2025

• Liu, R., Senior, A., Bao, Z., Koay, Y., Holmes, A., O'Sullivan, J. (2025). Multi-organ multi-omic and gut microbiome signatures of fat and sucrose dietary oversupply in cardiometabolic disease. iScience, 28(4), 111887. [More Information]

2024

• Ribeiro, R., Senior, A., Simpson, S., Tan, J., Raubenheimer, D., Le Couteur, D., Macia, L., Holmes, A., Eberhard, J., O'Sullivan, J., Koay, Y., Kanjrawi, A., Yang, J., Kim, T., Gosby, A. (2024). Rapid benefits in older age from transition to whole food diet regardless of protein source or fat to carbohydrate ratio: Arandomised control trial. Aging Cell, 23(11), e14276. [More Information]

2023

• Grech, A., Kizirian, N., Lal, R., Zankl, A., Birkner, K., Nasir, J., Muirhead, R., Sau-Harvey, R., Mosalman Haghighi, M., Collins, C., Holmes, A., Skilton, M., Simpson, S., Gordon, A. (2023). Cohort profile: the BABY1000 pilot prospective longitudinal birth cohort study based in Sydney, Australia. BMJ Open, 13(6), e068275. [More Information]
• Koemel, N., Senior, A., Benmarhnia, T., Holmes, A., Okada, M., Oulhote, Y., Parker, H., Shah, S., Simpson, S., Raubenheimer, D., Gill, T., Skilton, M., et al (2023). Diet Quality, Microbial Lignan Metabolites, and Cardiometabolic Health among US Adults. Nutrients, 15(6). [More Information]
• Thahir, A., Li, M., Holmes, A., Gordon, A. (2023). Exploring Factors Associated with Stunting in 6-Month-Old Children: A Population-Based Cohort Study in Sulawesi, Indonesia. Nutrients, 15(15). [More Information]
• Thahir, A., Nasir, S., Holmes, A., Li, M., Gordon, A. (2023). Mothers’ and Midwives’ Experiences of Maternal and Child Health Services during the COVID-19 Pandemic in Banggai, Indonesia: A Qualitative Study. International Journal of Community Based Nursing and Midwifery, 11(2), 96-109. [More Information]
• Xu, X., Lubomski, M., Holmes, A., Sue, C., Davis, R., Mueller, S., Yang, J. (2023). NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions. Microbiome, 11(1). [More Information]

2022

• Simpson, R., Shanahan, E., Batten, M., Reijers, I., Read, M., Da Silva, I., Versluis, J., Ribeiro, R., Angelatos, A., Tan, J., Adhikari, C., Menzies, A., Saw, R., Gonzalez, M., Shannon, K., Spillane, A., Velickovic, R., Macia, L., Holmes, A., Wilmott, J., Scolyer, R., Long, G., et al (2022). Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome. Nature Medicine, 28(11), 2344-2352. [More Information]
• Febinia, C., Malik, S., Djuwita, R., Weta, I., Wihandani, D., Maulida, R., Sudoyo, H., Holmes, A. (2022). Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization. Microbial Ecology, 83(3), 798-810. [More Information]
• Molina Ortiz, J., Read, M., McClure, D., Holmes, A., Dehghani, F., Shanahan, E. (2022). High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure. Gut Microbes, 14(1). [More Information]
• Luk, A., Mitchell, L., Koay, Y., O'Sullivan, J., O'Connor, H., Hackett, D., Holmes, A. (2022). Intersection of Diet and Exercise with the Gut Microbiome and Circulating Metabolites in Male Bodybuilders: A Pilot Study. Metabolites, 12(10). [More Information]
• Lubomski, M., Xu, X., Holmes, A., Mueller, S., Yang, J., Davis, R., Sue, C. (2022). Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease. Frontiers in Aging Neuroscience, 14, 881872-1-881872-16. [More Information]
• Cui, Z., Holmes, A., Zhang, W., Hu, D., Shao, Q., Wang, Z., Jiqi, L., Raubenheimer, D. (2022). Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items. Integrative Zoology, 17(6), 1147-1161. [More Information]
• Hu, D., Fuller, N., Caterson, I., Holmes, A., Reeves, P. (2022). Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Reports, 38(2), 110239. [More Information]
• Lubomski, M., Xu, X., Holmes, A., Mueller, S., Yang, J., Davis, R., Sue, C. (2022). The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies. Frontiers in Aging Neuroscience, 14(May 17 2022), 875261-1-875261-24. [More Information]
• Lubomski, M., Xu, X., Holmes, A., Yang, J., Sue, C., Davis, R. (2022). The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease. Journal of Neurology, 269(2), 780-795. [More Information]

2021

• Molina Ortiz, J., McClure, D., Shanahan, E., Dehghani, F., Holmes, A., Read, M. (2021). Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes, 13(1), 1965698. [More Information]
• Wali, J., Milner, A., Luk, A., Pulpitel, T., Dodgson, T., Facey, H., Wahl, D., Kebede, M., Senior, A., Sullivan, M., Brandon, A., Yau, B., Lockwood, G., Koay, Y., Ribeiro, R., Solon-Biet, S., Bell-Anderson, K., O'Sullivan, J., Macia, L., Cooney, G., Cogger, V., Holmes, A., Raubenheimer, D., Le Couteur, D., Simpson, S., et al (2021). Impact of dietary carbohydrate type and protein–carbohydrate interaction on metabolic health. Nature Metabolism, 3(6), 810-828. [More Information]
• Grech, A., Collins, C., Holmes, A., Lal, R., Duncanson, K., Taylor, R., Gordon, A. (2021). Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis. Gut Microbes, 13(1), 1-30. [More Information]
• Koay, Y., Chen, Y., Wali, J., Luk, A., Li, M., Doma, H., Reimark, R., Zaldivia, M., Habtom, H., Franks, A., Fusco-Allison, G., Yang, J., Holmes, A., Simpson, S., O'Sullivan, J., et al (2021). Plasma levels of trimethylamine-N-oxide can be increased with 'healthy' and 'unhealthy' diets and do not correlate with the extent of atherosclerosis but with plaque instability. Cardiovascular Research, 117(2), 435-449. [More Information]
• Gamage, H., Venturini, C., Tetu, S., Kabir, M., Nayyar, V., Ginn, A., Roychoudhry, B., Thomas, L., Brown, M., Holmes, A., Partridge, S., Seppelt, I., Iredell, J., et al (2021). Third generation cephalosporins and piperacillin/tazobactam have distinct impacts on the microbiota of critically ill patients. Scientific Reports, 11(1), 7252. [More Information]

2020

• Zoll, J., Read, M., Heywood, S., Estevez, E., Marshall, J., Kammoun, H., Allen, T., Holmes, A., Febbraio, M., Henstridge, D. (2020). Fecal microbiota transplantation from high caloric-fed donors alters glucose metabolism in recipient mice, independently of adiposity or exercise status. American Journal of Physiology - Endocrinology and Metabolism, 319(1), E203-E216. [More Information]
• Lubomski, M., Tan, A., Lim, S., Holmes, A., Davis, R., Sue, C. (2020). Parkinson's disease and the gastrointestinal microbiome. Journal of Neurology, 267(9), 2507-2523. [More Information]

2019

• Marques, F., Jama, H., Tsyganov, K., Gill, P., Rhys-Jones, D., Muralitharan, R., Muir, J., Holmes, A., Mackay, C. (2019). Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension. Hypertension, 74(6), 1279-1293. [More Information]
• Koay, Y., Wali, J., Luk, A., Macia, L., Cogger, V., Pulpitel, T., Wahl, D., Solon-Biet, S., Holmes, A., Simpson, S., O'Sullivan, J. (2019). Ingestion of resistant starch by mice markedly increases microbiome-derived metabolites. The FASEB Journal, 33(7), 8033-8042. [More Information]

2018

• McCarl, V., Somerville, M., Ly, M., Henry, R., Liew, E., Wilson, N., Holmes, A., Coleman, N. (2018). Heterologous expression of Mycobacterium alkene monooxygenases in Gram-positive and Gram-negative bacterial hosts. Applied and Environmental Microbiology, 84(15), 1-16. [More Information]

2017

• Holmes, A., Chew, Y., Colakoglu, F., Cliff, J., Klaassens, E., Read, M., Solon-Biet, S., McMahon, A., Cogger, V., Ruohonen, K., Raubenheimer, D., Le Couteur, D., Simpson, S. (2017). Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints. Cell Metabolism, 25(1), 140-151. [More Information]
• Read, M., Holmes, A. (2017). Towards an integrative understanding of diet-host-gut microbiome interactions. Frontiers in Immunology, 8, 1-9. [More Information]

2016

• Cogger, V., Mohamad, M., Solon-Biet, S., Senior, A., Warren, A., O'Reilly, J., Tung, B., Svistounov, D., McMahon, A., Fraser, R., Raubenheimer, D., Holmes, A., Simpson, S., Le Couteur, D. (2016). Dietary Macronutrients and the Aging Liver Sinusoidal Endothelial Cell. American Journal of Physiology - Heart and Circulatory Physiology, 310(9), H1064-H1070. [More Information]

2015

• Wong, A., Holmes, A., Ponton, F., Lihoreau, M., Wilson, K., Raubenheimer, D., Simpson, S. (2015). Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior. Frontiers in Microbiology, 6, 1-8. [More Information]
• Lam, Y., Ha, C., Hoffmann, J., Oscarsson, J., Dinudom, A., Mather, T., Cook, D., Hunt, N., Caterson, I., Holmes, A., Storlien, L. (2015). Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice. Obesity, 23(7), 1429-1439. [More Information]
• Gofton, A., Oskam, C., Lo, N., Beninati, T., Wei, G., McCarl, V., Murray, D., Paparini, A., Greay, T., Holmes, A., et al (2015). Inhibition of the endosymbiont "Candidatus Midichloria mitochondrii" during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia. Parasites and Vectors, 8(1), 1-11. [More Information]
• Ponton, F., Wilson, K., Holmes, A., Raubenheimer, D., Robinson, K., Simpson, S. (2015). Macronutrients mediate the functional relationship between Drosophila and Wolbachia. Proceedings of the Royal Society B: Biological Sciences, 282, 1-9. [More Information]
• Read, M., Holmes, A., Hartill-Law, M., Solon-Biet, S., Raubenheimer, D., Simpson, S. (2015). Simulating the Influence of Diet on the Intestinal Microbiome Composition. The 13th European Conference on Artificial Life (ECAL 2015), York, UK: The MIT Press. [More Information]
• Le Couteur, D., Tay, S., Solon-Biet, S., Bertolino, P., McMahon, A., Cogger, V., Colakoglu, F., Warren, A., Holmes, A., Pichaud, N., Raubenheimer, D., Simpson, S., et al (2015). The influence of macronutrients on splanchnic and hepatic lymphocytes in aging mice. Journals of Gerontology. Series A: Biological Sciences and Medical Sciences, 70(12), 1499-1507. [More Information]

2014

• Coleman, N., Richardson, J., Wilson, N., Holmes, A. (2014). Insertion sequence ISPst4 activates pUC plasmid replication in Pseudomonas stutzeri. FEMS Microbiology Letters, 356(2), 242-249. [More Information]
• Ha, C., Lam, Y., Holmes, A. (2014). Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health. World Journal of Gastroenterology, 20(44), 16498-16517. [More Information]
• Liew, E., Tong, D., Coleman, N., Holmes, A. (2014). Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity. Microbiology, 160(Pt 6), 1267-1277. [More Information]
• Chew, Y., Holmes, A., Cliff, J. (2014). Visualization of Metabolic Properties of Bacterial Cells Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS). In Ian T. Paulsen and Andrew J. Holmes (Eds.), Environmental Microbiology: Methods and Protocols, (pp. 133-146). New York: Humana Press. [More Information]

2013

• Islam, A., Labbate, M., Djordjevic, S., Alam, M., Darling, A., Melvold, J., Holmes, A., Johura, F., Cravioto, A., Charles, I., et al (2013). Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic. Open Biology, 3(2), 1-12. [More Information]
• Ponton, F., Wilson, K., Holmes, A., Cotter, S., Raubenheimer, D., Simpson, S. (2013). Integrating nutrition and immunology: A new frontier. Journal of Insect Physiology, 59(2), 130-137. [More Information]
• Tetu, S., Breakwell, K., Elbourne, L., Holmes, A., Gillings, M., Paulsen, I. (2013). Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism. The ISME Journal, 7(6), 1227-1236. [More Information]
• Cheung, S., McCarl, V., Holmes, A., Coleman, N., Rutledge, P. (2013). Substrate range and enantioselectivity of epoxidation reactions mediated by the ethene-oxidising Mycobacterium strain NBB4. Applied Microbiology and Biotechnology, 97(3), 1131-1140. [More Information]

2012

• Fuller, N., Lau, N., Denyer, G., Simpson, A., Gerofi, J., Wu, M., Holmes, A., Markovic, T., Kang, J., Caterson, I. (2012). A 12-week, randomised, controlled trial to examine the acceptability of the Korean diet and its effectiveness on weight and metabolic parameters in an Australian overweight and obese population. Obesity Research & Clinical Practice, 6(1), e71-e83. [More Information]
• Coleman, N., Le, N., Ly, M., Ogawa, H., McCarl, V., Wilson, N., Holmes, A. (2012). Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily. The ISME Journal, 6(1), 171-182. [More Information]
• Lam, Y., Ha, C., Campbell, C., Mitchell, A., Dinudom, A., Oscarsson, J., Cook, D., Hunt, N., Caterson, I., Holmes, A., Storlien, L. (2012). Increased Gut Permeability and Microbiota Change Associate with Mesenteric Fat Inflammation and Metabolic Dysfunction in Diet-induced Obese Mice. PloS One, 7(3), 1-10. [More Information]
• Lam, Y., Ha, C., Holmes, A. (2012). Insulin resistance pathogenesis in visceral fat and gut organisms. In Louise A. Baur, Stephen M. Twigg, Roger S.Magnusson (Eds.), A Modern Epidemic: Expert Perspectives on Obesity and Diabetes, (pp. 46-69). Sydney, Australia: Sydney University Press. [More Information]

2011

• Lam, Y., Mitchell, A., Holmes, A., Denyer, G., Gummesson, A., Caterson, I., Hunt, N., Storlien, L. (2011). Role of the Gut in Visceral Fat Inflammation and Metabolic Disorders. Obesity, 19(11), 2113-2120. [More Information]
• Coleman, N., Yau, S., Wilson, N., Nolan, L., Migocki, M., Ly, M., Crossett, B., Holmes, A. (2011). Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. Environmental Microbiology Reports, 3(3), 297-307. [More Information]

2010

• Thompson, C., Hofer, M., Campbell, I., Holmes, A. (2010). Community Dynamics in the Mouse Gut Microbiota: A Possible Role for IRF9-Regulated Genes in Community Homeostasis. PloS One, 5(4), e10335-1-e10335-9. [More Information]

2009

• Thompson, C., Holmes, A. (2009). A window of environmental dependence is evident in multiple phylogenetically distinct subgroups in the faecal community of piglets. FEMS Microbiology Letters, 290(1), 91-97. [More Information]
• Chew, Y., Holmes, A. (2009). Suppression subtractive hybridisation allows selective sampling of metagenomic subsets of interest. Journal of Microbiological Methods, 78(2), 136-143. [More Information]
• Holmes, A. (2009). The Diversity of Soluble Di-iron Monooxygenases with Bioremediation Applications. In Ajay Singh, Ramesh C. Kuhad, Owen P. Ward (Eds.), Advances in Applied Bioremediation, Soil Biology 17, (pp. 91-102). Germany: Springer. [More Information]

2008

• Tetu, S., Holmes, A. (2008). A Family Of Insertion Sequences That Impacts Integrons By Specific Targeting Of Gene Cassette Recombination Sites, The IS1111-attc Group. Journal of Bacteriology, 190(11), 4959-4970. [More Information]
• Holmes, A., Coleman, N. (2008). Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts. Antonie van Leeuwenhoek: international journal of general and molecular microbiology, 94(1), 75-84. [More Information]
• Gillings, M., Boucher, Y., Labbate, M., Holmes, A., Krishnan, S., Holley, M., Stokes, H. (2008). The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance. Journal of Bacteriology, 190(14), 5095-5100. [More Information]
• Thompson, C., Wang, B., Holmes, A. (2008). The immediate environment during postnatal development has long-term impact on gut community structure in pigs. The ISME Journal, 2, 739-748. [More Information]

2007

• Longford, S., Tujula, N., Crocetti, G., Holmes, A., Holmstrom, C., Kjelleberg, S., Steinberg, P., Taylor, M. (2007). Comparisons of diversity of bacterial communities associated with three sessile marine eukaryotes. Aquatic Microbial Ecology, 48(3), 217-229. [More Information]
• Hall, R., Holmes, A., Roy, P., Stokes, H. (2007). What are superintegrons? Nature Reviews Microbiology, 5 (Feb 2007) doi:10.1038/nrmicro1462-c1(2), 1-2. [More Information]

2006

• Coleman, N., Le, N., Holmes, A. (2006). Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments. Environmental Microbiology, 8(7), 1228-1239. [More Information]

2005

• Robinson, A., Wu, P., Harrop, S., Schaeffer, P., Doszta´nyi, Z., Gillings, M., Holmes, A., Nevalainen, H., Stokes, H., Otting, G., et al (2005). Integron-associated Mobile Gene Cassettes Code for Folded Proteins: The Structure of Bal32a, a New Member of the Adaptable α + β Barrel Family. Journal of Molecular Biology, 346, 1229-1241. [More Information]
• Gillings, M., Holley, M., Stokes, H., Holmes, A. (2005). Integrons in Xanthomonas: a source of species genome diversity. Proceedings of the National Academy of Sciences of the United States of America, 102(12), 4419-4424. [More Information]
• Coleman, N., Holmes, A. (2005). The native Pseudomonas stutzeri strain Q chromosomal integron can capture and express cassette-associated genes. Microbiology, 151(6), 1853-1864. [More Information]

2004

• Coleman, N., Tetu, S., Wilson, N., Holmes, A. (2004). An unusual integron in Treponema denticola. Microbiology, 150(11), 3524-3526. [More Information]
• Holmes, A. (2004). Analysis Of Microbial Communities In The Plant Environment. In Michael Gillings, Andrew Holmes (Eds.), Plant Microbiology, (pp. 243-268). United States: Taylor and Francis.
• Oliver, I., Holmes, A., Dangerfield, M., Gillings, M., Pik, A., Britton, D., Holley, M., Montgomery, M., Raison, M., Logan, V., et al (2004). Land systems as surrogates for biodiversity in conservation planning. Ecological Applications, 14(2), 485-503. [More Information]
• Michael, C., Gillings, M., Holmes, A., Hughes, L., Andrew, N., Holley, M., Stokes, H. (2004). Mobile Gene Cassettes: A Fundamental Resource For Bacterial Evolution. The American Naturalist, 164(1), 1-12. [More Information]
• Nield, B., Willows, R., Torda, A., Gillings, M., Holmes, A., Nevalainen, H., Stokes, H., Mabbutt, B. (2004). New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and an RNA-methyltransferase. Protein Science, 13, 1651-1659. [More Information]
• Green, J., Holmes, A., Westoby, M., Oliver, I., Briscoe, D., Dangerfield, M., Gillings, M., Beattie, A. (2004). Spatial Scaling Of Microbial Eukaryote Diversity. Nature, 432(7018), 747-750. [More Information]

2003

• Dangerfield, M., Pik, A., Britton, D., Holmes, A., Gillings, M., Oliver, I., Briscoe, D., Beattie, A. (2003). Patterns of invertebrate biodiversity across a natural edge. Austral Ecology, 28, 227-236. [More Information]
• Holmes, A., Holley, M., Mahon, A., Nield, B., Gillings, M., Stokes, H. (2003). Recombination Activity of a Distinctive Integron-Gene Cassette System Associated with Pseudomonas stutzeri Populations in Soil. Journal of Bacteriology, 185(3), 918-928. [More Information]
• Holmes, A., Gillings, M., Nield, B., Mabbutt, B., Nevalainen, H., Stokes, H. (2003). The gene cassette metagenome is a basic resource for bacterial genome evolution. Environmental Microbiology, 5(5), 383-394. [More Information]