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
2019
Conference Publication
The Role of the Gastrointestinal Microbiome in Lung Cancer Pathogenesis
Budden, Kurtis, Shukla, Shakti, Rehman, Saima Firdous, Sahu, Priyanka, Donovan, Chantal, Bowerman, Kate L., Dennis, Paul G., Hugenholtz, Philip and Hansbro, Philip M. (2019). The Role of the Gastrointestinal Microbiome in Lung Cancer Pathogenesis. 2019 Hunter Cancer Research Symposium, Newcastle, NSW Australia, 8 November 2019. Chichester, West Sussex United Kingdom: Wiley-Blackwell.
2019
Conference Publication
Dietary fibre elevates SCFAS and protects against experimental COPD
Budden, K., Shukla, S., Rehman, Firdous S., Donvan, C., Bowerman, K., Dennis, P., Hugenholtz, P. and Hansbro, P. (2019). Dietary fibre elevates SCFAS and protects against experimental COPD. TSANZSRS 2019 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting, Gold Coast, QLD, Australia, 29 March–2 April 2019. Richmond, VIC, Australia : Wiley-Blackwell Publishing Asia. doi: 10.1111/resp.13492
2018
Journal Article
Minimum information about an uncultivated virus genome (MIUViG)
Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R ... Eloe-Fadrosh, Emiley A (2018). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37 (1), 29-37. doi: 10.1038/nbt.4306
2018
Journal Article
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018). A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 13 (3), 663-675. doi: 10.1038/s41396-018-0282-y
2018
Journal Article
A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes
Wood, David L. A., Lachner, Nancy, Tan, Jean-Marie, Tang, Stephanie, Angel, Nicola, Laino, Antonia, Linedale, Richard, Lê Cao, Kim-Anh, Morrison, Mark, Frazer, Ian H., Soyer, H. Peter and Hugenholtz, Philip (2018). A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes. MBio, 9 (5) e01432-18. doi: 10.1128/mBio.01432-18
2018
Journal Article
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, Donovan H., Chuvochina, Maria, Waite, David W., Rinke, Christian, Skarshewski, Adam, Chaumeil, Pierre-Alain and Hugenholtz, Philip (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36 (10), 996-1004. doi: 10.1038/nbt.4229
2018
Journal Article
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size
Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018). Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7
2018
Journal Article
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 (7), 660-660. doi: 10.1038/nbt0718-660a
2018
Journal Article
Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Waite, David W., Dsouza, Melissa, Sekiguchi, Yuji, Hugenholtz, Philip and Taylor, Michael W. (2018). Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. Scientific Reports, 8 (1) 8128, 8128. doi: 10.1038/s41598-018-26484-4
2018
Journal Article
American gut: an open platform for citizen science microbiome research
McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua ... Knight, Rob (2018). American gut: an open platform for citizen science microbiome research. mSystems, 3 (3) e00031-18. doi: 10.1128/mSystems.00031-18
2018
Journal Article
Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid
Laloo, Andrew E., Wei, Justin, Wang, Dongbo, Narayanasamy, Shaman, Vanwonterghem, Inka, Waite, David, Steen, Jason, Kaysen, Anne, Heintz-Buschart, Anna, Wang, Qilin, Schulz, Benjamin, Nouwens, Amanda, Wilmes, Paul, Hugenholtz, Philip, Yuan, Zhiguo and Bond, Philip L. (2018). Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid. Environmental science & technology, 52 (9), 5386-5397. doi: 10.1021/acs.est.7b04273
2018
Journal Article
Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017)
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772
2018
Journal Article
Recipient mucosal-associated invariant T cells control GVHD within the colon
Varelias, Antiopi, Bunting, Mark D., Ormerod, Kate L., Koyama, Motoko, Olver, Stuart D., Straube, Jasmin, Kuns, Rachel D., Robb, Renee J., Henden, Andrea S., Cooper, Leanne, Lachner, Nancy, Gartlan, Kate H., Lantz, Olivier, Kjer-Nielsen, Lars, Mak, Jeffrey Y. W., Fairlie, David P., Clouston, Andrew D., McCluskey, James, Rossjohn, Jamie, Lane, Steven W., Hugenholtz, Philip and Hill, Geoffrey R. (2018). Recipient mucosal-associated invariant T cells control GVHD within the colon. Journal of Clinical Investigation, 128 (5), 1919-1936. doi: 10.1172/JCI91646
2018
Journal Article
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017)
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Goeker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2018). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Nature Biotechnology, 36 (4), 368-368. doi: 10.1038/nbt0418-368c
2018
Journal Article
Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57
Schofield, Benjamin J., Lachner, Nancy, Le, Oanh T., McNeill, David M., Dart, Peter, Ouwerkerk, Diane, Hugenholtz, Philip and Klieve, Athol V. (2018). Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57. Journal of Applied Microbiology, 124 (3), 855-866. doi: 10.1111/jam.13688
2018
Book Chapter
Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization
Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029
2018
Conference Publication
Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon
Varelias, Antiopi, Bunting, Mark, Ormerod, Kate, Koyama, Motoko, Olver, Stuart, Straube, Jasmin, Kuns, Rachel, Robb, Renee, Henden, Andrea, Cooper, Leanne, Lachner, Nancy, Gartlan, Kate, Lantz, Olivier J., Kjer-Nielsen, Lars, Mak, Jeffrey, Fairlie, David, Clouston, Andrew, McCluskey, James, Rossjohn, Jamie, Lane, Steven, Hugenholtz, Phil and Hill, Geoff (2018). Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon. Immunology Meeting, Austin Tx, 4-8 May 2018. Bethesda, MD United States: American Association of Immunologists.
2017
Journal Article
Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 (2), 253-253. doi: 10.1038/s41564-017-0083-5
2017
Journal Article
Atmospheric trace gases support primary production in Antarctic desert surface soil
Ji, Mukan, Greening, Chris, Vanwonterghem, Inka, Carere, Carlo R., Bay, Sean K., Steen, Jason A., Montgomery, Kate, Lines, Thomas, Beardall, John, van Dorst, Josie, Snape, Ian, Stott, Matthew B., Hugenholtz, Philip and Ferrari, Belinda C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552 (7685), 400-403. doi: 10.1038/nature25014
2017
Journal Article
Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence
Yeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8
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
-
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
-
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
-
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
-
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
-
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
-
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
Media
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