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 on molecular microbial ecology and evolution.
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 marsupial and insect guts, biomining, marine and genomic mapping of the microbial tree of life.
Current research includes:
- A Genome Taxonomy Database for the Kingdom Fungi
- Tracing the emergence of cellular complexity in the phylum Planctomycetota
- Dual-function ribonucleases: unexpected agents of antibiotic resistance
- Breaking critical barriers in soil formation of bauxite residues
- Changing the classification status quo with a global genome-based taxonomy
- GBR Microbial Genomic Database
In 2018, Phil co-founded a start-up company, Microba Life Sciences (microba.com), which is focused on metagenome-based diagnostics and therapeutics.
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 outgoing President (2024-2026) 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 2019-2024.
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
2020
Other Outputs
Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem
Chen, Ya-Jou, Leung, Pok Man, Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Cook, Perran L. M. and Greening, Chris (2020). Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem. doi: 10.1101/2020.02.12.945220
2020
Journal Article
Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice
Bowerman, Kate L., Varelias, Antiopi, Lachner, Nancy, Kuns, Rachel D., Hill, Geoffrey R. and Hugenholtz, Philip (2020). Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. Gut Microbes, 11 (4), 1-17. doi: 10.1080/19490976.2019.1705729
2020
Conference Publication
Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives
Cuiv, Paraic O., Krause, Lutz, Wood, David, Hugenholtz, Phil and Tyson, Gene (2020). Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives. FNM 2020 ‐ 4th Meeting of the Federation of Neurogastroenterology and Motility, Adelaide, SA Australia, 25 - 28 March 2020. Chichester, West Sussex United Kingdom: Wiley-Blackwell.
2020
Conference Publication
Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease
Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark and Holtmann, Gerald J. (2020). Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Crohn's and Colitis Congress, Austin, TX, United States, 23-25 January 2020. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(20)32052-7
2020
Conference Publication
Diet influences COPD pathogenesis by regulating microbial metabolism
Budden, K., Rehman, Firdous S., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Sahu, P., Alemao, C., Holmes, A., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2020). Diet influences COPD pathogenesis by regulating microbial metabolism. TSANZSRS 2020 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health & Respiratory Science, Melbourne, VIC Australia, 27–31 March 2020. Richmond, VIC Australia: Wiley-Blackwell.
2020
Journal Article
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
Waite, David W., Chuvochina, Maria, Pelikan, Claus, Parks, Donovan H., Yilmaz, Pelin, Wagner, Michael, Loy, Alexander, Naganuma, Takeshi, Nakai, Ryosuke, Whitman, William B., Hahn, Martin W., Kuever, Jan and Hugenholtz, Philip (2020). Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. International Journal of Systematic and Evolutionary Microbiology, 70 (11) 004213, 5972-6016. doi: 10.1099/ijsem.0.004213
2020
Journal Article
Roadmap for naming uncultivated Archaea and Bacteria
Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5 (8), 987-994. doi: 10.1038/s41564-020-0733-x
2019
Conference Publication
2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study
Tsutsumi, Tamao, Shah, Alok, Lam, Lisa M T, Schlebusch, Sanmarie, Krueger, Annika, Frazer, Ian, Hugenholtz, Phil, Soyer, H Peter, Morrison, Mark, Hill, Michelle, Sedman, Jacqueline and Ismail, Ashraf (2019). 2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study. IDWeek 2019, Washington, DC, United States, 2-6 October 2019. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ofid/ofz360.1805
2019
Journal Article
Functional effects of the microbiota in chronic respiratory disease
Budden, Kurtis F., Shukla, Shakti D., Rehman, Saima Firdous, Bowerman, Kate L., Keely, Simon, Hugenholtz, Philip, Armstrong-James, Darius P. H., Adcock, Ian M., Chotirmall, Sanjay H., Chung, Kian Fan and Hansbro, Philip M. (2019). Functional effects of the microbiota in chronic respiratory disease. Lancet Respiratory Medicine, 7 (10), 907-920. doi: 10.1016/S2213-2600(18)30510-1
2019
Journal Article
Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains
Whitman, William B., Klenk, Hans-Peter, Arahal, David R., Aznar, Rosa, Garrity, George, Pester, Michael and Hugenholtz, Philip (2019). Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains. Microbiology Australia, 40 (3), 125-129. doi: 10.1071/MA19034
2019
Journal Article
Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala
Blyton, Michaela D. J., Soo, Rochelle M., Whisson, Desley, Marsh, Karen J., Pascoe, Jack, Le Pla, Mark, Foley, William, Hugenholtz, Philip and Moore, Ben D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Animal Microbiome, 1 (1) 6, 6. doi: 10.1186/s42523-019-0008-0
2019
Journal Article
Defining the human gut host–phage network through single-cell viral tagging
Džunková, Mária, Low, Soo Jen, Daly, Joshua N., Deng, Li, Rinke, Christian and Hugenholtz, Philip (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4 (12), 2192-2203. doi: 10.1038/s41564-019-0526-2
2019
Journal Article
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Low, Soo Jen, Džunková, Mária, Chaumeil, Pierre-Alain, Parks, Donovan H. and Hugenholtz, Philip (2019). Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales. Nature Microbiology, 4 (8), 1306-1315. doi: 10.1038/s41564-019-0448-z
2019
Journal Article
Consent insufficient for data release Response
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Consent insufficient for data release Response. Science, 364 (6439), 446-446. doi: 10.1126/science.aax7509
2019
Journal Article
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments
Kessler, Adam J., Chen, Ya-Jou, Waite, David W., Hutchinson, Tess, Koh, Sharlynn, Popa, M. Elena, Beardall, John, Hugenholtz, Philip, Cook, Perran L. M. and Greening, Chris (2019). Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nature Microbiology, 4 (6), 1014-1023. doi: 10.1038/s41564-019-0391-z
2019
Journal Article
IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota
Rehaume, Linda M., Matigian, Nicholas, Mehdi, Ahmed M., Lachner, Nancy, Bowerman, Kate L., Daly, Joshua, Lê Cao, Kim-Anh, Hugenholtz, Philip and Thomas, Ranjeny (2019). IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota. Annals of the Rheumatic Diseases, 78 (4), 494-503. doi: 10.1136/annrheumdis-2018-214381
2019
Journal Article
Toward unrestricted use of public genomic data
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Toward unrestricted use of public genomic data. Science, 363 (6425), 350-352. doi: 10.1126/science.aaw1280
2019
Journal Article
An evolving view of methane metabolism in the Archaea
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7
2019
Journal Article
The importance of designating type material for uncultured taxa
Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2019). The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42 (1), 15-21. doi: 10.1016/j.syapm.2018.07.003
2019
Journal Article
Evolution of photosynthesis and aerobic respiration in the cyanobacteria
Soo, Rochelle M., Hemp, James and Hugenholtz, Philip (2019). Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radical Biology and Medicine, 140, 200-205. doi: 10.1016/j.freeradbiomed.2019.03.029
Funding
Current funding
Past funding
Supervision
Availability
- Professor Phil Hugenholtz is:
- Available for supervision
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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
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
Characterization of Uncultured Basal Clades of Planctomycetota
Principal Advisor
Other advisors: Dr Kate Bowerman
-
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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Doctor Philosophy
Changing the prokaryotic classification status quo with a global genome-based taxonomy
Principal Advisor
Other advisors: Professor Mikael Boden
-
Doctor Philosophy
Use of structural phylogeny and reconciliation in molecular phylogenetics
Principal Advisor
Other advisors: Professor David Ascher, Dr Kate Bowerman
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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
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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
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Doctor Philosophy
Building a better understanding of acetogen's metabolism
Associate Advisor
Other advisors: Dr Kate Bowerman, Dr Paul Evans
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Doctor Philosophy
Identification and characterisation of virally-encoded, antibiotic-degrading metalloenzymes
Associate Advisor
Other advisors: Professor Gary Schenk
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Doctor Philosophy
Dual-function ribonucleases: unexpected agents of antibiotic resistance
Associate Advisor
Other advisors: Professor Mikael Boden
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Doctor Philosophy
Protein structure guided precision medicine
Associate Advisor
Other advisors: Dr Stephanie Portelli, Professor David Ascher
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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
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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
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
A phylogenomic investigation of the largely uncharacterised Firmicutes classes, Dehalobacteriia and TC1
Principal Advisor
Other advisors: Professor Ulrike Kappler
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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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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
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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
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2024
Doctor Philosophy
The ecology and evolution of non-photosynthetic Cyanobacteria
Associate Advisor
Other advisors: Dr Paul Evans
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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
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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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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
Viral/bacterial respiratory tract co-infections in children
Associate Advisor
Other advisors: Professor Keith Chappell
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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
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