
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
2005
Book Chapter
Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117. Bergey's manual of systematic bacteriology: The proteobacteria. Part C. The alpha-, beta-, delta-, and epsilonproteobacteria. (pp. 258-263) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer. doi: 10.1007/0-387-29298-5_70
2005
Book Chapter
Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. Bergey's manual of systematic bacteriology. (pp. 452-459) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer.
2004
Journal Article
Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)
Hugenholtz, Philip and Stackebrandt, Erko (2004). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). International Journal of Systematic and Evolutionary Microbiology, 54 (6), 2049-2051. doi: 10.1099/ijs.0.03028-0
2004
Journal Article
Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia
Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip and Janssen, Peter H. (2004). Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Applied and Environmental Microbiology, 70 (10), 5875-5881. doi: 10.1128/AEM.70.10.5875-5881.2004
2004
Conference Publication
Magnetocardiography predicts coronary artery disease in patients presenting with acute chest pain
Park, JW, Hill, P, Hugenholtz, P, Chung, N and Jung, F (2004). Magnetocardiography predicts coronary artery disease in patients presenting with acute chest pain. In: ESC Congress 2004, Munich Germany, (303-304). Aug 28-Sep 01, 2004.
2004
Journal Article
Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria
Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip and Janssen, Peter H. (2004). Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Applied and Environmental Microbiology, 70 (7), 4363-4366. doi: 10.1128/AEM.70.7.4363-4366.2004
2004
Journal Article
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Huber, T, Faulkner, G and Hugenholtz, P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20 (14), 2317-2319. doi: 10.1093/bioinformatics/bth226
2004
Journal Article
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 (6978), 37-43. doi: 10.1038/nature02340
2004
Conference Publication
The tree of life - An overview
Baldauf, SL, Bhattacharya, D, Cockrill, J, Hugenholtz, P, Pawlowski, J and Simpson, AGB (2004). The tree of life - An overview. Conference on Assembling the Tree of Life, New York Ny, May 30-Jun 01, 2002. NEW YORK: OXFORD UNIV PRESS.
2004
Journal Article
Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
Ginige, MP, Hugenholtz, P, Daims, H, Wagner, M, Keller, J and Blackall, LL (2004). Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied And Environmental Microbiology, 70 (1), 588-596. doi: 10.1128/AEM.70.1.588-596.2004
2004
Book Chapter
The tree of life: An overview
Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, Philip, Pawlowski, J. and Simpson, A.G. (2004). The tree of life: An overview. Assembling the tree of life. (pp. 43-75) New York: Oxford University Press.
2003
Journal Article
Laboratory cultivation of widespread and previously uncultured soil bacteria
Joseph, SJ, Hugenholtz, P, Sangwan, P, Osborne, CA and Janssen, PH (2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Applied and Environmental Microbiology, 69 (12), 7210-7215. doi: 10.1128/AEM.69.12.7210-7215.2003
2003
Journal Article
Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes
Baker, BJ, Hugenholtz, P, Dawson, SC and Banfield, JF (2003). Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Applied and Environmental Microbiology, 69 (9), 5512-5518. doi: 10.1128/AEM.69.9.5512-5518.2003
2003
Journal Article
Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.
Zhang, H, Sekiguchi, Y, Hanada, S, Hugenholtz, P, Kim, H, Kamagata, Y and Nakamura, K (2003). Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.. International Journal of Systematic and Evolutionary Microbiology, 53 (4), 1155-1163. doi: 10.1099/ijs.0.02520-0
2003
Journal Article
Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae
Janssen, PH and Hugenholtz, P (2003). Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae. Archives of Microbiology, 179 (5), 321-328. doi: 10.1007/s00203-003-0528-5
2003
Journal Article
PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues
Uzal, FA, Hugenholtz, P, Blackall, LL, Petray, S, Moss, S, Assis, RA, Miyakawa, MF and Carloni, G (2003). PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Veterinary Microbiology, 91 (2-3), 239-248. doi: 10.1016/S0378-1135(02)00291-2
2003
Journal Article
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
Hugenholtz, P and Huber, T (2003). Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic And Evolutionary Microbiology, 53 (1), 289-293. doi: 10.1099/ijs.0.02441-0
2003
Journal Article
Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community
Rossetti, S, Blackall, LL, Majone, M, Hugenholtz, P, Plumb, JJ and Tandoi, V (2003). Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology-sgm, 149 (2), 459-469. doi: 10.1099/mic.0.26018-0
2002
Journal Article
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys
Sait, M, Hugenholtz, P and Janssen, PH (2002). Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environmental Microbiology, 4 (11), 654-666. doi: 10.1046/j.1462-2920.2002.00352.x
2002
Journal Article
Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal
Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 (8), 2309-2318. doi: 10.1099/00221287-148-8-2309
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
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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
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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
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
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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
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
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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
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
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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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