Associate Professor Andrew Holmes

Associate Professor

G08 - Biochemistry and Microbiology Building
The University of Sydney

Telephone 9351 2530

Website Room 4113, D17 - The Hub, Charles Perkins Centre

Research interests

Microorganisms are the most abundant and the most diverse group of organisms on Earth. They are also the most poorly known. As such the microbiota represent the largest unexplored biological resource on Earth. Andrew's research interests focus on three distinct aspects of microbial diversity:

1. The role of gut microbial diversity in human health; 2. Exploring microbial diversity for new biological resources; 3. The underlying evolutionary origins of microbial diversity

Selected grants

2013

  • IMELDA: Indonesian Model for Epidemic Lifestyle Disease Associations; Holmes A, Simpson S, Sudoyo H, Malik S, Suastika K; DVC International/IPDF Grant.
  • Ecological effects of antibiotics; Iredell J, Paulsen I, Partridge S, Seppelt I, Holmes A; National Health and Medical Research Council (NHMRC)/Project Grants.
  • Integrating nutritional immunology; Simpson S, Holmes A, Ponton F, Wilson K; Australian Research Council (ARC)/Discovery Projects (DP).

2012

  • Sydney Infectious Diseases and Biosecurity Network (SIBRN); Sorrell T, Bennett B, Booy R, Crawford J, Dwyer D, Gilbert G, Giles F, Holmes A, Hossain L, Iredell J, Jones C, Kesson A, Kerridge I, Marais B, Simpson S, Sintchenko V, Ward M, Werder O, Britton W, Dhand N, Hunter C, Kamradt-Scott A, Mor S, Salkeld G, Shaw T, Smith F, Wood N; DVC Research/Research Network Scheme (SyReNS).
  • Determinants of substrate preferences and environmental applications of the copper membrane monooxygenases; Holmes A, Coleman N, Bodrossy L, Abell G; Australian Research Council (ARC)/Discovery Projects (DP).
  • Identification of microbiome control of weight loss during dietary intervention in obesity; Holmes A, Paulsen I, Caterson I, Reeves P; National Health and Medical Research Council (NHMRC)/Project Grants.

2009

  • The ongoing Evolution of Class 1 Integrons and the Recruitment of New Resistance and Virtulence Genes into Pathogens; Gillings M, Stokes H, Holmes A, Iredell J, Partridge S; National Health and Medical Research Council (NHMRC)/Project Grants.

2008

  • DNA-stable isotope probing, gene mining and expression of soluble; Holmes A, Murrell J, Murrell J; DVC Research/International Visiting Research Fellowship (IVRF).
  • Bacterial monooxygenases as new biocatalysts; Holmes A, Coleman N, Guss M; Australian Research Council (ARC)/Discovery Projects (DP).

2007

  • An integron model for evolution of genetic networks in bacteria; Holmes A; University of Sydney/Bridging Support.

2005

  • Exploring And Harnessing Mobile Dna: Integrons And Gene Cassettes In Natural Populations Of Bacteria; Holmes A, Stokes H; Australian Research Council (ARC)/Discovery Projects (DP).
  • Recovery and characterization of mono-oxygenases for biocatalysis and bioremediation through development of Novel DNA and protein based technology; Coleman N, Holmes A; Australian Research Council (ARC)/Discovery Projects (DP).

2004

  • Intergrating morphological and molecular approaches to describe the taxonomy and phylogeny of symbiotic dinoflagellates (zooxanthellae) from the Great Barrier Reef - 204-53; Carter D, Salih A, Holmes A, Paul R; Environment Australia - (ABRS)/Research Grant.

2003

  • Investigation of the role of integron-mediated gene transfer in metabolic pathway evolution; Holmes A; DVC Research/Research and Development Scheme: Newly Appointed Staff (NAS).

Selected publications

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Book Chapters

  • 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.
  • 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.
  • 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.
  • 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.

Journals

  • Coleman, N., Harris, 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]
  • 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]
  • 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]
  • 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., 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]
  • 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]
  • 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]
  • 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]
  • 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(DOI 10.1007/s10482-008-9227-1), 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]
  • 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.
  • 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.
  • 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]
  • 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 (PNAS) 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]
  • Coleman, N., Tetu, S., Wilson, N., Holmes, A. (2004). An unusual integron in Treponema denticola. Microbiology, 150(11), 3524-3526.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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: a journal of ecology in the Southern Hemisphere, 28, 227-236.
  • 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.
  • 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.

2014

  • Coleman, N., Harris, 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]
  • 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.

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.

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]
  • 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.

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(DOI 10.1007/s10482-008-9227-1), 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.
  • 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.

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 (PNAS) 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.
  • 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.
  • 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.
  • 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.
  • 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.

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: a journal of ecology in the Southern Hemisphere, 28, 227-236.
  • 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.
  • 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.

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