Research Group Publications

Google Scholar Profile https://scholar.google.com.au/citations?hl=en&user=XPfyb78AAAAJ&view_op=list_works&sortby=pubdate

·         Wilkinson, N., Hughes, R.J., Bajagai, Y.S., Aspden, W.J., Van, T.T.H., Moore, R.J., and Stanley, D. Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences. Heliyon Heliyon 6 (1), e03213 (2020)

·         Bauer, B.W., Gangadoo, S., Bajagai, Y.S., Van, T.T.H., Moore, R.J., and  Stanley, D. Oregano powder reduces Streptococcus and increases SCFA concentration in a mixed bacterial culture assay of chicken, PloS One  (2019)

·         Willson, N., Van, T.T.H., Lever, J., Moore, R.J., and  Stanley, D. Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus, Applied Microbiology and Biotechnology 103 (21-22), 8977-8985, (2019)

·         Bauer, B.W., Radovanovic, A., Willson, N., Bajagai, Y.S., Van, T.T.H., Moore, R.J., and  Stanley D. Oregano: A potential prophylactic treatment for the intestinal microbiota, Heliyon 5 (10), e02625, (2019)

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

·         Pinget, G., Tan, J.,  Janac, B., Kaakoush, N.O., Angelatos, A.S., O'Sullivan, J., Koay, Y.C., Sierro, F., Davis, J., Divakarla, S.K.,  Khanal, D., Moore, R.J., Stanley, D., Chrzanowski, W., Macia, L. Impact of the food additive titanium dioxide (E171) on gut microbiota-host interaction, Frontiers in Nutrition, 6, 57, (2019)

·         Willson, N., Van, T.T.H., Bhattarai, S.P.,  Courtice, J.M.,  McIntyre, J.R., Prasai, T.P., Moore, R.J., Walsh, K., and Stanley, D. Feed supplementation with biochar may reduce poultry pathogens, including Campylobacter hepaticus, the causative agent of Spotty Liver Disease, PloS One 14 (4), e0214471, (2019)

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

·         Khalesi, S., Bellissimo, N., Vandelanotte, C., Williams, S., Stanley, D., Irwin, C. A review of probiotic supplementation in healthy adults: helpful or hype? European journal of clinical nutrition, 1, (2018)

·         Willson, N., Nattrass, G.S., Hughes, RJ., Moore, RJ., Stanley, D., Hynd, PI., and Forder, R.E.A. Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry. Applied Microbiology and Biotechnology, (DOI: 10.1007/s00253-018-9281-1), (2018).

·         Wilkinson, N., Dinev, I., Aspden, W.J., Hughes, R.J., Christiansen, I., Chapman, J., Gangadoo, S., Moore, R.J., and Stanley, D. Ultrastructure of the gastro intestinal tract of healthy Japanese quail (Coturnix japonica) using light and scanning electron microscopy.  Animal Nutrition, (DOI: 10.1016/j.aninu.2018.06.006), (2018)

·         Baldwin, S., Hughes, RJ., Van, T.T.H.,  Moore, R.J.,  Stanley, D.  At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota PloS one 13 (3), e0194825 (2018)

·         Shen, S.J., Prame Kumar, K., Stanley, D.,  Moore, R.J, Van, T.T.H., Wen, S.W., Wong, C,H,W. Invariant natural killer T cells shape the gut microbiota and regulate neutrophil recruitment and function during intestinal inflammation. Frontiers in Immunology 9, 999 (2018)

·         Stanley, D., Moore, R.J., Wong, C.H.Y. An insight into intestinal mucosal microbiota disruption after stroke. Scientific reports 8 (1), 568 (2018). Veterinary microbiology 227, 119-126

·         Lacey, J.A., Stanley, D., Keyburn, A.L., Ford, M., Chen, H., Johanesen, P., Lyras, D., and Moore, R.J. Clostridium perfringens-mediated necrotic enteritis is not influenced by the pre-existing microbiota but is promoted by large changes in the post-challenge microbiota,

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

·         Abudabos, A.M., Al-Atiyat, R.M., Albatshan, H.A., Aljassim, R., Aljumaah, M.R., Alkhulaifi, M.M., and Stanley, D.  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 (2017).

·         Abudabos, A.M., Al-Atiyat, R.M., Stanley, D., Aljassim, R., and Albatshan, H.A. 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) 21412–21. (2017).

·         Reynolds, A.C., Paterson, J.L., Ferguson, S.A., Stanley, D., Wright, K.P., and Dawson, D. 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. 12 (2017).

·         Donaldson, E.E., Stanley, D., Hughes, R.J., and Moore, R.J. The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs. PeerJ 5, e3587. (2017)

·         Prasai, T. P., Walsh, K. B., Bhattarai, S. P., Midmore D. J., Van T. T., Moore R. J. and Stanley, D. Zeolite food supplementation reduces abundance of enterobacteria. Microbiological Research 195: 24-30. (2017).

·         Mariño, E., Richards, J., McLeod, K., Stanley, D., Yap, Y.E., Knight, J., McKenzie, C., Kranich, J., Oliveira, A., Rossello, F., Krishnamurthy, B., Nefzger, C., Macia, L., Thorburn, A., Baxter, A., Morahan, G., Wong, L., Polo, J.M., Moore, R.J., Lockett, T., Clarke, J., Topping, D., Harrison, L., and Mackay, C.R. (2017) "Gut microbial metabolites limit autoimmune T cell frequencies and protect against type 1 diabetes", Nature Immunology, doi:10.1038/ni.3713, (2017).

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

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

·         Batacan, R., Fenning, A., Dalbo, V.J., Scanlan, A.T., Duncan1,M., Moore, R.J., and Stanley, D. A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats. Journal of Applied Microbiology; DOI: 10.1111/jam.13442 (2017)

·         Stanley, D., L. J. Mason, K. E. Mackin, Y. N. Srikhanta, D. Lyras, M. D. Prakash, K. Nurgali, A. Venegas, M. D. Hill, R. J. Moore and C. H. Wong. Translocation and dissemination of commensal bacteria in post-stroke infection. Nature Medicine 22(11): 1277-1284 (2016).

·         Stanley D., Hughes R.J., Geier M.S., and Moore R.J. 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(187) (2016).

·         Wilkinson N., Hughes R.J., Aspden W.J., Chapman J., Moore R.J and Stanley D.  The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica. Applied Microbiology and Biotechnology 15:51 1/13 1:9 (2016).

·         Crisol-Martinez, E., Moreno-Moyano, L. T., Wilkinson, N., Prasai, T., Brown, P. H., Moore, R. J. and Stanley, D. A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica).  PeerJ 4: e2002 (2016)

·         Crisol-Martinez, E., Moreno-Moyano, L. T., Wormington, K. R., Brown P. H., and Stanley D. 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): e0150159 (2016).

·         Gangadoo, S., Stanley, D., Hughes, B., Moore R. J. and Chapman J. (2016). Nanoparticles in feed: progress and prospects in poultry research. (2016) Trends in Food Science & Technology 58: 115-126.

·         Moore, R. J. and Stanley, D. Experimental design considerations in microbiota/inflammation studies. Clinical and Translational Immunology 5 (7), e92 (2016).

·         Prasai, T. P., Walsh, K. B., Bhattarai, S. P., Midmore, D. J., Van, T. T., Moore, R. J. and Stanley, D. Biochar, Bentonite and Zeolite Supplemented Feeding of Layer Chickens Alters Intestinal Microbiota and Reduces Campylobacter Load. PLoS One 11(4): e0154061. (2016).

·         Reynolds, A. C., Paterson, J. L., Ferguson, S. A., Stanley, D., Wright, D., K. P., Jr. and Dawson D. 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. DOI: 10.1016/j.smrv.2016.06.009 (2016).

·          Thorburn, A.N., McKenzie, C.I., Shen, S., Stanley, D., Macia, L., Mason, L.J., Roberts, L.K., Wong, C.H.Y., Shim, R., Robert, R., Chevalier, N., Tan, J.K., Mariño, E., Moore, R.J., Wong, L., McConville, M.J., Tull, D.L., Wood, L.G., Murphy, V.A., Mattes, J., Gibson, P.R. & Mackay, C.R.   Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nature Communications -6:7320 (2015).

·         Macia L., Vieira1 A.T., Tan .J., Stanley D., Canesso M.C.C., Luong S., Maruya M., Hijikata A., Binge L., Thorburn A., Maslowski K., Chevallier N., Mariño E., Robert R., Offermanns S., Teixeira M., da Silva Barcelos B., Moore R., Fagarasan S. and Mackay C.R. Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome Nature Communicatios 6:6734 (2015).

·         Stanley D., Geier M.S., Hughes R.J., and Moore R.J.  Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences BMC Microbiology 15:51  (2015).

·         Stanley D., Wu S., Rodgers N., Swick R.A., and Moore R.J.  Differential responses of cecal microbiota to fishmeal, Eimeria and Clostridium perfringens in a necrotic enteritis challenge model in chickens. Plos One, 9, 8, e104739 (2014).

·         Wu, S.B., Stanley, D., Rodgers, N., Swick, R.A. & Moore, R.J. Two necrotic enteritis predisposing factors, dietary fishmeal and Eimeria infection, induce large changes in the caecal microbiota of broiler chickens. Veterinary Microbiology 169, 188-197 (2014).

·         Stanley, D., Hughes, R.J. & Moore, R.J. Microbiota of the chicken gastrointestinal tract: Influence on health, productivity and disease. Applied Microbiology and Biotechnology 98(10):4301-10. (2014).

·         Stanley, D., Watson-Haigh, N.S., Cowled, C.J. and Moore, R.J. Genetic architecture of gene expression in the chicken. BMC Genomics 14, 13 (2013).

·         Stanley, D., Geier, M.S., Hughes, R.J., Denman, S.E. and Moore, R.J. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS One 8, e84290 (2013).

·         Stanley, D., Denman S.E., Hughes R.J., Geier M.S., Crowley T.M., Chen H., Haring V.R., and Moore R.J. Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed. Veterinary Microbiology 164, 85-92 (2013).

·         Gillespie, M.J., Crowley T.M., Haring V.R., Wilson S., Harper J.A., Payne J.S., Stanley D., Green D., Monaghan P., Donald J., Nicholas K.R. and Moore R.J. Transcriptome analysis of pigeon milk production - role of cornification and triglyceride synthesis genes. BMC Genomics 14, 169 (2013).

·         Konsak, B.M., Stanley, D., Haring V.R., Geier M.S., Hughes R.J., Howarth G.S., Crowley T.M., and Moore R.J. Identification of differential duodenal gene expression levels and microbiota abundance correlated with differences in energy utilisation in chickens. Animal Production Science 53, 12:19 (2013).

·         Stanley, D., Keyburn, A.L., Denman, S.E. & Moore, R.J. Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. Veterinary Microbiology 159, 155-162 (2012).

·         Stanley, D., Denman S.E., Hughes R.J., Geier M.S., Crowley T.M., Chen. H., Haring V.R., and Moore R.J. Intestinal microbiota associated with differential feed conversion efficiency in chickens. Applied Microbiology and Biotechnology 96, 1361-1369 (2012).

·         Gillespie, M.J., Stanley, D., Chen, H., Donald, J.A., Nicholas, K.R., Moore, R.J., and Crowley, T.M. Functional similarities between pigeon 'milk' and mammalian milk: induction of immune gene expression and modification of the microbiota. PLoS One 7, e48363 (2012).

·         Stanley, D., Fraser, S., Stanley, G.A. & Chambers, P.J. Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 87, 1447-1454 (2010).

·         Stanley, D., Fraser, S., Chambers, P.J., Rogers, P. & Stanley, G.A. Generation and characterisation of stable ethanol-tolerant mutants of Saccharomyces cerevisiae. Journal of Industrial Microbiology and Biotechnology 37, 139-149 (2010).

·         Stanley, D., Chambers, P.J., Stanley, G.A., Borneman, A. & Fraser, S. Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 88, 231-239 (2010).

·         Stanley, D., Bandara, A., Fraser, S., Chambers, P.J. & Stanley, G.A. The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae. Journal of Applied Microbiology 109, 13-24 (2010).

Conference Proceedings

 ·         Bauer, B.W., Bajagai, Y.S., Alsemgeest, J., Willson, N.L., Van, T.T.H., Moore, R.J., and  Stanley, D. Functional analysis of changes in gut microbiota genetic potential in broilers supplemented with 2% oregano. Australian Poultry Science Symposium (Sydney 2020).

·          Bajagai, Y.S., Bauer, B.W., Alsemgeest, J., Willson, N.L., Van, T.T.H., Moore, R.J., and  Stanley, D. Effects of supplemented oregano on the maturation of broiler microbiota. Australian Poultry Science Symposium (Sydeny 2020).

·         Stanley, D., Bajagai, Y.S., Van, T.T.H., and Moore, R.J. The importance of gut microbiome in layer chickens with particular emphasis on the field situation., Australian Poultry Science Symposium, (2019)

·         Moore, R.J., Stanley, D., Konsak B.M., Haring V.R., Hughe s R.J., Geier M.S., Crowley T.M. Correlations between variable broiler performance, gene expression and microflora in the gut.  Australian Poultry Science Symposium 22, 9-16 (2011).

·         Stanley, D., Geier, M.S., Hughes, R.J. & Moore, R.J. The role of gastrointestinal tract microbiota in chicken productivity. Australian Poultry Science Symposium 23, 262-265 (2012).

·         Marino, E., Richards, J., McLeod, K., Yap, Y., Stanley, D., Mackay, C. Gut microbial metabolites regulate autoimmune T cell responses and protect against type 1 diabetes. European Journal Of Immunology, 46, 538-538 (2016).

·         McLeod, K., Stanley, D., Richards, J., Moore, R., Mackay, C., Marino, E. Changes of microbiota, and their metabolites, in in the development of T1D. European Journal Of Immunology, 46, 290-290 (2016).

·         Wong, C., Stanley, D., Mackin, K., Lyras, D., Prakash, M., Nurgali, K., Hill, M., Moore, R. Translocation and dissemination of commensal bacteria as a source of infection after stroke. European Journal Of Immunology, 46, 704-704 (2016).

·         Jordan, M.A., Gresle, M., Laverick, L., Stanley, D., Smith, L.,Spelman, T., Field, J., Johnson, L., Butzkueven, H., Baxter, A.G. Unravelling the multiple sclerosis complex disease trait through an immune transcriptional regulatory network approach. European Journal Of Immunology, 46, 292-293 (2016).

·         Jordan, M.A., Stanley, D., Moore, R., Baxter, A.G. The effect of microbiome/Toll-like receptor interactions on susceptibility to type 1 diabetes, European Journal Of Immunology, 46, 921-921 (2016).

·         Moore, R.J., Stanley, D., and Hughes, R.J. Microbiota studies in poultry: the black hole of complexity! Australian Poultry Science Symposium 28, 8-11 (2017).

Most Recent Conference Presentations

·         Stanley, D., Bajagai, Y.S., Van, T.T.H., and Moore, R.J. The importance of gut microbiome in layer chickens with particular emphasis on the field situation., Invited presentation, Australian Poultry Science Symposium, APSS, Sydney, 2019.

·         Stanley, D. Gut flora of laying hens. Invited presentation, Australian Eggs Industry Forum. Adelaide, 2019.

·         Stanley, D. Alternatives to antibiotic growth promoters and implications to poultry intestinal health. Invited presentation, Australian Veterinary Poultry Association , AVPA, Adeliade, 2019.

·         Stanley, D. The importance of gut microbota. Invited presentation, A Symposium: Reimagining Human Health: The Microbiome, Farming, and Medicine. Bard College, New York USA (2019)

·         Stanley, D. Microbial manipulation through nutrition. Invited presentation, Nutrition Society Australia, Annual Society Meeting. Newcastle, 2019.

·         Stanley, D. Alternatives to antibiotic growth promoters and poultry intestinal health. Invited presentation, The Asia nutrition forum, Tokyo, Japan, 2019

·         Stanley, D. Alternatives to antibiotic growth promoters and poultry intestinal health. Invited presentation, The Asia nutrition forum, Seoul. South Korea, 2019

·         Stanley, D. Alternatives to antibiotic growth promoters and poultry intestinal health. Invited presentation, The Asia nutrition forum, Wuxi, China, 2019

·         Stanley, D Gut microflora in layers. Invited presentation, Australian Veterinary Poultry Association , AVPA, Sydney, 2018.

·         Stanley, D., Morre R.J., and Wong C. Immune suppression after stroke: Evidence of bacterial translocation. Invited presentation, Microbial Food and Feed Ingredients (MiFFI), Copenhagen, 2018.

·         Moore, R.J., Stanley, D., and Hughes, R.J. Microbiota studies in poultry: the black hole of complexity! Australian Poultry Science Symposium, APSS, Sydney, 2017.

·         Stanley, D., Translocation and dissemination of intestinal bacteria after stroke: the role of gut mucosal microbiota and Akkermansia muciniphila.  Theo Murphy Australian Frontiers of Science. Invited presentation, Adelaide, Australia, 2016.

·         Stanley, D., Short Chain Fatty Acids can Remodel Intestinal Microbiota to Protect from Type 1 Diabetes, Invited speaker, 2nd Microbiome R&D and Business Collaboration Congress, Kuala Lumpur, 2016

·         Marino, E., Richards, J., McLeod, K., Yap, Y., Stanley, D., Mackay, C. 2016. Gut microbial metabolites regulate autoimmune T cell responses and protect against type 1 diabetes. Invited presentation, International Congress of Immunology Melbourne, Australia, 2016

·         McLeod, K., Stanley, D., Richards, J., Yap, Y., Moore, R., Mackay, C., Marino, E. Changes of microbiota, and their metabolites, in in the development of T1D. International Congress of Immunology, 2016, Melbourne, Australia, 2016.

·         Wong, C., Stanley, D., Mackin, K., Lyras, D., Prakash, M., Nurgali, K., Hill, M., Moore, R. 2016. Translocation and dissemination of commensal bacteria as a source of infection after stroke. International Congress of Immunology, 2016, Melbourne, Australia, 2016.

·         Jordan, M.A., Stanley, D., Moore, R., Crowley, B., Baxter, A.G. The effect of microbiome/Toll-like receptor interactions on susceptibility to type 1 diabetes, International Congress of Immunology, 2016, Melbourne, Australia, 2016.

·         Jordan, M.A., Gresle, M., Laverick, L., Stanley, D., Smith, L.,Spelman, T., Field, J., Johnson, L., Butzkueven, H., Baxter, A.G. Unravelling the multiple sclerosis complex disease trait through an immune transcriptional regulatory network approach, International Congress of Immunology, Melbourne, Australia, 2016.