Nichols, B. et al. (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119(4), pp. 885-895. (doi: 10.1016/j.ajcnut.2023.12.027) (PMID:38569785) (PMCID:PMC11007740)

Gul, F., Herrema, H., Davids, M., Keating, C. , Nasir, A., Ijaz, U. Z. and Javed, S. (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16, 5. (doi: 10.1186/s13099-024-00596-x)

Aqueel, R., Badar, A., Roy, N., Mushtaq, Q., Ali, A. F., Bashir, A., Ijaz, U. Z. and Malik, K. A. (2023) Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated. npj Biofilms and Microbiomes, 9(1), 100. (doi: 10.1038/s41522-023-00470-9) (PMID:38097579) (PMCID:PMC10721634)

Vignola, M. , Lenselink, J., Quinn, D., Ijaz, U. Z. , Pereira, R., Sloan, W. T. , Connelly, S. , Moore, G., Gauchotte-Lindsay, C. and Smith, C. J. (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72(10), pp. 1837-1851. (doi: 10.2166/aqua.2023.036)

Ameer, A., Cheng, Y., Saleem, F., Uzma, , McKenna, A., Richmond, A., Gundogdu, O., Sloan, W. T. , Javed, S. and Ijaz, U. Z. (2023) Temporal stability and community assembly mechanisms in healthy broiler cecum. Frontiers in Microbiology, 14, 1197838. (doi: 10.3389/fmicb.2023.1197838) (PMID:37779716) (PMCID:PMC10534011)

Singh, S., Keating, C. , Ijaz, U. Z. and Hassard, F. (2023) Molecular insights informing factors affecting low temperature anaerobic applications: diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems. Science of the Total Environment, 874, 162420. (doi: 10.1016/j.scitotenv.2023.162420) (PMID:36842571)

Lan, J. , Zhao, D. and Tian, D. (2023) Safe and robust data-driven cooperative control policy for mixed vehicle platoons. International Journal of Robust and Nonlinear Control, 33(7), pp. 4171-4190. (doi: 10.1002/rnc.6412)

Aziz, I., Noreen, Z., Ijaz, U. Z. , Gundogdu, O., Hamid, M. H., Muhammad, N., Khan, A. and Bokhari, H. (2023) A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Scientific Reports, 13, 6802. (doi: 10.1038/s41598-023-32491-x)

Batool, M., Keating, C. , Javed, S., Nasir, A., Muddassar, M. and Ijaz, U. Z. (2023) A cross-sectional study of potential antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of young normoweight Pakistani individuals. Microorganisms, 11(2), 279. (doi: 10.3390/microorganisms11020279) (PMID:36838244) (PMCID:PMC9965051)

Carboni, M. F., Mills, S., Arriaga, S., Collins, G., Ijaz, U. Z. and Lens, P. N.L. (2022) Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donors. Environmental Technology and Innovation, 28, 102878. (doi: 10.1016/j.eti.2022.102878)

Bain, K. A., Nichols, B., Kerbiriou, C., Moffat, F., Ijaz, U. Z. , Gerasimidis, K. , McInnes, I. B. , Åstrand, A., Holmes, S. and Milling, S. W. F. (2022) Stratification of alopecia areata reveals involvement of CD4 T cell populations and altered faecal microbiota. Clinical and Experimental Immunology, 210(2), pp. 175-186. (doi: 10.1093/cei/uxac088) (PMID:36200950) (PMCID:PMC9750826)

Birlanga, V. B., McCormack, G., Ijaz, U. Z. , MacCarthy, E., Smith, C. and Collins, G. (2022) Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Scientific Reports, 12, 16719. (doi: 10.1038/s41598-022-17008-2) (PMID:36202859) (PMCID:PMC9537138)

Trego, A., Keating, C. , Nzeteu, C., Graham, A., O'Flaherty, V. and Ijaz, U. Z. (2022) Beyond basic diversity estimates – analytical tools for mechanistic interpretations of amplicon sequencing data. Microorganisms, 10(10), 1961. (doi: 10.3390/microorganisms10101961) (PMID:36296237) (PMCID:PMC9609705)

Mills, S., Dessì, P., Pant, D., Farràs, P., Sloan, W. T. , Collins, G. and Ijaz, U. Z. (2022) A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis. npj Biofilms and Microbiomes, 8, 73. (doi: 10.1038/s41522-022-00337-5) (PMID:36138044) (PMCID:PMC9500080)

Ijaz, U. Z. et al. (2022) Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate. Frontiers in Microbiology, 13, 960747. (doi: 10.3389/fmicb.2022.960747) (PMID:36212864) (PMCID:PMC9539666)

Cholet, F., Lisik, A., Agogué, H., Ijaz, U. Z. , Pineau, P., Lachaussée, N. and Smith, C. J. (2022) Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method. mSphere, 7(4), e0032422. (doi: 10.1128/msphere.00324-22) (PMID:35938727) (PMCID:PMC9429940)

Kazlauskaite, R. et al. (2022) Deploying an in vitro gut model to assay the impact of the mannan-oligosaccharide prebiotic bio-mos on the Atlantic Salmon (Salmo salar) gut microbiome. Microbiology Spectrum, 10(3), e0195321. (doi: 10.1128/spectrum.01953-21) (PMID:35532227) (PMCID:PMC9241627)

Logan, M. , Mackinder, M., Clark, C. M., Kountouri, A., Jere, M., Ijaz, U. Z. , Hansen, R., McGrogan, P., Russell, R. K. and Gerasimidis, K. (2022) Intestinal fatty acid binding protein is a disease biomarker in paediatric coeliac disease and Crohn’s disease. BMC Gastroenterology, 22, 260. (doi: 10.1186/s12876-022-02334-6) (PMID:35606704) (PMCID:PMC9125891)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. and Ijaz, U.Z. (2022) Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet. npj Biofilms and Microbiomes, 8, 36. (doi: 10.1038/s41522-022-00296-x) (PMID:35508464) (PMCID:PMC9068720)

Thom, C., Smith, C. J. , Moore, G., Weir, P. and Ijaz, U. Z. (2022) Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap. Water Research, 212, 118106. (doi: 10.1016/j.watres.2022.118106) (PMID:35091225)

Khan, A., Akbar, S., Okonkwo, V., Smith, C. , Khan, S., Shah, A. A., Adnan, F., Ijaz, U. Z. , Ahmed, S. and Badshah, M. (2022) Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor. Bioresource Technology, 345, 126219. (doi: 10.1016/j.biortech.2021.126219) (PMID:34813923)

Tatti, E., Duff, A., Kostrysia, A., Cholet, F., Ijaz, U. and Smith, C. (2022) Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine, Coastal and Shelf Science, 264, 107666. (doi: 10.1016/j.ecss.2021.107666)

Kostrytsia, A., Papirio, S., Khodzhaev, M., Morrison, L., Collins, G., Lens, P. N.L., Ijaz, U. Z. and Esposito, G. (2022) Biofilm carrier type affects biogenic sulfur-driven denitrification performance and microbial community dynamics in moving-bed biofilm reactors. Chemosphere, 287(Part 1), 131975. (doi: 10.1016/j.chemosphere.2021.131975)

Singh, S., Rinta-Kanto, J. M., Lens, P. N. L., Kokko, M., Rintala, J., O’Flaherty, V., Ijaz, U. Z. and Collins, G. (2022) Microbial community assembly and dynamics in granular, fixed-biofilm and planktonic microbiomes valorizing long-chain fatty acids at 20ºC. Bioresource Technology, 343, 126098. (doi: 10.1016/j.biortech.2021.126098) (PMID:34626764)

Rashid, A., Mirza, S. A., Keating, C. , Ijaz, U. Z. , Ali, S. and Campos, L. C. (2022) Machine learning approach to predict quality parameters for bacterial consortium-treated hospital wastewater and phytotoxicity assessment on radish, cauliflower, hot pepper, rice and wheat crops. Water, 14(1), 116. (doi: 10.3390/w14010116)

Gkikas, K. et al. (2021) Dietary triggers of gut inflammation following exclusive enteral nutrition in children with Crohn’s disease: a pilot study. BMC Gastroenterology, 21, 454. (doi: 10.1186/s12876-021-02029-4) (PMID:34861829)

Trego, A. C., Conall Holohan, B., Keating, C. , Graham, A., O'Connor, S., Gerardo, M., Hughes, D., Ijaz, U. Z. and O'Flaherty, V. (2021) First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater. Bioresource Technology, 341, 125786. (doi: 10.1016/j.biortech.2021.125786) (PMID:34523560)

Nikolova, C., Ijaz, U. Z. and Gutierrez, T. (2021) Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant‐assisted oil biodegradation. Ecology and Evolution, 11(20), pp. 13862-13874. (doi: 10.1002/ece3.8091) (PMCID:PMC8525123)

Nikolova, C. N., Ijaz, U. Z. , Magill, C., Kleindienst, S., Joye, S. B. and Gutierrez, T. (2021) Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants. Microbiome, 9(1), 191. (doi: 10.1186/s40168-021-01143-5) (PMID:34548108) (PMCID:PMC8456599)

Cheaib, B. et al. (2021) Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon. Aquaculture, 541, 736772. (doi: 10.1016/j.aquaculture.2021.736772) (PMID:34471330) (PMCID:PMC8192413)

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Ijaz, U.Z. and Smith, C.J. (2021) Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Animal Microbiome, 3, 7. (doi: 10.1186/s42523-020-00065-1) (PMID:33500003) (PMCID:PMC7934267)

Mills, S., Trego, A. C., Lens, P. N.L., Ijaz, U. and Collins, G. (2021) A distinct, flocculent, acidogenic microbial community accompanies methanogenic granules in anaerobic digesters. Microbiology Spectrum, 9(3), e00784-21. (doi: 10.1128/Spectrum.00784-21) (PMID:34756083) (PMCID:PMC8579839)

Mittell, E. A., Cobbold, C. A. , Ijaz, U. Z. , Kilbride, E. A., Moore, K. A. and Mable, B. K. (2020) Feral populations of Brassica oleracea along Atlantic coasts in western Europe. Ecology and Evolution, 10(20), pp. 11810-11825. (doi: 10.1002/ece3.6821) (PMID:33145003) (PMCID:PMC7593181)

Trego, A. C., O'Sullivan, S., Quince, C., Mills, S., Ijaz, U. Z. and Collins, G. (2020) Size shapes the active microbiome of the methanogenic granules, corroborating a biofilm life cycle. mSystems, 5(5), e00323-20. (doi: 10.1128/mSystems.00323-20) (PMID:32994285)

McKenna, A. et al. (2020) Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter. Microbiome, 8, 128. (doi: 10.1186/s40168-020-00908-8) (PMID:32907634) (PMCID:PMC7488076)

Trego, A. C. et al. (2020) Growth and break-up of methanogenic granules suggests mechanisms for biofilm and community development. Frontiers in Microbiology, 11, 1126. (doi: 10.3389/fmicb.2020.01126) (PMID:32582085) (PMCID:PMC7285868)

Cholet, F., Ijaz, U. Z. and Smith, C. J. (2020) Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22(6), pp. 2383-2402. (doi: 10.1111/1462-2920.15017) (PMID:32285609)

Logan, M. et al. (2020) Analysis of 61 exclusive enteral nutrition formulas used in management of active Crohn's disease - new insights into dietary disease triggers. Alimentary Pharmacology and Therapeutics, 51(10), pp. 935-947. (doi: 10.1111/apt.15695) (PMID:32249975)

Heys, C. , Cheaib, B. , Busetti, A., Kazlauskaite, R., Maier, L., Sloan, W.T. , Ijaz, U.Z. , Kaufmann, J., McGinnity, P. and Llewellyn, M.S. (2020) Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar. Applied and Environmental Microbiology, 86(8), e02283-19. (doi: 10.1128/AEM.02283-19) (PMID:32033945) (PMCID:PMC7117918)

Cheaib, B. , Seghouani, H., Ijaz, U. and Derome, N. (2020) Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. Microbiome, 8, 14. (doi: 10.1186/s40168-020-0789-0) (PMID:32041654) (PMCID:PMC7011381)

Jukes, C., Ijaz, U. Z. , Buckley, A., Spencer, J., Irvine, J., Li, J. V., Marchesi, J. R., Candlish, D. and Douce, G. (2020) Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease. Gut Microbes, 11(3), pp. 481-496. (doi: 10.1080/19490976.2019.1678996) (PMID:31793403) (PMCID:PMC7524298)

Frau, A. et al. (2019) DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies. Scientific Reports, 9, 9328. (doi: 10.1038/s41598-019-44974-x) (PMID:31249384) (PMCID:PMC6597572)

Trego, A. C. et al. (2019) De novo growth of methanogenic granules indicates a biofilm life-cycle with complex ecology. bioRxiv, (doi: 10.1101/667386) (Submitted)