Kayal, A., Yu, S. J., Van, T. T. H., Bajagai, Y. S., & Stanley, D. (2025). Effect of early gut microbiota intervention using pre-designed poultry microbiota substitute on broiler health and performance. Animal Production Science, 65(4), 1-8. doi:10.1071/AN24354

Yu, S. J., Morris, A., Kayal, A., Milošević, I., Van, T. T. H., Bajagai, Y. S., & Stanley, D. (2024). Pioneering gut health improvements in piglets with phytogenic feed additives. Applied Microbiology and Biotechnology, 108(1), 108-142. doi:10.1007/s00253-023-12925-2

Ren, X., Whitton, M. M., Trotter, T., Ashwath, N., Stanley, D., & Bajagai, Y. S. (2024). Enhancing soil health and carbon sequestration through phytogenic treatment: Insights into microbial functional pathways in pasture dieback affected soil. Plant and Soil, 503(1-2), 433-449. doi:10.1007/s11104-024-06594-x

Petranyi, F., Whitton, M. M., Lobo, E., Ramirez, S., Radovanović, A., Bajagai, Y. S., & Stanley, D. (2024). Precision glycan supplementation: A strategy to improve performance and intestinal health of laying hens in high-stress commercial environments. Journal of Animal Physiology and Animal Nutrition, 108(5), 1498-1509. doi:10.1111/jpn.13996

Ren, X., Yu, S. J., Brewer, P. B., Ashwath, N., Bajagai, Y. S., Stanley, D., & Trotter, T. (2024). Unveiling microbial dynamics and gene expression in legume–Buffel grass coculture systems for sustainable agriculture. Agronomy, 14(9), 1-20. doi:10.3390/agronomy14092172

Batacan, R., Briskey, D., Bajagai, Y. S., Smith, C., Stanley, D., & Rao, A. (2024). Effect of palmitoylethanolamide compared to a placebo on the gut microbiome and biochemistry in an overweight adult population: A randomised, placebo controlled, double-blind study. Biomedicines, 12(7), 1-19. doi:10.3390/biomedicines12071620

Horyanto, D., Bajagai, Y. S., von Hellens, J., Chen, X., Van, T. T. H., Dunlop, M. W., & Stanley, D. (2024). The association between brmoiler litter microbiota and the supplementation of bacillus probiotics in a leaky gut model. Animals, 14(12), 1-15. doi:10.3390/ani14121758

Ren, X., Trotter, T., Ashwath, N., Stanley, D., Bajagai, Y. S., & Brewer, P. B. (2024). Transcriptomic insights: Phytogenic modulation of buffel grass (Cenchrus ciliaris) seedling emergence. Plants, 13(9), 1-16. doi:10.3390/plants13091174

Bajagai, Y. S., Van, T. T. H., Joat, N., Chousalkar, K., Moore, R. J., & Stanley, D. (2024). Layer chicken microbiota: A comprehensive analysis of spatial and temporal dynamics across all major gut sections. Journal of Animal Science and Biotechnology, 15(1), 1-15. doi:10.1186/s40104-023-00979-1

Horyanto, D., Bajagai, Y. S., Kayal, A., von Hellens, J., Chen, X., Van, T. T. H., . . . Stanley, D. (2024). Bacillus amyloliquefaciens probiotics mix supplementation in a broiler leaky gut model. Microorganisms, 12(2), 1-16. doi:10.3390/microorganisms12020419

Yu, S. J., Morris, A., Kayal, A., Hao Van, T. T., Stanley, D., & Bajagai, Y. S. (2024). Enhancing gut health and performance of grower-finisher pigs: Assessing the efficacy of the mixture of microencapsulated essential oils and saponins. Animal Production Science, 64(1), 1-10. doi:10.1071/AN23215

Lobo, E., Bajagai, Y. S., Kayal, A., Ramirez, S., Nikolić, A., Valientes, R., & Stanley, D. (2024). Precision glycan supplementation improves gut microbiota diversity, performance, and disease outbreak resistance in broiler chickens. Animals, 14(1), 1-17. doi:10.3390/ani14010032

Joat, N., Bajagai, Y. S., Hao Van, T. T., Stanley, D., Chousalkar, K., & Moore, R. J. (2023). The temporal fluctuations and development of faecal microbiota in commercial layer flocks. Animal Nutrition, 15, 197-209. doi:10.1016/j.aninu.2023.07.006

Ren, X., Whitton, M. M., Yu, S. J., Trotter, T., Bajagai, Y. S., & Stanley, D. (2023). Application of phytogenic liquid supplementation in soil microbiome restoration in Queensland Pasture Dieback. Microorganisms, 11(3), 1-20. doi:10.3390/microorganisms11030561

Whitton, M. M., Ren, X., Yu, S. J., Irving, A. D., Trotter, T., Bajagai, Y. S., & Stanley, D. (2023). Humate application alters microbiota–mineral interactions and assists in pasture dieback recovery. Heliyon, 9(2), 1-14. doi:10.1016/j.heliyon.2023.e13327

Whitton, M. M., Ren, X., Yu, S. J., Trotter, T., Stanley, D., & Bajagai, Y. S. (2022). Remediation of Pasture Dieback Using Plant Growth Promotant. Agronomy, 12(12), 1-14. doi:10.3390/agronomy12123153

Kayal, A., Stanley, D., Radovanovic, A., Horyanto, D., Van, T. T. H., & Bajagai, Y. S. (2022). Controlled Intestinal Microbiota Colonisation in Broilers under the Industrial Production System. Animals, 12(23), 1-19. doi:10.3390/ani12233296

Whitton, M. M., Ren, X., Yu, S. J., Irving, A. D., Trotter, T., Bajagai, Y. S., & Stanley, D. (2022). Sea Minerals Reduce Dysbiosis, Improve Pasture Productivity and Plant Morphometrics in Pasture Dieback Affected Soils. Sustainability, 14(22), 1-18. doi:10.3390/su142214873

Stanley, D., Batacan, R., & Bajagai, Y. S. (2022). Rapid growth of antimicrobial resistance: the role of agriculture in the problem and the solutions. Applied Microbiology and Biotechnology, 106(21), 6953-6962. doi:10.1007/s00253-022-12193-6

Stanley, D., & Bajagai, Y. S. (2022). Feed Safety and the Development of Poultry Intestinal Microbiota. Animals, 12(20), 1-14. doi:10.3390/ani12202890

Yu, S. J., Bajagai, Y. S., Petranyi, F., de las Heras-Saldana, S., Van, T. T. H., & Stanley, D. (2022). Phytogenic Blend Improves Intestinal Health and Reduces Obesity, Diabetes, Cholesterol and Cancers: A Path toward Customised Supplementation. Antibiotics, 11(10), 1-14. doi:10.3390/antibiotics11101428

Yu, S. J., Bajagai, Y. S., Petranyi, F., & Stanley, D. (2022). Phytogen Improves Performance during Spotty Liver Disease by Impeding Bacterial Metabolism and Pathogenicity. Applied and Environmental Microbiology, 88(18), 1-10. doi:10.1128/aem.00758-22

Bajagai, Y. S., Trotter, M., Williams, T. M., Costa, D. F. A., Whitton, M. M., Ren, X., . . . Stanley, D. (2022). The role of microbiota in animal health and productivity: Misinterpretations and limitations. Animal Production Science, 62(11), A-M. doi:10.1071/AN21515

Bajagai, Y., Petranyi, F., Yu, S., Lobo, E., Batacan, R., Kayal, A., . . . Stanley, D. (2022). Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers. Scientific Reports, 12(1), 1-13. doi:10.1038/s41598-022-14925-0

Bajagai, Y. S., Petranyi, F., Horyanto, D., Batacan, R., Lobo, E., Ren, X., . . . Stanley, D. (2022). Ileum transcriptional response to prolonged supplementation with phytogenic product containing menthol, carvacrol and carvone. Heliyon, 8(3), 1-9. doi:10.1016/j.heliyon.2022.e09131

Dinh, X. T., Stanley, D., Smith, L. D., Moreau, M., Berzins, S. P., Gemiarto, A., . . . Jordan, M. A. (2021). Modulation of TCR signalling components occurs prior to positive selection and lineage commitment in iNKT cells. Scientific Reports, 11, 1-23. doi:10.1038/s41598-021-02885-w

Nowland, T. L., Stanley, D., Kirkwood, R. N., Torok, V. A., Bajagai, Y. S., Gannon, N. J., & Plush, K. J. (2021). Maternal supplementation with phytogenic additives influenced the faecal microbiota and reproductive potential in sows. AMB Express, 11(1), 1-11. doi:10.1186/s13568-021-01268-8

Joat, N., Van, T. T. H., Stanley, D., Moore, R. J., & Chousalkar, K. (2021). Temporal dynamics of gut microbiota in caged laying hens: A field observation from hatching to end of lay. Applied Microbiology and Biotechnology, 105(11), 4719-4730. doi:10.1007/s00253-021-11333-8

Abudabos, A. M., Abdelrahman, M. M., Alatiyat, R. M., Aljumaah, M. R., Al Jassim, R., & Stanley, D. (2021). Effect of dietary inclusion of graded levels of distillers dried grains with solubles on the performance, blood profile and rumen microbiota of Najdi lambs. Heliyon, 7(1), 1-10. doi:10.1016/j.heliyon.2020.e05683

Bajagai, Y. S., Steel, J. C., Radovanovic, A., & Stanley, D. (2021). Prolonged continual consumption of oregano herb interferes with the action of steroid hormones and several drugs, and effects signaling across the brain-gut axis. Food and Function, 12(2), 726-738. doi:10.1039/d0fo02988b

Shen, S., Prame Kumar, K., Wen, S. W., Shim, R., Wanrooy, B. J., Stanley, D., . . . Wong, C. H. Y. (2021). Deficiency of dietary fiber modulates gut microbiota composition, neutrophil recruitment and worsens experimental colitis. Frontiers in Immunology, 12, 1-14. doi:10.3389/fimmu.2021.619366

Bajagai, Y. S., Radovanovic, A., Steel, J. C., & Stanley, D. (2021). The effects of continual consumption of origanum vulgare on liver transcriptomics. Animals, 11(2), 1-15. doi:10.3390/ani11020398

Bajagai, Y. S., Alsemgeest, J. C., Moore, R. J., Van, T. T. H., & Stanley, D. (2020). Phytogenic products, used as alternatives to antibiotic growth promoters, modify the intestinal microbiota derived from a range of production systems: An in vitro model. Applied Microbiology and Biotechnology, 104(24), 10631-10640. doi:10.1007/s00253-020-10998-x

Haberecht, S., Bajagai, Y. S., Moore, R. J., Van, T. T. H., & Stanley, D. (2020). Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation. AMB Express, 10(1), 1-10. doi:10.1186/s13568-020-01077-5

Aljumaah, M. R., Alkhulaifi, M. M., Aljumaah, R. S., Abudabos, A. M., Abdullatif, A. A., Suliman, G. M., . . . Stanley, D. (2020). Influence of sanguinarine-based phytobiotic supplementation on post necrotic enteritis challenge recovery. Heliyon, 6(11), 1-10. doi:10.1016/j.heliyon.2020.e05361

Khan, S., Moore, R. J., Stanley, D., & Chousalkar, K. K. (2020). The gut microbiota of laying hens and its manipulation with prebiotics and probiotics to enhance gut health and food safety. Applied and Environmental Microbiology, 86(13), 1-18. doi:10.1128/AEM.00600-20

Aljumaah, M. R., Alkhulaifi, M. M., Abudabos, A. M., Aljumaah, R. S., Alsaleh, A. N., & Stanley, D. (2020). Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge. PLoS ONE, 15(6), 1-18. doi:10.1371/journal.pone.0232781

Aljumaah, M. R., Alkhulaifi, M. M., Abudabos, A. M., Alabdullatifb, A., El-Mubarak, A. H., Al Suliman, A. R., & Stanley, D. (2020). Organic acid blend supplementation increases butyrate and acetate production in Salmonella enterica serovar Typhimurium challenged broilers. PLoS ONE, 15(6), 1-14. doi:10.1371/journal.pone.0232831

Gangadoo, S., Dinev, I., Willson, N. -L., Moore, R. J., Chapman, J. M., & Stanley, D. (2020). Nanoparticles of selenium as high bioavailable and non-toxic supplement alternatives for broiler chickens. Environmental Science and Pollution Research, 27(14), 16159-16166. doi:10.1007/s11356-020-07962-7

Wilkinson, N. E., Hughes, R. J., Bajagai, Y. S., Aspden, W. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2020). Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences in Japanese quail. Heliyon, 6(1), 1-7. doi:10.1016/j.heliyon.2020.e03213

Bauer, B. W., Gangadoo, S., Bajagai, Y. S., Van, T. T. H., Moore, R. J., & Stanley, D. (2019). Oregano powder reduces Streptococcus and increases SCFA concentration in a mixed bacterial culture assay. PLoS ONE, 14(12), 1-16. doi:10.1371/journal.pone.0216853

Gangadoo, S., Bauer, B. W., Bajagai, Y. S., Van, T. T. H., Moore, R. J., & Stanley, D. (2019). In vitro growth of gut microbiota with selenium nanoparticles. Animal Nutrition, 5(4), 424-431. doi:10.1016/j.aninu.2019.06.004

Willson, N. -L., Van, T. T. H., Lever, J., Moore, R. J., & Stanley, D. (2019). Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus. Applied Microbiology and Biotechnology, 103(21), 8977-8985. doi:10.1007/s00253-019-10143-3

Bauer, B. W., Radovanovic, A., Willson, N. -L., Bajagai, Y. S., Hao Van, T. T., Moore, R. J., & Stanley, D. (2019). Oregano: A potential prophylactic treatment for the intestinal microbiota. Heliyon, 5(10), 1-11. doi:10.1016/j.heliyon.2019.e02625

Pinget, G., Tan, J., Janac, B., Kaakoush, N. O., Angelatos, A. S., O'Sullivan, J., . . . Macia, L. (2019). Impact of the food additive titanium dioxide (e171) on gut microbiota-host interaction. Frontiers in Nutrition, 6, 1-13. doi:10.3389/fnut.2019.00057

Willson, N. -L., Van, T. T. H., Bhattarai, S. P., Courtice, J. M., McIntyre, J. R., Prasai, T. P., . . . Stanley, D. (2019). Feed supplementation with biochar may reduce poultry pathogens, including Campylobacter hepaticus, the causative agent of Spotty Liver Disease. PLoS ONE, 14(4), 1-16. doi:10.1371/journal.pone.0214471

Khalesi, S., Bellissimo, N., Vandelanotte, C., Williams, S., Stanley, D., & Irwin, C. (2019). A review of probiotic supplementation in healthy adults: helpful or hype?. European Journal of Clinical Nutrition, 73(1), 24-37. doi:10.1038/s41430-018-0135-9

Stanley, D., Moore, R. J., & Wong, C. H. Y. (2018). An insight into intestinal mucosal microbiota disruption after stroke. Scientific Reports, 8, 1-12. doi:10.1038/s41598-017-18904-8

Lacey, J. A., Stanley, D., Keyburn, A. L., Ford, M., Chen, H., Johanesen, P., . . . Moore, R. J. (2018). Clostridium perfringens-mediated necrotic enteritis is not influenced by the pre-existing microbiota but is promoted by large changes in the post-challenge microbiota. Veterinary Microbiology, 227, 119-126. doi:10.1016/j.vetmic.2018.10.022

Wilkinson, N. E., Dinev, I., Aspden, W. J., Hughes, R. J., Christiansen, I., Chapman, J., . . . Stanley, D. (2018). Ultrastructure of the gastro intestinal tract of healthy Japanese quail (Coturnix japonica) using light and scanning electron microscopy. Animal Nutrition, 4(4), 378-387. doi:10.1016/j.aninu.2018.06.006

Willson, N. -L., Nattrass, G. S., Hughes, R. J., Moore, R. J., Stanley, D., Hynd, P. I., & Forder, R. E. A. (2018). Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry. Applied Microbiology and Biotechnology, 102(21), 9317-9329. doi:10.1007/s00253-018-9281-1

Shen, S., Kumar, K. P., Stanley, D., Moore, R. J., Hao Van, T. T., Wen, S. W., . . . Wong, C. H. Y. (2018). Invariant natural killer T cells shape the gut microbiota and regulate neutrophil recruitment and function during intestinal inflammation. Frontiers in Immunology, 9(May 2018), 1-15. doi:10.3389/fimmu.2018.00999

Baldwin, S., Hughes, R. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2018). At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota. PLoS ONE, 13(3), 1-14. doi:10.1371/journal.pone.0194825

Gangadoo, S., Dinev, I., Chapman, J., Hughes, R. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2018). Selenium nanoparticles in poultry feed modify gut microbiota and increase abundance of Faecalibacterium prausnitzii. Applied Microbiology and Biotechnology, 102(3), 1455-1466. doi:10.1007/s00253-017-8688-4

Jordan, M., Gresle, M. M., Laverick,, L., Stanley, D., Gemiarto, A., Smith, L. D., . . . Baxter, A. G. (2017). Dissecting the "killer module" and its role in Multiple Sclerosis. Multiple Sclerosis Journal, 23(13), N29-NP29. Retrieved from http://journals.sagepub.com/doi/full/10.1177/1352458517734699

Abudabos, A. M., Al-Atiyat, R. M., Albatshan, H. A., Aljassim, R., Aljumaah, M. R., Alkhulaifi, M. M., & Stanley, D. M. (2017). Effects of concentration of corn distillers dried grains with solubles and enzyme supplementation on cecal microbiota and performance in broiler chickens. Applied Microbiology and Biotechnology, 101(18), 7017-7026. doi:10.1007/s00253-017-8448-5

Abudabos, A. M., Al-Atiyat, R. M., Stanley, D., Aljassim, R., & Albatshan, H. A. (2017). The effect of corn distiller's dried grains with solubles (DDGS) fortified with enzyme on growth performance of broiler. Environmental Science and Pollution Research, 24(26), 21412-21421. doi:10.1007/s11356-017-9808-5

Donaldson, E. E., Stanley, D., Hughes, R. J., & Moore, R. J. (2017). The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs. PeerJ, 5, 1-19. doi:10.7717/peerj.3587

Batacan, R. B., Fenning, A. S., Dalbo, V. J., Scanlan, A. T., Duncan, M. J., Moore, R. J., & Stanley, D. (2017). A gut reaction: the combined influence of exercise and diet on gastrointestinal microbiota in rats. Journal of Applied Microbiology, 122(6), 1627-1638. doi:10.1111/jam.13442

Crisol-Martínez, E., Stanley, D., Geier, M. S., Hughes, R. J., & Moore, R. J. (2017). Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: Linking gut microbiota and growth performance in chickens. Applied Microbiology and Biotechnology, 101(11), 4547-4559. doi:10.1007/s00253-017-8193-9

Crisol-Martínez, E., Stanley, D., Geier, M. S., Hughes, R. J., & Moore, R. J. (2017). Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens. PeerJ, (3), 1-20. doi:10.7717/peerj.3071

Mariño, E., Richards, J. L., McLeod, K. H., Stanley, D., Yap, Y. A., Knight, J., . . . Mackay, C. R. (2017). Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nature Immunology, 18(5), 552-562. doi:10.1038/ni.3713

Gangadoo, S., Stanley, D., Hughes, R. J., Moore, R. J., & Chapman, J. (2017). The synthesis and characterisation of highly stable and reproducible selenium nanoparticles. Inorganic and Nano-Metal Chemistry, 47(11), 1568-1576. doi:10.1080/24701556.2017.1357611

Prasai, T. P., Walsh, K. B., Bhattarai, S. P., Midmore, D. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2017). Zeolite food supplementation reduces abundance of enterobacteria. Microbiological Research, 195, 24-30. doi:10.1016/j.micres.2016.11.006

Gangadoo, S., Stanley, D., Hughes, R. J., Moore, R. J., & Chapman, J. (2016). Nanoparticles in feed: Progress and prospects in poultry research. Trends in Food Science and Technology, 58, 115-126. doi:10.1016/j.tifs.2016.10.013

Stanley, D., Mason, L. J., Mackin, K. E., Srikhanta, Y. N., Lyras, D., Prakash, M. D., . . . Wong, C. H. Y. (2016). Translocation and dissemination of commensal bacteria in post-stroke infection. Nature Medicine, 22(11), 1277-1284. doi:10.1038/nm.4194

Reynolds, A., Paterson, J., Stanley, D., Burke, K., Wright, K., Preece, H., . . . Ferguson, S. (2016). Sleep loss and the human gut microbiome: Preliminary investigation of a novel mechanistic link between shiftwork and metabolic disease. Journal of Sleep Research, 25(S2), 12. doi:10.1111/jsr.12453

Moore, R. J., & Stanley, D. (2016). Experimental design considerations in microbiota/inflammation studies. Clinical and Translational Immunology, 5, 1-7. doi:10.1038/cti.2016.41

Crisol-Martínez, E., Moreno-Moyano, L. T., Wilkinson, N., Prasai, T., Brown, P. H., Moore, R. J., & Stanley, D. (2016). A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica). PeerJ, 2016(5), 1-23. doi:10.7717/peerj.2002

Wilkinson, N., Hughes, R. J., Aspden, W. J., Chapman, J., Moore, R. J., & Stanley, D. (2016). The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica. Applied Microbiology and Biotechnology, 100(9), 4201-4209. doi:10.1007/s00253-015-7280-z

Prasai, T. P., Walsh, K., Bhattarai, S. P., Midmore, D. J., Van Thi, T. H., Moore, R. J., & Stanley, D. (2016). Biochar, bentonite and zeolite supplemented feeding of layer chickens alters intestinal microbiota and reduces campylobacter load. PLoS ONE, 11(4), 1-13. doi:10.1371/journal.pone.0154061

Crisol-Martínez, E., Moreno-Moyano, L. T., Wormington, K. R., Brown, P. H., & Stanley, D. (2016). Using next-generation sequencing to contrast the diet and explore pest-reduction services of sympatric bird species in macadamia orchards in Australia. PLoS ONE, 11(3), 1-19. doi:10.1371/journal.pone.0150159

Stanley, D., Hughes, R. J., Geier, M. S., & Moore, R. J. (2016). Bacteria within the gastrointestinal tract microbiota correlated with improved growth and feed conversion: Challenges presented for the identification of performance enhancing probiotic bacteria. Frontiers in Microbiology, 7, 1-13. doi:10.3389/fmicb.2016.00187

Reynolds, A. C., Paterson, J. L., Ferguson, S. A., Stanley, D., Wright, K. P., & Dawson, D. (2017). The shift work and health research agenda: Considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease. Sleep Medicine Reviews, 34, 3-9. doi:10.1016/j.smrv.2016.06.009

Thorburn, A., Shen, S., Stanley, D., Macia, L., Mason, L., Roberts, L., . . . Mackay, C. (2015). Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nature communications., 6, 1-13. doi:10.1038/ncomms8320

Macia, L., Vieira, A., Leach, K., Stanley, D., Luong, S., Maruya, M., . . . Mackay, C. (2015). Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome. Nature communications., 6, 1-15. doi:10.1038/ncomms7734

Stanley, D., Geier, M., Chen, H., Hughes, R., & Moore, R. (2015). Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC microbiology., 15(1), 51-61. doi:10.1186/s12866-015-0388-6

Gillespie, M. J., Crowley, T. M., Haring, V. R., Wilson, S. L., Harper, J. A., Payne, J. S., . . . Moore, R. J. (2014). Correction: Transcriptome analysis of pigeon milk production - role of cornification and triglyceride synthesis genes. BMC Genomics, 15(1), 185. doi:10.1186/1471-2164-15-185

Stanley, D., Wu, S. B., Rodgers, N., Swick, R., & Moore, R. (2014). Differential responses of cecal microbiota to fishmeal, Eimeria and Clostridium perfringens in a necrotic enteritis challenge model in chickens. PLoS ONE., 9(8), 1-10. doi:10.1371/journal.pone.0104739

Stanley, D., Hughes, R., & Moore, R. (2014). Microbiota of the chicken gastrointestinal tract : influence on health, productivity and disease. Applied microbiology and biotechnology., 98(10), 4301-4310. doi:10.1007/s00253-014-5646-2

Wu, S. B., Stanley, D., Rodgers, N., Swick, R., & Moore, R. (2014). Two necrotic enteritis predisposing factors, dietary fishmeal and Eimeria infection, induce large changes in the caecal microbiota of broiler chickens. Veterinary microbiology., 169(3-4), 188-197. doi:10.1016/j.vetmic.2014.01.007

Stanley, D., Watson-Haigh, N., Cowled, C., & Moore, R. (2013). Genetic architecture of gene expression in the chicken. BMC genomics., 14, 13-22. doi:10.1186/1471-2164-14-13

Stanley, D., Geier, M., Hughes, R., Denman, S., & Moore, R. (2013). Highly variable microbiota development in the chicken gastrointestinal tract. PLoS ONE., 8(12), 1-7. doi:10.1371/journal.pone.0084290

Stanley, D., Geier, M., Denman, S., Haring, V., Crowley, T., Hughes, R., & Moore, R. (2013). Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed. Veterinary microbiology., 164(1-2), 85-92. doi:10.1016/j.vetmic.2013.01.030

Konsak, B., Stanley, D., Haring, V., Geier, M., Hughes, R., Howarth, G., . . . Moore, R. (2013). Identification of differential duodenal gene expression levels and microbiota abundance correlated with differences in energy utilisation in chickens. Animal production science., 53(12), 1269-1275. doi:10.1071/AN12426

Gillespie, M. J., Stanley, D., Chen, H., Donald, J. A., Nicholas, K. R., Moore, R. J., & Crowley, T. M. (2012). Functional similarities between pigeon ‘milk’ and mammalian milk: Induction of immune gene expression and modification of the microbiota. PLoS ONE, 7(10), 1-10. doi:10.1371/journal.pone.0048363

Stanley, D., Keyburn, A., Denman, S., & Moore, R. (2012). Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. Veterinary microbiology., 159(1-2), 155-162. doi:10.1016/j.vetmic.2012.03.032

Stanley, D., Denman, S., Hughes, R., Geier, M., Crowley, T., Chen, H., . . . Moore, R. (2012). Intestinal microbiota associated with differential feed conversion efficiency in chickens. Applied microbiology and biotechnology., 96(5), 1361-1369. doi:10.1007/s00253-011-3847-5

Stanley, D., Chambers, P., Stanley, G., Borneman, A., & Fraser, S. (2010). Transcriptional changes associated with ethanol tolerance in saccharomyces cerevisiae. Applied microbiology and biotechnology., 88, 231-239. doi:10.1007/s00253-010-2760-7

Stanley, D., Fraser, S., Stanley, G., & Chambers, P. (2010). Retrotransposon expression in ethanol-stressed saccharomyces cerevisiae. Applied microbiology and biotechnology., 87(4), 1447-1454. doi:10.1007/s00253-010-2562-y

Stanley, D., Fraser, S., Chambers, P., Rogers, P., & Stanley, G. (2010). Generation and characterisation of stable ethanol-tolerant mutants of Saccharomyces cerevisiae. Journal of industrial microbiology and biotechnology., 37, 139-149. doi:10.1007/s10295-009-0655-3

Stanley, D., Bandara, A., Fraser, S., Chambers, P., & Stanley, G. (2010). The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae. Journal of applied microbiology., 109, 13-24. doi:10.1111/j.1365-2672.2009.04657.x

Sharma Bajagai, Y., Petrany, F., & Stanley, D. (2025). Microbiome-host interaction in avian pasteurellosis. In Proceedings of the Australian Poultry Science Symposium: Volume 36, 2025 Vol. 36 (pp. 152-155). Brownlow Hill, NSW: Poultry Research Foundation. Retrieved from https://apss.sydney.edu.au/past-proceedings/

Horyanto, D., Sharma Bajagai, Y., Von Hellens, J., Chen, X., Van, T. T. H., Radovanovic, A., & Stanley, D. (2025). Influence of Bacillus Subtilis probiotic on gut integrity and gene expression in broilers. In Proceedings of the Australian Poultry Science Symposium: Volume 36, 2025 Vol. 36 (pp. 55-58). Brownlow Hill, NSW: Poultry Research Foundation. Retrieved from https://apss.sydney.edu.au/past-proceedings/

Yu, S. J., Bajagai, Y. S., Petrany, F., & Stanley, D. (2023). Influence of phytogenic supplement on layer production during the peak of heat stress. In Proceedings of the Australian Poultry Science Symposium, Volume 34 2023 Vol. 34 (pp. 147-150). Camden, NSW: The University of Sydney. Retrieved from https://poultry-research.sydney.edu.au/publications/

Petrany, F., Bajagai, Y., Ramirez, S., & Stanley, D. (2022). Influence of precision glycans on layer cecal community. In Proceedings of the Australian Poultry Science Symposium Vol. 33 (pp. 54-57). Online: University of Sydney. Retrieved from https://poultry-research.sydney.edu.au/

Bauer, B. W., Bajagai, Y. S., Alsemgeest, J., Willson, N. -L., Van, T. T. H., Moore, R., & Stanley, D. (2020). Effects of supplemented oregano on the maturation of broiler faecal microbiota. In https://www.apss2024.com.au/proceedings Vol. 31 (pp. 170-173). Camden, Australia: The University of Queensland. Retrieved from https://poultry-research.sydney.edu.au/

Bajagai, Y. S., Bauer, B. W., Alsemgeest, J., Willson, N. -L., Van, T. T. H., Moore, R., & Stanley, D. (2020). Functional analysis of changes in gut microbiota genetic potential in broilers supplemented with 2% oregano. In 31st Australian Poultry Science Symposium (pp. 112-115). Camden, Australia: The University of Sydney. Retrieved from https://www.apss2024.com.au/proceedings