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Items: 41

1.

A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078.

Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Marwick CA, Coia J, Brown D, Buchanan S, Ijaz UZ, Goswami C, Douce G, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Crook DW.

MBio. 2019 Mar 12;10(2). pii: e02790-18. doi: 10.1128/mBio.02790-18.

2.

Differential ratio amplicons (Ramp ) for the evaluation of RNA integrity extracted from complex environmental samples.

Cholet F, Ijaz UZ, Smith CJ.

Environ Microbiol. 2019 Feb;21(2):827-844. doi: 10.1111/1462-2920.14516. Epub 2019 Feb 12.

3.

Treatment of Active Crohn's Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition.

Svolos V, Hansen R, Nichols B, Quince C, Ijaz UZ, Papadopoulou RT, Edwards CA, Watson D, Alghamdi A, Brejnrod A, Ansalone C, Duncan H, Gervais L, Tayler R, Salmond J, Bolognini D, Klopfleisch R, Gaya DR, Milling S, Russell RK, Gerasimidis K.

Gastroenterology. 2018 Dec 11. pii: S0016-5085(18)35398-8. doi: 10.1053/j.gastro.2018.12.002. [Epub ahead of print]

4.

NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

Calus ST, Ijaz UZ, Pinto AJ.

Gigascience. 2018 Dec 1;7(12). doi: 10.1093/gigascience/giy140.

5.

Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion.

De Vrieze J, Ijaz UZ, Saunders AM, Theuerl S.

Sci Rep. 2018 Nov 14;8(1):16818. doi: 10.1038/s41598-018-34921-7.

6.

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.

Ijaz UZ, Sivaloganathan L, McKenna A, Richmond A, Kelly C, Linton M, Stratakos AC, Lavery U, Elmi A, Wren BW, Dorrell N, Corcionivoschi N, Gundogdu O.

Front Microbiol. 2018 Oct 15;9:2452. doi: 10.3389/fmicb.2018.02452. eCollection 2018.

7.

Biokinetics of microbial consortia using biogenic sulfur as a novel electron donor for sustainable denitrification.

Kostrytsia A, Papirio S, Morrison L, Ijaz UZ, Collins G, Lens PNL, Esposito G.

Bioresour Technol. 2018 Dec;270:359-367. doi: 10.1016/j.biortech.2018.09.044. Epub 2018 Sep 11.

8.

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights.

Koci O, Logan M, Svolos V, Russell RK, Gerasimidis K, Ijaz UZ.

PeerJ. 2018 Jul 26;6:e5047. doi: 10.7717/peerj.5047. eCollection 2018.

9.

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus.

Reich I, Ijaz UZ, Gormally M, Smith CJ.

Sci Rep. 2018 Jul 10;8(1):10402. doi: 10.1038/s41598-018-28720-3.

10.

Comparison of Clinical Methods With the Faecal Gluten Immunogenic Peptide to Assess Gluten Intake in Coeliac Disease.

Gerasimidis K, Zafeiropoulou K, Mackinder M, Ijaz UZ, Duncan H, Buchanan E, Cardigan T, Edwards CA, McGrogan P, Russell RK.

J Pediatr Gastroenterol Nutr. 2018 Sep;67(3):356-360. doi: 10.1097/MPG.0000000000002062.

PMID:
29916953
11.

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.

Keating C, Hughes D, Mahony T, Cysneiros D, Ijaz UZ, Smith CJ, O'Flaherty V.

FEMS Microbiol Ecol. 2018 Jul 1;94(7). doi: 10.1093/femsec/fiy095.

12.

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.

Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O'Flaherty V, Abram F.

Front Microbiol. 2018 Mar 21;9:540. doi: 10.3389/fmicb.2018.00540. eCollection 2018.

13.

Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans.

Pedersen C, Ijaz UZ, Gallagher E, Horton F, Ellis RJ, Jaiyeola E, Duparc T, Russell-Jones D, Hinton P, Cani PD, La Ragione RM, Robertson MD.

Physiol Rep. 2018 Apr;6(7):e13649. doi: 10.14814/phy2.13649.

14.

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.

De Vrieze J, Pinto AJ, Sloan WT, Ijaz UZ.

Microbiome. 2018 Apr 2;6(1):63. doi: 10.1186/s40168-018-0449-9.

15.

Effect of Laser Irradiation on Cell Function and Its Implications in Raman Spectroscopy.

Yuan X, Song Y, Song Y, Xu J, Wu Y, Glidle A, Cusack M, Ijaz UZ, Cooper JM, Huang WE, Yin H.

Appl Environ Microbiol. 2018 Apr 2;84(8). pii: e02508-17. doi: 10.1128/AEM.02508-17. Print 2018 Apr 15.

16.

Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's disease.

Logan M, Ijaz UZ, Hansen R, Gerasimidis K, Russell RK.

Aliment Pharmacol Ther. 2017 Dec;46(11-12):1119-1120. doi: 10.1111/apt.14351. No abstract available.

PMID:
29105140
17.

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use.

Parsons BN, Ijaz UZ, D'Amore R, Burkitt MD, Eccles R, Lenzi L, Duckworth CA, Moore AR, Tiszlavicz L, Varro A, Hall N, Pritchard DM.

PLoS Pathog. 2017 Nov 2;13(11):e1006653. doi: 10.1371/journal.ppat.1006653. eCollection 2017 Nov.

18.

IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization.

Ritchie ND, Ijaz UZ, Evans TJ.

BMC Genomics. 2017 Oct 23;18(1):807. doi: 10.1186/s12864-017-4215-3.

19.

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences.

Ijaz AZ, Jeffries TC, Ijaz UZ, Hamonts K, Singh BK.

PeerJ. 2017 Oct 10;5:e3827. doi: 10.7717/peerj.3827. eCollection 2017.

20.

Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes.

Cho SK, Jung KW, Kim DH, Kwon JC, Ijaz UZ, Shin SG.

Biotechnol Prog. 2017 Sep;33(5):1226-1234. doi: 10.1002/btpr.2540. Epub 2017 Sep 6.

PMID:
28840641
21.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors.

Connelly S, Shin SG, Dillon RJ, Ijaz UZ, Quince C, Sloan WT, Collins G.

Front Microbiol. 2017 May 1;8:664. doi: 10.3389/fmicb.2017.00664. eCollection 2017.

22.

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred.

Ijaz UZ, Quince C, Hanske L, Loman N, Calus ST, Bertz M, Edwards CA, Gaya DR, Hansen R, McGrogan P, Russell RK, Gerasimidis K.

PLoS One. 2017 Feb 21;12(2):e0172605. doi: 10.1371/journal.pone.0172605. eCollection 2017.

23.

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure.

De Vrieze J, Christiaens MER, Walraedt D, Devooght A, Ijaz UZ, Boon N.

Water Res. 2017 Mar 15;111:109-117. doi: 10.1016/j.watres.2016.12.042. Epub 2016 Dec 26.

24.

Seqenv: linking sequences to environments through text mining.

Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E.

PeerJ. 2016 Dec 20;4:e2690. doi: 10.7717/peerj.2690. eCollection 2016.

25.

Host-microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake.

Pedersen C, Gallagher E, Horton F, Ellis RJ, Ijaz UZ, Wu H, Jaiyeola E, Diribe O, Duparc T, Cani PD, Gibson GR, Hinton P, Wright J, La Ragione R, Robertson MD.

Br J Nutr. 2016 Dec;116(11):1869-1877. doi: 10.1017/S0007114516004086. Epub 2016 Dec 15.

PMID:
27974055
26.

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab).

Varsos C, Patkos T, Oulas A, Pavloudi C, Gougousis A, Ijaz UZ, Filiopoulou I, Pattakos N, Vanden Berghe E, Fernández-Guerra A, Faulwetter S, Chatzinikolaou E, Pafilis E, Bekiari C, Doerr M, Arvanitidis C.

Biodivers Data J. 2016 Nov 1;(4):e8357. eCollection 2016.

27.

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

Ray JL, Althammer J, Skaar KS, Simonelli P, Larsen A, Stoecker D, Sazhin A, Ijaz UZ, Quince C, Nejstgaard JC, Frischer M, Pohnert G, Troedsson C.

Mol Ecol. 2016 Nov;25(21):5585-5602. doi: 10.1111/mec.13844. Epub 2016 Oct 20.

PMID:
27662431
28.

The effect of DNA extraction methodology on gut microbiota research applications.

Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, Calus S, Loman N, Ijaz UZ.

BMC Res Notes. 2016 Jul 26;9:365. doi: 10.1186/s13104-016-2171-7.

29.

Response to Kaakoush et al.

Gerasimidis K, Ijaz UZ, Edwards C, Russell RK, Quince C, Hansen R.

Am J Gastroenterol. 2016 Jul;111(7):1033-4. doi: 10.1038/ajg.2016.169. No abstract available.

PMID:
27356826
30.

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System.

Pinto AJ, Marcus DN, Ijaz UZ, Bautista-de Lose Santos QM, Dick GJ, Raskin L.

mSphere. 2015 Dec 30;1(1). pii: e00054-15. doi: 10.1128/mSphere.00054-15. eCollection 2016 Jan-Feb.

31.

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.

Schirmer M, D'Amore R, Ijaz UZ, Hall N, Quince C.

BMC Bioinformatics. 2016 Mar 11;17:125. doi: 10.1186/s12859-016-0976-y.

32.

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.

33.

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.

D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.

BMC Genomics. 2016 Jan 14;17:55. doi: 10.1186/s12864-015-2194-9.

34.

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K.

Am J Gastroenterol. 2015 Dec;110(12):1718-29; quiz 1730. doi: 10.1038/ajg.2015.357. Epub 2015 Nov 3.

35.

Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment.

Couto JM, Ijaz UZ, Phoenix VR, Schirmer M, Sloan WT.

Curr Microbiol. 2015 Aug;71(2):296-302. doi: 10.1007/s00284-015-0846-2. Epub 2015 Jun 5.

36.

Bacterial diversity along a 2600 km river continuum.

Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AK, Farnleitner AH, Eiler A.

Environ Microbiol. 2015 Dec;17(12):4994-5007. doi: 10.1111/1462-2920.12886. Epub 2015 Jun 11.

37.

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C.

Nucleic Acids Res. 2015 Mar 31;43(6):e37. doi: 10.1093/nar/gku1341. Epub 2015 Jan 13.

38.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
39.

Multidirectional scattering models for 3-dimensional ultrasound imaging.

Ijaz UZ, Housden RJ, Treece GM, Prager RW, Gee AH.

J Ultrasound Med. 2013 Apr;32(4):699-714.

PMID:
23525397
40.

Three-dimensional ultrasound imaging.

Prager RW, Ijaz UZ, Gee AH, Treece GM.

Proc Inst Mech Eng H. 2010;224(2):193-223. Review.

PMID:
20349815
41.

Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation processes using three-dimensional electrical impedance tomography.

Khambampati AK, Rashid A, Ijaz UZ, Kim S, Soleimani M, Kim KY.

Philos Trans A Math Phys Eng Sci. 2009 Aug 13;367(1900):3095-120. doi: 10.1098/rsta.2009.0081.

PMID:
19581257

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