By Associate Professor Nadeem Omar Kaakoush

Journal articles

Wark G; Kaakoush NO; Samocha-Bonet D; Ghaly S; Danta M, 2025, 'Oral microbial diversity is associated with biologic treatment and metabolic health status but not with disease activity in patients with inflammatory bowel disease', Crohn's & Colitis 360, pp. otaf047, http://dx.doi.org/10.1093/crocol/otaf047

Hasebe K; Kendig MD; Kaakoush NO; Tajaddini A; Hesam-Shariati S; Frederick Westbrook R; Morris MJ, 2025, 'Pregnancy-related changes in microbiome are disrupted by obesogenic diet exposure: implications for offspring microbiome development', Food and Function, 16, pp. 4023 - 4034, http://dx.doi.org/10.1039/d4fo05674d

Desai I; Pandit A; Smith-Ryan AE; Simar D; Candow DG; Kaakoush NO; Hagstrom AD, 2025, 'The Effect of Creatine Supplementation on Lean Body Mass with and Without Resistance Training', Nutrients, 17, http://dx.doi.org/10.3390/nu17061081

Chen-Liaw A; Aggarwala V; Mogno I; Haifer C; Li Z; Eggers J; Helmus D; Hart A; Wehkamp J; Lamousé-Smith ESN; Kerby RL; Rey FE; Colombel JF; Kamm MA; Olle B; Norman JM; Menon R; Watson AR; Crossette E; Terveer EM; Keller JJ; Borody TJ; Grinspan A; Paramsothy S; Kaakoush NO; Dubinsky MC; Faith JJ, 2025, 'Author Correction: Gut microbiota strain richness is species specific and affects engraftment (Nature, (2025), 637, 8045, (422-429), 10.1038/s41586-024-08242-x)', Nature, 638, pp. E4, http://dx.doi.org/10.1038/s41586-024-08566-8

Porcari S; Mullish BH; Asnicar F; Ng SC; Zhao L; Hansen R; O'Toole PW; Raes J; Hold G; Putignani L; Hvas CL; Zeller G; Koren O; Tun H; Valles-Colomer M; Collado MC; Fischer M; Allegretti J; Iqbal T; Chassaing B; Keller J; Baunwall SM; Abreu M; Barbara G; Zhang F; Ponziani FR; Costello SP; Paramsothy S; Kao D; Kelly C; Kupcinskas J; Youngster I; Franceschi F; Khanna S; Vehreschild M; Link A; De Maio F; Pasolli E; Miguez AB; Brigidi P; Posteraro B; Scaldaferri F; Stojanovic MR; Megraud F; Malfertheiner P; Masucci L; Arumugam M; Kaakoush N; Segal E; Bajaj J; Leong R; Cryan J; Weersma RK; Knight R; Guarner F; Shanahan F; Cani PD; Elinav E; Sanguinetti M; de Vos WM; El-Omar E; Dorè J; Marchesi J; Tilg H; Sokol H; Segata N; Cammarota G; Gasbarrini A; Ianiro G, 2025, 'International consensus statement on microbiome testing in clinical practice', Lancet Gastroenterology and Hepatology, 10, pp. 154 - 167, http://dx.doi.org/10.1016/S2468-1253(24)00311-X

Chen-Liaw A; Aggarwala V; Mogno I; Haifer C; Li Z; Eggers J; Helmus D; Hart A; Wehkamp J; Lamousé-Smith ESN; Kerby RL; Rey FE; Colombel JF; Kamm MA; Olle B; Norman JM; Menon R; Watson AR; Crossett E; Terveer EM; Keller JJ; Borody TJ; Grinspan A; Paramsothy S; Kaakoush NO; Dubinsky MC; Faith JJ, 2025, 'Gut microbiota strain richness is species specific and affects engraftment', Nature, 637, pp. 422 - 429, http://dx.doi.org/10.1038/s41586-024-08242-x

Bénard MV; de Goffau MC; Blonk J; Hugenholtz F; van Buuren J; Paramsothy S; Kaakoush NO; D'Haens GRAM; Borody TJ; Kamm MA; Ponsioen CY, 2025, 'Gut Microbiota Features in Relation to Fecal Microbiota Transplantation Outcome in Ulcerative Colitis: A Systematic Review and Meta-Analysis', Clinical Gastroenterology and Hepatology, http://dx.doi.org/10.1016/j.cgh.2024.10.001

Yin J; Kaakoush NO; Massey J; Danta M, 2025, 'Understanding the microbiome in autologous haemopoietic stem cell transplant for multiple sclerosis.', Front Immunol, 16, pp. 1590601, http://dx.doi.org/10.3389/fimmu.2025.1590601

Luu LDW; Pandey A; Paramsothy S; Ngo C; Castaño-Rodríguez N; Liu C; Kamm MA; Borody TJ; Man SM; Kaakoush NO, 2024, 'Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-46983-5

Majzoub ME; Paramsothy S; Haifer C; Parthasarathy R; Borody TJ; Leong RW; Kamm MA; Kaakoush NO, 2024, 'The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-53454-4

Shen C; Pandey A; Enosi Tuipulotu D; Mathur A; Liu L; Yang H; Adikari NK; Ngo C; Jing W; Feng S; Hao Y; Zhao A; Kirkby M; Kurera M; Zhang J; Venkataraman S; Liu C; Song R; Wong JJL; Schumann U; Natoli R; Wen J; Zhang L; Kaakoush NO; Man SM, 2024, 'Inflammasome protein scaffolds the DNA damage complex during tumor development', Nature Immunology, 25, pp. 2085 - 2096, http://dx.doi.org/10.1038/s41590-024-01988-6

Wark G; Kaakoush NO; Samocha-Bonet D; Ghaly S; Danta M, 2024, 'Dietary Determinants of Metabolic and Gut Microbial Health in Patients with Inflammatory Bowel Disease', Nutrients, 16, http://dx.doi.org/10.3390/nu16193233

Majzoub ME; Luu LDW; Haifer C; Paramsothy S; Borody TJ; Leong RW; Thomas T; Kaakoush NO, 2024, 'Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling', Msystems, 9, http://dx.doi.org/10.1128/msystems.00746-24

Chetwood JD; Paramsothy S; Haifer C; Borody TJ; Kamm MA; Leong RW; Kaakoush NO, 2024, 'Key metabolomic alterations are associated with ulcerative colitis disease state and activity: A validation analysis', Gut, 73, pp. 1392 - 1393, http://dx.doi.org/10.1136/gutjnl-2023-330196

Pandey A; Shen C; Feng S; Tuipulotu DE; Ngo C; Liu C; Kurera M; Mathur A; Venkataraman S; Zhang J; Talaulikar D; Song R; Wong JJL; Teoh N; Kaakoush NO; Man SM, 2024, 'Ku70 senses cytosolic DNA and assembles a tumor-suppressive signalosome', Science Advances, 10, http://dx.doi.org/10.1126/sciadv.adh3409

Benard M; de Goffau M; Blonk J; Hugenholtz F; van Buuren J; Paramsothy S; Kaakoush N; Borody T; Kamm M; Ponsioen C, 2024, 'P1205 Features of the gut microbiota that associate with clinical outcomes of fecal microbiota transplantation in Ulcerative Colitis: a systematic review and meta-analysis', Journal of Crohn's and Colitis, 18, pp. i2131 - i2132, http://dx.doi.org/10.1093/ecco-jcc/jjad212.1335

Wark G; Kaakoush NO; Samocha-Bonet D; Ghaly S; Danta M, 2024, 'P1233 Serum insulin is associated with c-reactive protein and gut microbial diversity in inflammatory bowel disease', Journal of Crohn's and Colitis, 18, pp. i2171 - i2171, http://dx.doi.org/10.1093/ecco-jcc/jjad212.1363

Parthasarathy R; Wakefield D; Santiago FS; Kaakoush NO; Tedla N, 2024, 'Horizontal gene transfer and endogenous retroviruses as mechanisms for molecular mimicry', Lancet Microbe, 5, pp. e4 - e5, http://dx.doi.org/10.1016/S2666-5247(23)00316-6

Hasebe K; Kendig MD; Kaakoush NO; Tajaddini A; Hesam-Shariati S; Westbrook F; Morris MJ, 2024, 'Impact of maternal obesogenic diet on maternal and offspring microbiome development', Obesity Research & Clinical Practice, 18, pp. S6 - S6, http://dx.doi.org/10.1016/j.orcp.2024.09.015

Desai I; Wewege MA; Jones MD; Clifford BK; Pandit A; Kaakoush NO; Simar D; Hagstrom AD; Hagstrom M, 2024, 'The Effect of Creatine Supplementation on Resistance Training-Based Changes to Body Composition: A Systematic Review and Meta-analysis', Journal of Strength and Conditioning Research, 38, pp. 1813 - 1821, http://dx.doi.org/10.1519/JSC.0000000000004862

Shalaby N; Samocha-Bonet D; Kaakoush NO; Danta M, 2023, 'The Role of the Gastrointestinal Microbiome in Liver Disease', Pathogens, 12, http://dx.doi.org/10.3390/pathogens12091087

Clifford BK; Kaakoush NO; Tedla N; Goldstein D; Simar D, 2023, 'The effect of exercise intensity on the inflammatory profile of cancer survivors: A randomised crossover study', European Journal of Clinical Investigation, 53, pp. e13984, http://dx.doi.org/10.1111/eci.13984

Mathur A; Kay C; Xue Y; Pandey A; Lee J; Jing W; Enosi Tuipulotu D; Lo Pilato J; Feng S; Ngo C; Zhao A; Shen C; Rug M; Miosge LA; Atmosukarto II; Price JD; Ali SA; Gardiner EE; Robertson AAB; Awad MM; Lyras D; Kaakoush NO; Man SM, 2023, 'Clostridium perfringens virulence factors are nonredundant activators of the NLRP3 inflammasome', EMBO Reports, 24, http://dx.doi.org/10.15252/embr.202254600

Kendig MD; Leigh SJ; Hasebe K; Kaakoush NO; Westbrook RF; Morris MJ, 2023, 'Obesogenic Diet Cycling Produces Graded Effects on Cognition and Microbiota Composition in Rats', Molecular Nutrition and Food Research, 67, http://dx.doi.org/10.1002/mnfr.202200809

Enosi Tuipulotu D; Feng S; Pandey A; Zhao A; Ngo C; Mathur A; Lee J; Shen C; Fox D; Xue Y; Kay C; Kirkby M; Lo Pilato J; Kaakoush NO; Webb D; Rug M; Robertson AAB; Tessema MB; Pang S; Degrandi D; Pfeffer K; Augustyniak D; Blumenthal A; Miosge LA; Brüstle A; Yamamoto M; Reading PC; Burgio G; Man SM, 2023, 'Immunity against Moraxella catarrhalis requires guanylate-binding proteins and caspase-11-NLRP3 inflammasomes', EMBO Journal, 42, http://dx.doi.org/10.15252/embj.2022112558

Clifford BK; Amorim N; Kaakoush N; Boysen L; Tedla N; Goldstein D; Hardeman E; Simar D, 2023, 'Irradiation-Induced Dysbiosis: The Compounding Effect ofHigh-Fat Diet on Metabolic and Immune Functions in Mice', International Journal of Molecular Sciences, 24, pp. 5631 - 5631, http://dx.doi.org/10.3390/ijms24065631

Parthasarathy R; Santiago F; McCluskey P; Kaakoush NO; Tedla N; Wakefield D, 2023, 'The microbiome in HLA-B27-associated disease: implications for acute anterior uveitis and recommendations for future studies', Trends in Microbiology, 31, pp. 142 - 158, http://dx.doi.org/10.1016/j.tim.2022.08.008

Haifer C; Luu LDW; Paramsothy S; Borody TJ; Leong RW; Kaakoush NO, 2023, 'Microbial determinants of effective donors in faecal microbiota transplantation for UC', Gut, 72, pp. 90 - 100, http://dx.doi.org/10.1136/gutjnl-2022-327742

Kendig MD; Hasebe K; Tajaddini A; Kaakoush NO; Westbrook RF; Morris MJ, 2023, 'The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive, and Gut Microbiome Parameters Are Preserved in Adult Rat Offspring of Mothers Fed a High-Fat, High-Sugar Diet', Molecular Nutrition and Food Research, 67, http://dx.doi.org/10.1002/mnfr.202200318

Podlesny D; Durdevic M; Paramsothy S; Kaakoush NO; Högenauer C; Gorkiewicz G; Walter J; Fricke WF, 2022, 'Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics', Cell Reports Medicine, 3, http://dx.doi.org/10.1016/j.xcrm.2022.100711

Hasebe K; Kendig MD; Kaakoush NO; Tajaddini A; Westbrook RF; Morris MJ, 2022, 'The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat', Animal Microbiome, 4, http://dx.doi.org/10.1186/s42523-022-00185-w

Jing W; Pilato JL; Kay C; Feng S; Tuipulotu DE; Mathur A; Shen C; Ngo C; Zhao A; Miosge LA; Ali SA; Gardiner EE; Awad MM; Lyras D; Robertson AAB; Kaakoush NO; Man SM, 2022, 'Clostridium septicum α-toxin activates the NLRP3 inflammasome by engaging GPI-anchored proteins', Science Immunology, 7, http://dx.doi.org/10.1126/sciimmunol.abm1803

Kaakoush NO; Olzomer EM; Kosasih M; Martin AR; Fargah F; Lambie N; Susic D; Hoehn KL; Farrell R; Byrne FL, 2022, 'Differences in the Active Endometrial Microbiota across Body Weight and Cancer in Humans and Mice', Cancers, 14, pp. 2141, http://dx.doi.org/10.3390/cancers14092141

Haifer C; Paramsothy S; Kaakoush NO; Leong RW, 2022, 'Oral faecal microbiota transplantation in ulcerative colitis – Authors' reply', The Lancet Gastroenterology and Hepatology, 7, pp. 286 - 287, http://dx.doi.org/10.1016/S2468-1253(22)00045-0

Haifer C; Paramsothy S; Kaakoush NO; Saikal A; Ghaly S; Yang T; Luu LDW; Borody TJ; Leong RW, 2022, 'Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial', Lancet Gastroenterology and Hepatology, 7, pp. 141 - 151, http://dx.doi.org/10.1016/S2468-1253(21)00400-3

Lu LDW; Singh H; Castaño-Rodríguez N; Leach ST; Riordan SM; Tedla N; Krishnan U; Kaakoush NO, 2022, 'Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia', Microbial Genomics, 8, http://dx.doi.org/10.1099/mgen.0.000870

Rodriguez Paris V; Wong XYD; Solon-Biet SM; Edwards MC; Aflatounian A; Gilchrist RB; Simpson SJ; Handelsman DJ; Kaakoush NO; Walters KA, 2022, 'The interplay between PCOS pathology and diet on gut microbiota in a mouse model', Gut Microbes, 14, http://dx.doi.org/10.1080/19490976.2022.2085961

Don Wai Luu L; Kaakoush NO; Castaño-Rodríguez N, 2022, 'The role of ATG16L2 in autophagy and disease', Autophagy, 18, pp. 2537 - 2546, http://dx.doi.org/10.1080/15548627.2022.2042783

Deshpande NP; Riordan SM; Gorman CJ; Nielsen S; Russell TL; Correa-Ospina C; Fernando BSM; Waters SA; Castaño-Rodríguez N; Man SM; Tedla N; Wilkins MR; Kaakoush NO, 2021, 'Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus', Genome Medicine, 13, pp. 133, http://dx.doi.org/10.1186/s13073-021-00951-6

Haifer C; Saikal A; Paramsothy R; Kaakoush NO; Leong RW; Borody TJ; Kamm MA; Paramsothy S, 2021, 'Response to faecal microbiota transplantation in ulcerative colitis is not sustained long term following induction therapy', Gut, 70, pp. 2210 - 2211, http://dx.doi.org/10.1136/gutjnl-2020-323581

Haifer C; Saikal A; Paramsothy R; Kaakoush NO; Leong RW; Borody TJ; Kamm MA; Paramsothy S, 2021, 'Response to faecal microbiota transplantation in ulcerative colitis is not sustained long term following induction therapy', GUT, 70, pp. 2210 - 2210, http://dx.doi.org/10.1136/gutjnl-2020-323581

An H; Richardson A; Rajasekariah P; Zhong L; Fernando BSM; Macmillan A; Klotzsch E; Bryant K; Kaakoush NO; Tedla N, 2021, 'Nuclear Leukocyte Immunoglobulin-like Receptor A3 Is Monomeric and Is Involved in Multiple Layers of Regulated Gene Expression and Translation', Journal of Proteome Research, 20, pp. 3078 - 3089, http://dx.doi.org/10.1021/acs.jproteome.0c00946

Haifer C; Saikal A; Paramsothy S; Borody TJ; Ghaly S; Kaakoush NO; Leong R, 2021, 'Lyophilised orally administered faecal microbiota transplantation for Active Ulcerative Colitis (LOTUS study)', JOURNAL OF CROHNS & COLITIS, 15, pp. S029 - S029, http://dx.doi.org/10.1093/ecco-jcc/jjab075.029

Haifer C; Paramsothy S; Borody TJ; Clancy A; Leong RW; Kaakoush NO, 2021, 'Long-term bacterial and fungal dynamics following oral lyophilized fecal microbiota transplantation in clostridioides difficile infection', Msystems, 6, http://dx.doi.org/10.1128/MSYSTEMS.00905-20

Haifer C; Saikal A; Paramsothy S; Borody TJ; Ghaly DS; Kaakoush NO; Leong RW, 2021, '680 LYOPHILIZED ORALLY ADMINISTERED FECAL MICROBIOTA TRANSPLANTATION IN THE MANAGEMENT OF ULCERATIVE COLITIS (LOTUS STUDY) – RESULTS FROM THE INDUCTION PHASE OF A RANDOMIZED CONTROLLED TRIAL', Gastroenterology, 160, pp. S - 135, http://dx.doi.org/10.1016/s0016-5085(21)01074-x

Fox D; Mathur A; Xue Y; Liu Y; Tan WH; Feng S; Pandey A; Ngo C; Hayward JA; Atmosukarto II; Price JD; Johnson MD; Jessberger N; Robertson AAB; Burgio G; Tscharke DC; Fox EM; Leyton DL; Kaakoush NO; Märtlbauer E; Leppla SH; Man SM, 2020, 'Bacillus cereus non-haemolytic enterotoxin activates the NLRP3 inflammasome', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-14534-3

Leigh SJ; Kaakoush NO; Bertoldo MJ; Westbrook RF; Morris MJ, 2020, 'Intermittent cafeteria diet identifies fecal microbiome changes as a predictor of spatial recognition memory impairment in female rats', Translational Psychiatry, 10, http://dx.doi.org/10.1038/s41398-020-0734-9

Leigh SJ; Kaakoush NO; Westbrook RF; Morris MJ, 2020, 'Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats', Translational Psychiatry, 10, http://dx.doi.org/10.1038/s41398-020-0774-1

Krishnan U; Singh H; Tedla N; Leach ST; Kaakoush NO, 2020, 'Presence of gastric pepsinogen in the trachea is associated with altered inflammation and microbial composition', Infection and Immunity, 88, http://dx.doi.org/10.1128/IAI.00455-20

Wasinger VC; Lu K; Yau YY; Nash J; Lee J; Chang J; Paramsothy S; Kaakoush NO; Mitchell HM; Leong RWL, 2020, 'Spp24 is associated with endocytic signalling, lipid metabolism, and discrimination of tissue integrity for ‘leaky-gut’ in inflammatory bowel disease', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-69746-w

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