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Biology and Biochemistry
Australia
2026

D-Index & Metrics

Biology and Biochemistry

D-Index
135
Citations
139043
World Ranking
345
National Ranking
7

Research.com Recognitions

  • 2026 - Research.com Biology and Biochemistry in Australia Leader Award
  • 2025 - Research.com Biology and Biochemistry in Australia Leader Award
  • 2023 - Research.com Biology and Biochemistry in Australia Leader Award
  • 2022 - Research.com Biology and Biochemistry in Australia Leader Award

Overview

Philip Hugenholtz is affiliated with the University of Queensland in Australia. Their research spans multiple fields primarily within Biochemistry, Genetics and Molecular Biology as well as Environmental Science.

The main subfields of study for Philip Hugenholtz include Molecular Biology, Ecology, Infectious Diseases, Food Science, and Renewable Energy, Sustainability and the Environment. Their work covers a variety of interconnected scientific topics such as Genomics and Phylogenetic Studies, Microbial Community Ecology and Physiology, Gut microbiota and health, Probiotics and Fermented Foods, Global Energy and Sustainability Research, Climate Change Communication and Perception, and Clostridium difficile and Clostridium perfringens research.

Philip Hugenholtz has authored and co-authored numerous papers in scientific venues with a focus on microbiology, molecular taxonomy, and environmental surveillance. Some of their recent papers include:

  • GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, 2021, Nucleic Acids Research
  • First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community, 2020, The Science of The Total Environment
  • A complete domain-to-species taxonomy for Bacteria and Archaea, 2020, Nature Biotechnology
  • GTDB-Tk v2: memory friendly classification with the genome taxonomy database, 2022, Bioinformatics
  • A unified catalog of 204,938 reference genomes from the human gut microbiome, 2020, Nature Biotechnology

The scientist collaborates regularly with several researchers, with frequent co-authors being Donovan H. Parks, Maria Chuvochina, Julian Zaugg, Thulani P. Makhalanyane, and Fengping Wang.

Philip Hugenholtz's publications have appeared repeatedly in well-known scientific journals and platforms including bioRxiv (Cold Spring Harbor Laboratory), Nature Microbiology, The ISME Journal, ISME Communications, and Nature Biotechnology.

Best Publications

  • Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

    Todd Z. DeSantis;Philip Hugenholtz;Neils Larsen;Mark Rojas

  • CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

    Donovan H. Parks;Michael Imelfort;Connor T. Skennerton;Philip Hugenholtz

  • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

    Daniel McDonald;Morgan N Price;Julia Goodrich;Julia Goodrich;Eric P Nawrocki

  • STAMP: statistical analysis of taxonomic and functional profiles

    Donovan H. Parks;Gene W. Tyson;Philip Hugenholtz;Robert G. Beiko

  • GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

    Pierre-Alain Chaumeil;Aaron J Mussig;Philip Hugenholtz;Donovan H Parks

  • Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity

    Philip Hugenholtz;Brett M. Goebel;Norman R. Pace

  • Defining the core Arabidopsis thaliana root microbiome

    Derek S. Lundberg;Sarah L. Lebeis;Sur Herrera Paredes;Scott Yourstone

  • A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

    Donovan H Parks;Maria Chuvochina;David W Waite;Christian Rinke

  • Community structure and metabolism through reconstruction of microbial genomes from the environment

    Gene W. Tyson;Jarrod Chapman;Jarrod Chapman;Philip Hugenholtz;Eric E. Allen

  • Insights into the phylogeny and coding potential of microbial dark matter

    Christian Rinke;Patrick Schwientek;Alexander Sczyrba;Alexander Sczyrba;Natalia N. Ivanova

  • Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

    Robert M. Bowers;Nikos C. Kyrpides;Ramunas Stepanauskas;Miranda Harmon-Smith

  • Comparative Metagenomics of Microbial Communities

    Susannah Green Tringe;Christian von Mering;Arthur Kobayashi;Asaf A. Salamov

  • First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community.

    Warish Ahmed;Nicola Angel;Janette Edson;Kyle Bibby

  • Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

    Thomas Huber;Geoffrey Faulkner;Philip Hugenholtz

  • Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

    Donovan H. Parks;Christian Rinke;Maria Chuvochina;Pierre-Alain Chaumeil

  • Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.

    Falk Warnecke;Peter Luginbühl;Natalia Ivanova;Majid Ghassemian

  • Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

    Victor Kunin;Anna Engelbrektson;Howard Ochman;Philip Hugenholtz

  • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

    Mads Albertsen;Philip Hugenholtz;Adam Skarshewski;Kåre Lehmann Nielsen

  • CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material

    Donovan H. Parks;Michael Imelfort;Connor T. Skennerton;Philip Hugenholtz

  • Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB

    T.Z. DeSantis;P. Hugenholtz;N. Larsen;M. Rojas

Frequent Co-Authors

Jonathan A. Eisen
Jonathan A. Eisen University of California, Davis
Lynne Goodwin
Lynne Goodwin Los Alamos National Laboratory
Miriam Land
Miriam Land Oak Ridge National Laboratory
Cliff Han
Cliff Han Los Alamos National Laboratory
Loren Hauser
Loren Hauser Digital Infuzion (United States)
John C. Detter
John C. Detter Los Alamos National Laboratory
Nikos C. Kyrpides
Nikos C. Kyrpides Joint Genome Institute
Natalia Ivanova
Natalia Ivanova Lawrence Berkeley National Laboratory
Alla Lapidus
Alla Lapidus Saint Petersburg State University
Jan Fang Cheng
Jan Fang Cheng Lawrence Berkeley National Laboratory

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