gundlach AL, Lawrence AJ.

PLoS One. 2015 Apr 7;10(4):e0122504. doi: 10.1371/journal.pone.0122504. eCollection 2015.


Microbiota that affect risk for shigellosis in children in low-income countries.

Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B, Walker AW, Paulson JN, Parkhill J, Omore R, Faruque AS, Das SK, Ikumapayi UN, Adeyemi M, Sanogo D, Saha D, Sow S, Farag TH, Nasrin D, Li S, Panchalingam S, Levine MM, Kotloff K, Magder LS, Hungerford L, Sommerfelt H, Pop M, Nataro JP, Stine OC.

Emerg Infect Dis. 2015 Feb;21(2):242-50. doi: 10.3201/eid2101.140795.


TLR signaling modulates side effects of anticancer therapy in the small intestine.

Frank M, Hennenberg EM, Eyking A, Rünzi M, Gerken G, Scott P, Parkhill J, Walker AW, Cario E.

J Immunol. 2015 Feb 15;194(4):1983-95. doi: 10.4049/jimmunol.1402481. Epub 2015 Jan 14.


Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hoffman LR, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.

J Cyst Fibros. 2015 Jul;14(4):464-7. doi: 10.1016/j.jcf.2014.10.004. Epub 2014 Oct 24.


Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW.

BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z.


Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, Kotloff K, Ikumapayi UN, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, Morris JG, Breiman RF, Saha D, Parkhill J, Nataro JP, Stine OC.

Genome Biol. 2014 Jun 27;15(6):R76. doi: 10.1186/gb-2014-15-6-r76.


Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hafiz T, Hoffman LR, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.

J Clin Microbiol. 2014 Aug;52(8):3011-6. doi: 10.1128/JCM.00764-14. Epub 2014 Jun 11.


Relaxin-3/RXFP3 networks: an emerging target for the treatment of depression and other neuropsychiatric diseases?

Smith CM, Walker AW, Hosken IT, Chua BE, Zhang C, Haidar M, Gundlach AL.

Front Pharmacol. 2014 Mar 21;5:46. doi: 10.3389/fphar.2014.00046. eCollection 2014. Review.


Phylogeny, culturing, and metagenomics of the human gut microbiota.

Walker AW, Duncan SH, Louis P, Flint HJ.

Trends Microbiol. 2014 May;22(5):267-74. doi: 10.1016/j.tim.2014.03.001. Epub 2014 Mar 31. Review.


Central injection of relaxin-3 receptor (RXFP3) antagonist peptides reduces motivated food seeking and consumption in C57BL/6J mice.

Smith CM, Chua BE, Zhang C, Walker AW, Haidar M, Hawkes D, Shabanpoor F, Hossain MA, Wade JD, Rosengren KJ, Gundlach AL.

Behav Brain Res. 2014 Jul 15;268:117-26. doi: 10.1016/j.bbr.2014.03.037. Epub 2014 Mar 25.


The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM, Louis P, Thomson JM; UK IBD Genetics Consortium, Satsangi J, Flint HJ, Parkhill J, Lees CW, Hold GL.

PLoS One. 2014 Feb 24;9(2):e88982. doi: 10.1371/journal.pone.0088982. eCollection 2014.

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