Professor Phil Hugenholtz
Professor

Phil Hugenholtz

Email: 
Phone: 
+61 7 336 53822

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

Microbiology

Qualifications

  • Bachelor (Honours) of Science (Advanced), The University of Queensland
  • Doctor of Philosophy, The University of Queensland

Research interests

  • Metagenomics

    culture-independent sequence-based characterisation of microbial communities

  • 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.

Search Professor Phil Hugenholtz’s works on UQ eSpace

538 works between 1990 and 2025
All (538) Journal Article (473) Book Chapter (13) Conference Publication (47) Other Outputs (5)

401 - 420 of 538 works

2009

Journal Article

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)

Herlemann, D. P. R., Geissinger, O., Ikeda-Ohtsubo, W., Kunin, V., Sun, H., Lapidus, A., Hugenholtz, P. and Brune, A. (2009). Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Applied and Environmental Microbiology, 75 (9), 2841-2849. doi: 10.1128/AEM.02698-08

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)

2009

Journal Article

Getting to the core of the gut microbiome

Tschop, MH, Hugenholtz, P and Karp, CL (2009). Getting to the core of the gut microbiome. Nature Biotechnology, 27 (4), 344-346. doi: 10.1038/nbt0409-344

Getting to the core of the gut microbiome

2009

Journal Article

A changing of the guard: Genomics update

Hugenholtz, P and Kyrpides, NC (2009). A changing of the guard: Genomics update. Environmental Microbiology, 11 (3), 551-553. doi: 10.1111/j.1462-2920.2009.01888.x

A changing of the guard: Genomics update

2009

Journal Article

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii

Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat and Kyrpides, Nikos C. (2009). Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One, 4 (1) e4192, e4192.1-e4192.8. doi: 10.1371/journal.pone.0004192

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii

2009

Journal Article

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

Clum, Alicia, Nolan, Matt, Lang, Elke, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Goeker, Markus, Spring, Stefan, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2009). Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences, 1 (1), 38-45. doi: 10.4056/sigs.1463

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

2009

Journal Article

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T))

Ivanova, Natalia, Gronow, Sabine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Rohde, Christine, Goeker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T)). Standards in Genomic Sciences, 1 (2), 126-132. doi: 10.4056/sigs.1854

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T))

2009

Journal Article

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

Mavrommatis, Konstantinos, Gronow, Sabine, Saunders, Elizabeth, Land, Miriam, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Bristow, James, Goeker, Markus, Rohde, Manfred ... Hugenholtz, Philip (2009). Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Standards in Genomic Sciences, 1 (2), 101-109. doi: 10.4056/sigs.15195

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

2009

Journal Article

Complete genome sequence of Halogeometricum borinquense type strain (PR3(T))

Malfatti, Stephanie, Tindall, Brian J., Schneider, Susanne, Faehnrich, Regine, Lapidus, Alla, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Anderson, Iain, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Chain, Patrick (2009). Complete genome sequence of Halogeometricum borinquense type strain (PR3(T)). Standards in Genomic Sciences, 1 (2), 150-158. doi: 10.4056/sigs.23264

Complete genome sequence of Halogeometricum borinquense type strain (PR3(T))

2009

Journal Article

Complete genome sequence of Rhodothermus marinus type strain (R-10(T))

Nolan, Matt, Gronow, Sabine, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Sims, David, Meincke, Linda, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Han, Cliff, Detter, John C., Ovchinikova, Galina, Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Chain, Patrick (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10(T)). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs46736

Complete genome sequence of Rhodothermus marinus type strain (R-10(T))

2009

Journal Article

Complete genome sequence of Saccharomonospora viridis type strain (P101(T))

Pati, Amrita, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Chain, Patrick, D'haeseleer, Patrik, Chen, Amy, Palaniappan, Krishna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Saccharomonospora viridis type strain (P101(T)). Standards in Genomic Sciences, 1 (2), 141-149. doi: 10.4056/sigs.20263

Complete genome sequence of Saccharomonospora viridis type strain (P101(T))

2009

Journal Article

Complete genome sequence of Kangiella koreensis type strain (SW-125(T))

Han, Cliff, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Goeker, Markus, Tindall, Brian J., Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Kangiella koreensis type strain (SW-125(T)). Standards in Genomic Sciences, 1 (3), 226-233. doi: 10.4056/sigs.36635

Complete genome sequence of Kangiella koreensis type strain (SW-125(T))

2009

Journal Article

Complete genome sequence of Actinosynnema mirum type strain (101(T))

Land, Miriam, Lapidus, Alla, Mayilraj, Shanmugam, Chen, Feng, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick, Tindall, Brian J. ... Klenk, Hans-Peter (2009). Complete genome sequence of Actinosynnema mirum type strain (101(T)). Standards in Genomic Sciences, 1 (1), 46-53. doi: 10.4056/sigs.21137

Complete genome sequence of Actinosynnema mirum type strain (101(T))

2009

Conference Publication

Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).

Pope, P., Denman, S., Tringe, S., Hinds, L., Hugenholtz, P., McSweeney, C. and Morrison, M. (2009). Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).. 2009 Conference on Gastrointestinal Function, Chicago, USA, 20-22 April, 2009. New York, NY, United States: Springer. doi: 10.1007/s00248-009-9496-x

Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).

2009

Journal Article

Correlative tem and fish imaging of microbial communities

Knierim, B., Webb, R., Wilmes, P., Hugenholtz, P., Liphardt, J., McDonald, K., Banfield, J. and Auer, M. (2009). Correlative tem and fish imaging of microbial communities. Microscopy and Microanalysis, 15 (Suppl. 2), 834-835. doi: 10.1017/S1431927609098250

Correlative tem and fish imaging of microbial communities

2009

Journal Article

Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T))

Saunders, Elizabeth, Pukall, Ruediger, Abt, Birte, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C. ... Han, Cliff (2009). Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T)). Standards in Genomic Sciences, 1 (2), 174-182. doi: 10.4056/sigs.33592

Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T))

2009

Journal Article

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T))

Pukall, Ruedieger, Gehrich-Schroeter, Gabriele, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Copeland, Alex, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Bruce, David, Goodwin, Lynne, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Goeker, Markus, Bristow, Jim ... Han, Cliff (2009). Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T)). Standards in Genomic Sciences, 1 (3), 262-269. doi: 10.4056/sigs.41646

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T))

2009

Journal Article

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)

Clum, Alicia, Tindall, Brian J., Sikorski, Johannes, Ivanova, Natalia, Mavrommatis, Konstantinos, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T). Standards in Genomic Sciences, 1 (3), 308-316. doi: 10.4056/sigs.51657

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)

2009

Journal Article

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T))

Lapidus, Alla, Pukall, Ruediger, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2009). Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T)). Standards in Genomic Sciences, 1 (1), 3-11. doi: 10.4056/sigs.492

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T))

2009

Journal Article

Complete genome sequence of Desulfomicrobium baculatum type strain (X-T)

Copeland, Alex, Spring, Stefan, Goeker, Markus, Schneider, Susanne, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff ... Lucas, Susan (2009). Complete genome sequence of Desulfomicrobium baculatum type strain (X-T). Standards in Genomic Sciences, 1 (1), 29-37. doi: 10.4056/sigs.13134

Complete genome sequence of Desulfomicrobium baculatum type strain (X-T)

2009

Journal Article

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T))

Han, Cliff, Spring, Stefan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Goeker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T)). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4506/sigs.22138

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T))

Current funding

  • 2025 - 2026
    A Facility for Accelerated Microbial Phenotyping in Southeast Queensland
    ARC Linkage Infrastructure, Equipment and Facilities
    Open grant
  • 2025 - 2028
    A Genome Taxonomy Database for the Kingdom Fungi
    ARC Discovery Projects
    Open grant
  • 2025 - 2028
    Tracing the emergence of cellular complexity in the phylum Planctomycetota
    ARC Discovery Projects
    Open grant
  • 2023 - 2025
    Molecular analysis of koala scats for diet composition, KoRV subtypes and microbiome composition
    University of the Sunshine Coast
    Open grant
  • 2023 - 2026
    Gut leak and microbiome contribution to severe dengue disease
    NHMRC e-ASIA Joint Research Program
    Open grant
  • 2022 - 2025
    Changing the classification status quo with a global genome-based taxonomy
    ARC Discovery Projects
    Open grant
  • 2022 - 2025
    Dual-function ribonucleases: unexpected agents of antibiotic resistance
    NHMRC IDEAS Grants
    Open grant
  • 2020 - 2025
    GBR Microbial Genomic Database
    Australian Institute of Marine Science
    Open grant

Past funding

  • 2023 - 2025
    Enhancing Australian biodiscovery molecule generation, storage and access (ARC LIEF administered by Griffith University)
    Griffith University
    Open grant
  • 2020 - 2024
    Breaking critical barriers in soil formation of bauxite residues
    ARC Linkage Projects
    Open grant
  • 2020 - 2024
    Development of koala probiotics to improve rehabilitation success
    BCC Koala Research Partnerships Program
    Open grant
  • 2020 - 2024
    Development of Phage Therapy to Combat Chronic Otitis Media in Indigenous Children
    NHMRC IDEAS Grants
    Open grant
  • 2020 - 2022
    Do bacteriophages increase pathogenicity of Pseudomonas infections in children with cystic fibrosis?
    The Children's Hospital Foundation
    Open grant
  • 2020 - 2024
    Understanding evolution of dominant bacteria inhabiting the rodent gut
    ARC Discovery Projects
    Open grant
  • 2019 - 2020
    National Volumetric Imaging Facility: Observing the Cell in its Native Environment (ARC LIEF project administered by UTS)
    University of Technology Sydney
    Open grant
  • 2018
    Epifluorescent and live-cell imaging microscopes for the investigation of host-pathogen interactions and for molecular and cellular biology
    UQ Major Equipment and Infrastructure
    Open grant
  • 2016 - 2019
    Rapid functional and taxonomic skin microbe characterisation
    ARC Linkage Projects
    Open grant
  • 2016
    Establishing a gnotobiotic germ-free mouse facility
    UQ Major Equipment and Infrastructure
    Open grant
  • 2016
    Instrumentation for the analysis of cellular and metabolic phenotypes
    UQ Major Equipment and Infrastructure
    Open grant
  • 2016
    The Australian human microbiota project-microbe isolation facility
    UQ Major Equipment and Infrastructure
    Open grant
  • 2015 - 2021
    Reconstructing the Universal Tree and Network of Life
    ARC Australian Laureate Fellowships
    Open grant
  • 2015
    Engaging Students through Big Picture Genomics-based Science
    Vice-Chancellor's Research and Teaching Fellowship
    Open grant
  • 2015 - 2018
    Understanding the koala microbiome: unlocking the secrets of koala health and dietary specialisation, and successful husbandry and translocation (ARC Linkage Project administered by UWS)
    University of Western Sydney
    Open grant
  • 2015 - 2016
    Developing next-generation bio-fertilisers
    UQ Collaboration and Industry Engagement Fund - Seed Research Grant
    Open grant
  • 2015 - 2017
    Evolution of the marsupial gut microbiome and adaptation to eucalypt toxins
    ARC Discovery Projects
    Open grant
  • 2015 - 2019
    Immunological therapies for cancer, chronic infection and autoimmunity
    NHMRC Program Grant
    Open grant
  • 2015
    UQ Travel Award 2015 - Prof Andrew Weightman
    UQ Travel Grants Scheme
    Open grant
  • 2014
    A confocal microscope for investigation of live bacterial and viral pathogens and for molecular cell biology
    UQ Major Equipment and Infrastructure
    Open grant
  • 2014 - 2018
    Determinants of progression of actinic keratoses to squamous cancer
    NHMRC Project Grant
    Open grant
  • 2014 - 2018
    Modification of the microbiome and utilisation of microbial products as novel treatments for COPD (NHMRC Project Grant administered by the University of Newcastle)
    University of Newcastle
    Open grant
  • 2014
    Novel treatments for inflammatory bowel disease
    UQ Collaboration and Industry Engagement Fund - Seed Research Grant
    Open grant
  • 2014 - 2015
    The normal pulmonary flora - fact or fiction?
    Prince Charles Hospital Foundation
    Open grant
  • 2014
    UQ Travel Award - Category 1 Dr Li Deng
    UQ Travel Awards for International Collaborative Research (Category 1)
    Open grant
  • 2013 - 2018
    Microscale experiments to understand a microscale world: Combining microfluidics and ecogenomics to investigate microbial processes in the ocean
    University of Technology Sydney
    Open grant
  • 2013 - 2015
    Microbial communities that reside in the human ocular
    Brien Holden Vision Institute
    Open grant
  • 2013 - 2018
    Evaluation of Bacillus amyloliquefaciens H57 as a probiotic in livestock using animal nutrition studies and metagenomics
    ARC Linkage Projects
    Open grant
  • 2013
    Accelerated crop development and environmental compliance of agricultural and food systems
    UQ Major Equipment and Infrastructure
    Open grant
  • 2013 - 2015
    The lung transplant mycobiome
    Prince Charles Hospital Foundation
    Open grant
  • 2013
    UQ Travel Awards - Category 1 - A/Prof Shana Goffredi
    UQ Travel Grants Scheme
    Open grant
  • 2012 - 2013
    Impact of pig gut microbiology on pig nutrition and health
    CRC for High Integrity Australian Pork
    Open grant
  • 2012 - 2015
    Future biofuels
    Queensland Government Smart Futures Research Partnerships Program
    Open grant
  • 2012 - 2013
    A high-throughput screening and sequencing facility for single cell genomics
    ARC Linkage Infrastructure, Equipment and Facilities
    Open grant
  • 2012 - 2014
    Ecogenomics of Queensland sugarcane soils
    Queensland Government Smart Futures Co-Investment Fund
    Open grant
  • 2012
    An intergrated fluidic circuit system for digital PCR analysis, single-cell gene- expression, and high-throughput preparation of next-generation sequencing libraries.
    UQ Major Equipment and Infrastructure
    Open grant
  • 2012 - 2013
    Scanning electron microscope to house 3-Dimensional Sectioning Facility
    UQ Major Equipment and Infrastructure
    Open grant
  • 2012 - 2014
    Toward a complete view of life on Earth via single cell genomics
    ARC Discovery Projects
    Open grant
  • 2011
    Travel award - Keynote speaker for the Ecological Society of Australia Conference in Hobart, 21-24 November 2011
    Grains Research & Development Corporation
    Open grant
  • 2011
    Anaerobic workstations for experimental and pure culture research.
    UQ Major Equipment and Infrastructure
    Open grant
  • 2011
    Metagenomic analysis of bronchoalveolar lavage fluid from children with cystic fibrosis and disease controls
    Royal Children's Hospital Foundation
    Open grant

Availability

Professor Phil Hugenholtz is:
Available for supervision

Before you email them, read our advice on how to contact a supervisor.

Available projects

  • 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

  • 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

  • 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

    Changing the prokaryotic classification status quo with a global genome-based taxonomy

    Principal Advisor

    Other advisors: Professor Mikael Boden

  • Doctor Philosophy

    Protein structure guided precision medicine

    Associate Advisor

    Other advisors: Dr Stephanie Portelli, Professor David Ascher

  • 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

    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

  • 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

  • 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

  • Doctor Philosophy

    Dual-function ribonucleases: unexpected agents of antibiotic resistance

    Associate Advisor

    Other advisors: Professor Mikael Boden

Completed supervision

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