Overview
Background
From a PhD in 1994 at the University of Queensland, Phil Hugenholtz developed a career in microbiology and genomics in the USA and in Australia. Phil’s last position in the USA was as Staff Scientist (2004-2010) at the Department of Energy, Joint Genome Institute. In late 2010 Phil returned home to establish the Australian Centre for Ecogenomics (ACE) at the University of Queensland. He has contributed to the field of culture-independent analysis of microorganisms through the discovery and characterisation of numerous previously unrecognised major bacterial and archaeal lineages each with greater evolutionary divergence than animals and plants combined. Phil has played important roles in the development and application of metagenomics, the genome-based characterisation of microbiomes, which has revolutionised our understanding of microbial ecology and evolution. This has resulted in several discoveries in environmental and clinical microbiology sometimes overturning decades of misdirected culture-based studies. He has applied his interest in comparative genomics and metagenomics to develop a systematic genome-based taxonomy for bacteria and archaea, which is facilitating scientific communication and endeavour. Phil has published over four hundred papers in molecular microbial ecology including ten Science & ten Nature papers.
As Professorial Research Fellow at UQ and Director of ACE, Phil has affiliate appointments with the Institute for Molecular Bioscience and the UQ Diamantina Institute, which supports collaborative research at ACE. Currently, Phil’s research interests include the microbial ecology and evolution of environmental and host-associated ecosystems including mining bioremediation, marine, marsupial and rodent guts, and genomic mapping of the microbial tree of life.
Current research includes:
- a genome based taxonomy for classification of bacteria and archaea;
- characterisation of integrated phages across the bacterial domain
- historical and prospective evolution of the rodent gut microbiome.
In 2018, Phil co-founded a start-up company, Microba (microba.com), which offers metagenome-based microbiome profiling direct to consumers and to research clinicians.
Phil received the Young Investigators Award from the International Society of Microbial Ecology (ISME) in 2016, was elected in 2012 as a Fellow of the American Academy of Microbiology (AAM), elected a Fellow of the Australian Academy of Science in 2017, is a Member of the International Scientific Advisory Board (Fachbeirat) of the Max Planck Institute for Marine Microbiology, Bremen and is the elected Vice President (2020-2021) and the President (2022-2023) and finally outgoing President (2024-2025) of the International Society for Microbial Ecology (ISME). Phil has been a Clarivate Highly Cited Researcher since 2014 and one of only ~300 researchers worldwide to be highly cited in two fields (Microbiology and Biology & Biochemistry) from 2019-2023.
Availability
- Professor Phil Hugenholtz is:
- Available for supervision
Fields of research
Qualifications
- Bachelor (Honours) of Science (Advanced), The University of Queensland
- Doctor of Philosophy, The University of Queensland
Research interests
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Metagenomics
culture-independent sequence-based characterisation of microbial communities
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Microbial diversity and evolution
with a focus on a systematic genome-based prokaryotic taxonomy
Research impacts
Phil has been at the forefront of major advances in molecular microbial ecology over the last 30 years, which now form the basis of this field. Our understanding of microbiology as a whole has been profoundly changed as a result of these advances. Beginning with the recognition that we have been ignorant of most microbial diversity due to a strong cultivation bias, he has systematically directed his research to characterise “microbial dark matter” with the ultimate goal of a holistic understanding of microbial evolution and ecology. He has made central contributions to this grand challenge in biology as evidenced by a series of landmark papers (57 Science & Nature series papers ) and he has established a premier research facility at The University of Queensland, the Australian Centre for Ecogenomics (ACE), dedicated to this mission.
Works
Search Professor Phil Hugenholtz’s works on UQ eSpace
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Sustainable Agriculture, 2 (1) 23. doi: 10.1038/s44264-024-00033-1
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Microbiology, 9 (12), 3084-3085. doi: 10.1038/s41564-024-01861-0
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Haggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadege Adouke, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Fems Microbiology Ecology, 100 (11) ARTN fiae144. doi: 10.1093/femsec/fiae144
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Haggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadege Adouke, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Isme Journal, 18 (1) ARTN wrae219. doi: 10.1093/ismejo/wrae219
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Biofilms and Microbiomes, 10 (1) 122. doi: 10.1038/s41522-024-00591-9
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Communications, 15 (1) 9637. doi: 10.1038/s41467-024-53680-w
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Biodiversity, 3 (1) 34. doi: 10.1038/s44185-024-00066-2
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications Earth & Environment, 5 (1) 672. doi: 10.1038/s43247-024-01817-6
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Reviews Microbiology, 2 (1) 23, 1-2. doi: 10.1038/s41579-024-01123-0
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Climate Action, 3 (1) 102. doi: 10.1038/s44168-024-00179-1
2024
Journal Article
Microbial solutions must be deployed against climate catastrophe
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications Biology, 7 (1) 1466. doi: 10.1038/s42003-024-07108-2
2024
Journal Article
Options and considerations for validation of prokaryotic names under the SeqCode
Venter, Stephanus N., Rodriguez-R, Luis M., Chuvochina, Maria, Palmer, Marike, Hugenholtz, Philip and Steenkamp, Emma T. (2024). Options and considerations for validation of prokaryotic names under the SeqCode. Systematic and Applied Microbiology, 47 (6) 126554, 126554. doi: 10.1016/j.syapm.2024.126554
2024
Journal Article
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
Williams, Tom A, Davin, Adrian A, Szánthó, Lénárd L, Stamatakis, Alexandros, Wahl, Noah A, Woodcroft, Ben J, Soo, Rochelle M, Eme, Laura, Sheridan, Paul O, Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip and Szöllősi, Gergely J (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18 (1) wrae129. doi: 10.1093/ismejo/wrae129
2024
Journal Article
Putative genome contamination has minimal impact on the GTDB taxonomy
Mussig, Aaron J., Chaumeil, Pierre-Alain, Chuvochina, Maria, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2024). Putative genome contamination has minimal impact on the GTDB taxonomy. Microbial Genomics, 10 (5) 001256. doi: 10.1099/mgen.0.001256
2024
Journal Article
Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data era
Yu Jiao, Jian-, Abdugheni, Rashidin, Zhang, Dao-Feng, Ahmed, Iftikhar, Ali, Mukhtiar, Chuvochina, Maria, Dedysh, Svetlana N, Dong, Xiuzhu, Göker, Markus, Hedlund, Brian P, Hugenholtz, Philip, Jangid, Kamlesh, Liu, Shuang-Jiang, Moore, Edward R B, Rao, Manik Prabhu Narsing, Oren, Aharon, Rossello-Mora, Ramon, Rekadwad, Bhagwan Narayan, Salam, Nimaichand, Shu, Wensheng, Sutcliffe, Iain C, Teo, Wee Fei Aaron, Trujillo, Martha E, Venter, Stephanus N, Whitman, William B, Zhao, Guoping and Li, Wen-Jun (2024). Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data era. National Science Review, 11 (7) nwae168, nwae168. doi: 10.1093/nsr/nwae168
2024
Journal Article
Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs
Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere, 9 (4), e0055523. doi: 10.1128/msphere.00555-23
2024
Journal Article
Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of <i>Tigheibacillus jepli</i> gen. nov., sp. nov
Miliotis, Georgios, Sengupta, Pratyay, Hameed, Asif, Chuvochina, Maria, McDonagh, Francesca, Simpson, Anna C., Parker, Ceth W., Singh, Nitin K., Rekha, Punchappady D., Morris, Dearbháile, Raman, Karthik, Kyrpides, Nikos C., Hugenholtz, Philip and Venkateswaran, Kasthuri (2024). Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio, 15 (4), e0018124. doi: 10.1128/mbio.00181-24
2024
Journal Article
Faecal microbial transfer and complex carbohydrates mediate protection against COPD
Budden, Kurtis F, Shukla, Shakti D, Bowerman, Kate L, Vaughan, Annalicia, Gellatly, Shaan L, Wood, David L A, Lachner, Nancy, Idrees, Sobia, Rehman, Saima Firdous, Faiz, Alen, Patel, Vyoma K, Donovan, Chantal, Alemao, Charlotte A, Shen, Sj, Amorim, Nadia, Majumder, Rajib, Vanka, Kanth S, Mason, Jazz, Haw, Tatt Jhong, Tillet, Bree, Fricker, Michael, Keely, Simon, Hansbro, Nicole, Belz, Gabrielle T, Horvat, Jay, Ashhurst, Thomas, van Vreden, Caryn, McGuire, Helen, Fazekas de St Groth, Barbara ... Hansbro, Philip M (2024). Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut, 73 (5), gutjnl-2023. doi: 10.1136/gutjnl-2023-330521
2024
Journal Article
Anaerobic gut fungal communities in marsupial hosts
Jones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2), e0337023. doi: 10.1128/mbio.03370-23
2024
Journal Article
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli
Field, Christian J., Bowerman, Kate L. and Hugenholtz, Philip (2024). Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microbial Genomics, 10 (1) 001176. doi: 10.1099/mgen.0.001176
Funding
Current funding
Past funding
Supervision
Availability
- Professor Phil Hugenholtz is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Available projects
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Dual-function ribonucleases: unexpected agents of antibiotic resistance
Bacterial pathogens use a group of enzymes called metallo-β-lactamases (or MBLs) that enable them to be multi-drug resistant. Our project aims to determine how MBLs have evolved from harmless and widespread ribonucleases, both deep in the past and potentially very recently in response to modern use of antibiotics. These insights will provide valuable functional and structural information that will enable the development of urgently needed strategies to combat β-lactam antibiotic resistance.
Supervision history
Current supervision
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Doctor Philosophy
Characterization of Uncultured Basal Clades of Planctomycetota
Principal Advisor
Other advisors: Dr Kate Bowerman
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Doctor Philosophy
Extant and Evolutionary Analysis of Uncultured Bacterial Lineages Phylogenetically Affiliated with the Orders Rickettsiales and Mycoplasmatales
Principal Advisor
Other advisors: Dr Kate Bowerman
-
Doctor Philosophy
Changing the prokaryotic classification status quo with a global genome-based taxonomy
Principal Advisor
Other advisors: Professor Mikael Boden
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Doctor Philosophy
Use of structural phylogeny and reconciliation in molecular phylogenetics
Principal Advisor
Other advisors: Professor David Ascher, Dr Kate Bowerman
-
Doctor Philosophy
Exploration of the Genome Taxonomy Database at the Species and Subspecies Level
Principal Advisor
-
Doctor Philosophy
Diversity, ecology and biotechnological potential of chain elongating microorganisms from natural and engineered ecosystems
Principal Advisor
Other advisors: Dr Paul Evans, Dr Kate Bowerman
-
Doctor Philosophy
Dual-function ribonucleases: unexpected agents of antibiotic resistance
Associate Advisor
Other advisors: Dr Gabriel Foley, Professor Mikael Boden
-
Doctor Philosophy
Understanding the metabolic capabilities and evolutionary relatiosnhips of novel microorganisms from hot springs
Associate Advisor
Other advisors: Associate Professor Cheong Xin Chan, Dr Paul Evans
-
Doctor Philosophy
Protein structure guided precision medicine
Associate Advisor
Other advisors: Dr Stephanie Portelli, Professor David Ascher
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Doctor Philosophy
The Role of Bacterially Induced Inflammation in Squamous Cell Carcinoma Development
Associate Advisor
Other advisors: Professor Mark Morrison, Dr Debottam Sinha, Dr Janin Chandra, Professor Ian Frazer
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Doctor Philosophy
Functionalisation of Metalloproteins and Applications in Biotechnology
Associate Advisor
Other advisors: Professor Gary Schenk
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Doctor Philosophy
Evolution of an efficient antibiotic resistance mechanism from a common enzymatic fold.
Associate Advisor
Other advisors: Professor Gary Schenk
-
Doctor Philosophy
Building a better understanding of acetogen's metabolism
Associate Advisor
Other advisors: Dr Kate Bowerman, Dr Paul Evans
-
Doctor Philosophy
Identification and characterisation of virally-encoded, antibiotic-degrading metalloenzymes
Associate Advisor
Other advisors: Professor Gary Schenk
Completed supervision
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2024
Doctor Philosophy
Extant and Evolutionary Analysis of Uncultured Bacterial Lineages Phylogenetically Affiliated with the Orders Rickettsiales and Mycoplasmatales
Principal Advisor
Other advisors: Dr Kate Bowerman
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2021
Doctor Philosophy
Classification and functional characterisation of the murine gut bacterial family Muribaculaceae
Principal Advisor
Other advisors: Dr Antiopi Varelias
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2021
Doctor Philosophy
A phylogenomic investigation of the largely uncharacterised Firmicutes classes, Dehalobacteriia and TC1
Principal Advisor
Other advisors: Professor Ulrike Kappler
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2020
Doctor Philosophy
Exploring a Genome-Based Taxonomy for Tailed Double-Stranded DNA Viruses
Principal Advisor
-
2016
Doctor Philosophy
Molecular Investigation of Australian Termites and their Gut Symbionts
Principal Advisor
-
2015
Doctor Philosophy
Investigation of root and associated soil microbiomes of sugarcane and other plants
Principal Advisor
Other advisors: Professor Susanne Schmidt
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-
2024
Doctor Philosophy
The Role of Bacterially Induced Inflammation in Squamous Cell Carcinoma Development
Associate Advisor
Other advisors: Professor Mark Morrison, Dr Debottam Sinha, Dr Janin Chandra, Professor Ian Frazer
-
2024
Doctor Philosophy
The ecology and evolution of non-photosynthetic Cyanobacteria
Associate Advisor
Other advisors: Dr Paul Evans, Dr Rochelle Soo
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2023
Doctor Philosophy
Culture-independent exploration of microbial dark matter with a focus on Asgardarchaeota
Associate Advisor
Other advisors: Dr Paul Evans
-
2017
Doctor Philosophy
Viral/bacterial respiratory tract co-infections in children
Associate Advisor
Other advisors: Professor Keith Chappell, Professor Paul Young
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2017
Doctor Philosophy
Functional and comparative studies of members of the genus Methanosphaera, and their adaptations to the gut environment
Associate Advisor
Other advisors: Professor Mark Morrison
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2017
Doctor Philosophy
Microbial Community Structure and Functionality in Ruminants Fed the Probiotic Bacillus amyloliquefaciens H57
Associate Advisor
Other advisors: Dr Peter Dart
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2016
Doctor Philosophy
Moving targets: Microevolution of pathogenic species within the laboratory and the human host
Associate Advisor
Other advisors: Professor James Fraser
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2015
Doctor Philosophy
Molecular characterisation of microbial communities involved in coal bed methane production
Associate Advisor
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2015
Doctor Philosophy
Molecular characterisation of microbial communities involved in nitrate-driven anaerobic oxidation of methane
Associate Advisor
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2014
Doctor Philosophy
Microbial Ecology of Fermentative Microbes in Anaerobic Granules
Associate Advisor
Other advisors: Professor Damien Batstone, Associate Professor Paul Jensen
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2013
Master Philosophy
The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community
Associate Advisor
Other advisors: Professor Bernard Degnan, Professor Sandie Degnan
Media
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