Philip Hugenholtz

Affiliations

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

ORCID: http://orcid.org/0000-0001-5386-7925

Publications (69)

A complete domain-to-species taxonomy for Bacteria and Archaea.

Nature biotechnology

Avec: Donovan H Parks , Maria Chuvochina , Pierre-Alain Chaumeil , Christian Rinke , Aaron J Mussig ,

Functional effects of the microbiota in chronic respiratory disease.

The Lancet. Respiratory medicine

Avec: Kurtis F Budden , Shakti D Shukla , Saima Firdous Rehman , Kate L Bowerman , Simon Keely , Darius P H Armstrong-James , Ian M Adcock , Sanjay H Chotirmall , Kian Fan Chung , Philip M Hansbro

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

The ISME journal

Avec: Christian Rinke , Francesco Rubino , Lauren F Messer , Noha Youssef , Donovan H Parks , Maria Chuvochina , Mark Brown , Thomas Jeffries , Gene W Tyson , Justin R Seymour ,

Characterization of the juvenile koala gut microbiome across wild populations.

Environmental microbiology

Avec: Michaela D J Blyton , Rochelle M Soo , Ben D Moore

Proposal to reclassify the proteobacterial classes

International journal of systematic and evolutionary microbiology

Avec: David W Waite , Maria Chuvochina , Claus Pelikan , Donovan H Parks , Pelin Yilmaz , Michael Wagner , Alexander Loy , Takeshi Naganuma , Ryosuke Nakai , William B Whitman , Martin W Hahn , Jan Kuever ,

Relative Time Inference Using Lateral Gene Transfers.

Methods in molecular biology (Clifton, N.J.)

Avec: Adrián A Davín , Dominik Schrempf , Tom A Williams , Gergely J Szöllősi

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

Genome biology and evolution

Avec: Tom A Williams , Adrián A Davín , Benoit Morel , Lénárd L Szánthó , Anja Spang , Alexandros Stamatakis , Gergely J Szöllősi

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.

Nature microbiology

Avec: Soo Jen Low , Mária Džunková , Pierre-Alain Chaumeil , Donovan H Parks ,

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Nature biotechnology

Avec: Simon Roux , Evelien M Adriaenssens , Bas E Dutilh , Eugene V Koonin , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Rob Lavigne , J Rodney Brister , Arvind Varsani , Clara Amid , Ramy K Aziz , Seth R Bordenstein , Peer Bork , Mya Breitbart , Guy R Cochrane , Rebecca A Daly , Christelle Desnues , Melissa B Duhaime , Joanne B Emerson , François Enault , Jed A Fuhrman , Pascal Hingamp , Bonnie L Hurwitz , Natalia N Ivanova , Jessica M Labonté , Kyung-Bum Lee , Rex R Malmstrom , Manuel Martinez-Garcia , Ilene Karsch Mizrachi , Hiroyuki Ogata , David Páez-Espino , Marie-Agnès Petit , Catherine Putonti , Thomas Rattei , Alejandro Reyes , Francisco Rodriguez-Valera , Karyna Rosario , Lynn Schriml , Frederik Schulz , Grieg F Steward , Matthew B Sullivan , Shinichi Sunagawa , Curtis A Suttle , Ben Temperton , Susannah G Tringe , Rebecca Vega Thurber , Nicole S Webster , Katrine L Whiteson , Steven W Wilhelm , K Eric Wommack , Tanja Woyke , Kelly C Wrighton , Pelin Yilmaz , Takashi Yoshida , Mark J Young , Natalya Yutin , Lisa Zeigler Allen , Nikos C Kyrpides , Emiley A Eloe-Fadrosh

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

Avec: Kate L Bowerman , Antiopi Varelias , Nancy Lachner , Rachel D Kuns , Geoffrey R Hill ,

Tracking seasonal changes in diversity of pollen allergen exposure: Targeted metabarcoding of a subtropical aerobiome.

The Science of the total environment

Avec: B C Campbell , J Al Kouba , V Timbrell , M J Noor , K Massel , E K Gilding , N Angel , B Kemish , P Hugenholtz , I D Godwin , J M Davies

Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala.

Animal microbiome

Avec: Michaela D J Blyton , Rochelle M Soo , Desley Whisson , Karen J Marsh , Jack Pascoe , Mark Le Pla , William Foley , Ben D Moore

A rooted phylogeny resolves early bacterial evolution.

Science (New York, N.Y.)

Avec: Gareth A Coleman , Adrián A Davín , Tara A Mahendrarajah , Lénárd L Szánthó , Anja Spang , Gergely J Szöllősi , Tom A Williams

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations.

The ISME journal

Avec: Mukan Ji , Timothy J Williams , Kate Montgomery , Hon Lun Wong , Julian Zaugg , Jonathan F Berengut , Andrew Bissett , Maria Chuvochina , Belinda C Ferrari

Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active-Site Glutamic Acid.

Antimicrobial agents and chemotherapy

Avec: Liam A Wilson , Esmée G Knaven , Marc T Morris , Marcelo Monteiro Pedroso , Christopher J Schofield , Thomas B Brück , Mikael Boden , David W Waite , Luke Guddat , Gerhard Schenk

Anaerobic gut fungal communities in marsupial hosts.

mBio

Avec: Adrienne L Jones , Carrie J Pratt , Casey H Meili , Rochelle M Soo , Mostafa S Elshahed , Noha H Youssef

- Invited Review - Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota.

Animal bioscience

Avec: Lex E X Leong , Stuart E Denman , Seungha Kang , Stanislas Mondot , Chris S McSweeney

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs.

mSphere

Avec: Jacoba I Bromfield , Julian Zaugg , Rodney C Straw , Julia Cathie , Annika Krueger , Debottam Sinha , Janin Chandra , Ian H Frazer

Faecal microbial transfer and complex carbohydrates mediate protection against COPD.

Gut

Avec: Kurtis F Budden , Shakti D Shukla , Kate L Bowerman , Annalicia Vaughan , Shaan L Gellatly , David L A Wood , Nancy Lachner , Sobia Idrees , Saima Firdous Rehman , Alen Faiz , Vyoma K Patel , Chantal Donovan , Charlotte A Alemao , Sj Shen , Nadia Amorim , Rajib Majumder , Kanth S Vanka , Jazz Mason , Tatt Jhong Haw , Bree Tillet , Michael Fricker , Simon Keely , Nicole Hansbro , Gabrielle T Belz , Jay Horvat , Thomas Ashhurst , Caryn van Vreden , Helen McGuire , Barbara Fazekas de St Groth , Nicholas J C King , Ben Crossett , Stuart J Cordwell , Lorenzo Bonaguro , Joachim L Schultze , Emma E Hamilton-Williams , Elizabeth Mann , Samuel C Forster , Matthew A Cooper , Leopoldo N Segal , Sanjay H Chotirmall , Peter Collins , Rayleen Bowman , Kwun M Fong , Ian A Yang , Peter A B Wark , Paul G Dennis , Philip M Hansbro

SeqCode: a nomenclatural code for prokaryotes described from sequence data.

Nature microbiology

Avec: Brian P Hedlund , Maria Chuvochina , Konstantinos T Konstantinidis , Alison E Murray , Marike Palmer , Donovan H Parks , Alexander J Probst , Anna-Louise Reysenbach , Luis M Rodriguez-R , Ramon Rossello-Mora , Iain C Sutcliffe , Stephanus N Venter , William B Whitman

Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.

BMC biology

Avec: James G Volmer , Rochelle M Soo , Paul N Evans , Emily C Hoedt , Ana L Astorga Alsina , Benjamin J Woodcroft , Gene W Tyson , Mark Morrison

A long-awaited taxogenomic investigation of the family

Frontiers in microbiology

Avec: Rafael R de la Haba , David R Arahal , Cristina Sánchez-Porro , Maria Chuvochina , Stijn Wittouck , Antonio Ventosa

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.

The ISME journal

Avec: Tom A Williams , Adrian A Davin , Lénárd L Szánthó , Alexandros Stamatakis , Noah A Wahl , Ben J Woodcroft , Rochelle M Soo , Laura Eme , Paul O Sheridan , Cecile Gubry-Rangin , Anja Spang , Gergely J Szöllősi

Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing.

Scientific reports

Avec: H M H N Bandara , D L A Wood , I Vanwonterghem , P Hugenholtz , B P K Cheung , L P Samaranayake

Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

The ISME journal

Avec: Christian Rinke , Francesco Rubino , Lauren F Messer , Noha Youssef , Donovan H Parks , Maria Chuvochina , Mark Brown , Thomas Jeffries , Gene W Tyson , Justin R Seymour ,

An evolving view of methane metabolism in the Archaea.

Nature reviews. Microbiology

Avec: Paul N Evans , Joel A Boyd , Andy O Leu , Ben J Woodcroft , Donovan H Parks , Gene W Tyson

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.

Nature microbiology

Avec: Adam J Kessler , Ya-Jou Chen , David W Waite , Tess Hutchinson , Sharlynn Koh , M Elena Popa , John Beardall , Perran L M Cook , Chris Greening

IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease.

Blood

Avec: Andrea S Henden , Motoko Koyama , Renee J Robb , Adriana Forero , Rachel D Kuns , Karshing Chang , Kathleen S Ensbey , Antiopi Varelias , Stephen H Kazakoff , Nicole Waddell , Andrew D Clouston , Rabina Giri , Jakob Begun , Bruce R Blazar , Mariapia A Degli-Esposti , Sergei V Kotenko , Steven W Lane , Kate L Bowerman , Ram Savan , Kate H Gartlan , Geoffrey R Hill

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem.

The ISME journal

Avec: Ya-Jou Chen , Pok Man Leung , Jennifer L Wood , Sean K Bay , Adam J Kessler , Guy Shelley , David W Waite , Ashley E Franks , Perran L M Cook , Chris Greening

Chemotaxis shapes the microscale organization of the ocean's microbiome.

Nature

Avec: Jean-Baptiste Raina , Bennett S Lambert , Donovan H Parks , Christian Rinke , Nachshon Siboni , Anna Bramucci , Martin Ostrowski , Brandon Signal , Adrian Lutz , Himasha Mendis , Francesco Rubino , Vicente I Fernandez , Roman Stocker , Gene W Tyson , Justin R Seymour

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.

Nature microbiology

Avec: Stephen Nayfach , David Páez-Espino , Lee Call , Soo Jen Low , Hila Sberro , Natalia N Ivanova , Amy D Proal , Michael A Fischbach , Ami S Bhatt , Nikos C Kyrpides

A standardized archaeal taxonomy for the Genome Taxonomy Database.

Nature microbiology

Avec: Christian Rinke , Maria Chuvochina , Aaron J Mussig , Pierre-Alain Chaumeil , Adrián A Davín , David W Waite , William B Whitman , Donovan H Parks ,

Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils.

Environmental microbiology

Avec: Kate Montgomery , Timothy J Williams , Merryn Brettle , Jonathan F Berengut , Angelique E Ray , Eden Zhang , Julian Zaugg , Belinda C Ferrari

Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient.

The ISME journal

Avec: Sean K Bay , David W Waite , Xiyang Dong , Osnat Gillor , Steven L Chown , Chris Greening

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.

Nucleic acids research

Avec: Donovan H Parks , Maria Chuvochina , Christian Rinke , Aaron J Mussig , Pierre-Alain Chaumeil ,

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N

The ISME journal

Avec: Søren Hallstrøm , Jean-Baptiste Raina , Martin Ostrowski , Donovan H Parks , Gene W Tyson , Roman Stocker , Justin R Seymour , Lasse Riemann

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.

Environmental science & technology

Avec: Xiaole Yin , Xi Chen , Xiao-Tao Jiang , Ying Yang , Bing Li , Marcus Ho-Hin Shum , Tommy T Y Lam , Gabriel M Leung , Joan Rose , Concepcion Sanchez-Cid , Timothy M Vogel , Fiona Walsh , Thomas U Berendonk , Janet Midega , Chibuzor Uchea , Dominic Frigon , Gerard D Wright , Carlos Bezuidenhout , Renata C Picão , Shaikh Z Ahammad , Per Halkjær Nielsen , Nicholas J Ashbolt , Gianluca Corno , Despo Fatta-Kassinos , Helmut Bürgmann , Heike Schmitt , Chang-Jun Cha , Amy Pruden , Kornelia Smalla , Eddie Cytryn , Yu Zhang , Min Yang , Yong-Guan Zhu , Arnaud Dechesne , Barth F Smets , David W Graham , Michael R Gillings , William H Gaze , Célia M Manaia , Mark C M van Loosdrecht , Pedro J J Alvarez , Martin J Blaser , James M Tiedje , Edward Topp , Tong Zhang

Greengenes2 unifies microbial data in a single reference tree.

Nature biotechnology

Avec: Daniel McDonald , Yueyu Jiang , Metin Balaban , Kalen Cantrell , Qiyun Zhu , Antonio Gonzalez , James T Morton , Giorgia Nicolaou , Donovan H Parks , Søren M Karst , Mads Albertsen , Todd DeSantis , Se Jin Song , Andrew Bartko , Aki S Havulinna , Pekka Jousilahti , Susan Cheng , Michael Inouye , Teemu Niiranen , Mohit Jain , Veikko Salomaa , Leo Lahti , Siavash Mirarab , Rob Knight

A unified catalog of 204,938 reference genomes from the human gut microbiome.

Nature biotechnology

Avec: Alexandre Almeida , Stephen Nayfach , Miguel Boland , Francesco Strozzi , Martin Beracochea , Zhou Jason Shi , Katherine S Pollard , Ekaterina Sakharova , Donovan H Parks , Nicola Segata , Nikos C Kyrpides , Robert D Finn

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers.

Journal of travel medicine

Avec: Warish Ahmed , Paul M Bertsch , Nicola Angel , Kyle Bibby , Aaron Bivins , Leanne Dierens , Janette Edson , John Ehret , Pradip Gyawali , Kerry A Hamilton , Ian Hosegood , Guangming Jiang , Masaaki Kitajima , Homa T Sichani , Jiahua Shi , Katja M Shimko , Stuart L Simpson , Wendy J M Smith , Erin M Symonds , Kevin V Thomas , Rory Verhagen , Julian Zaugg , Jochen F Mueller

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

Bioinformatics (Oxford, England)

Avec: Pierre-Alain Chaumeil , Aaron J Mussig , Donovan H Parks

Defining the human gut host-phage network through single-cell viral tagging.

Nature microbiology

Avec: Mária Džunková , Soo Jen Low , Joshua N Daly , Li Deng , Christian Rinke ,

IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota.

Annals of the rheumatic diseases

Avec: Linda M Rehaume , Nicholas Matigian , Ahmed M Mehdi , Nancy Lachner , Kate L Bowerman , Joshua Daly , Kim-Anh Lê Cao , Ranjeny Thomas

Annals of the rheumatic diseases

Avec: Rabia Moentadj , Yiwen Wang , Kate Bowerman , Linda Rehaume , Hendrik Nel , Paraic O Cuiv , Juliette Stephens , Amalina Baharom , Muralidhara Maradana , Vanessa Lakis , Mark Morrison , Timothy Wells , Helen Benham , Kim-Anh Le Cao , Ranjeny Thomas

Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease.

Nature communications

Avec: Kate L Bowerman , Saima Firdous Rehman , Annalicia Vaughan , Nancy Lachner , Kurtis F Budden , Richard Y Kim , David L A Wood , Shaan L Gellatly , Shakti D Shukla , Lisa G Wood , Ian A Yang , Peter A Wark , Philip M Hansbro

Roadmap for naming uncultivated Archaea and Bacteria.

Nature microbiology

Avec: Alison E Murray , John Freudenstein , Simonetta Gribaldo , Roland Hatzenpichler , Peter Kämpfer , Konstantinos T Konstantinidis , Christopher E Lane , R Thane Papke , Donovan H Parks , Ramon Rossello-Mora , Matthew B Stott , Iain C Sutcliffe , J Cameron Thrash , Stephanus N Venter , William B Whitman , Silvia G Acinas , Rudolf I Amann , Karthik Anantharaman , Jean Armengaud , Brett J Baker , Roman A Barco , Helge B Bode , Eric S Boyd , Carrie L Brady , Paul Carini , Patrick S G Chain , Daniel R Colman , Kristen M DeAngelis , Maria Asuncion de Los Rios , Paulina Estrada-de Los Santos , Christopher A Dunlap , Jonathan A Eisen , David Emerson , Thijs J G Ettema , Damien Eveillard , Peter R Girguis , Ute Hentschel , James T Hollibaugh , Laura A Hug , William P Inskeep , Elena P Ivanova , Hans-Peter Klenk , Wen-Jun Li , Karen G Lloyd , Frank E Löffler , Thulani P Makhalanyane , Duane P Moser , Takuro Nunoura , Marike Palmer , Victor Parro , Carlos Pedrós-Alió , Alexander J Probst , Theo H M Smits , Andrew D Steen , Emma T Steenkamp , Anja Spang , Frank J Stewart , James M Tiedje , Peter Vandamme , Michael Wagner , Feng-Ping Wang , Pablo Yarza , Brian P Hedlund , Anna-Louise Reysenbach

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome.

Frontiers in microbiology

Avec: Donovan H Parks , Fabio Rigato , Patricia Vera-Wolf , Lutz Krause , Gene W Tyson , David L A Wood

Secreted Toxins From

Frontiers in microbiology

Avec: Annika Krueger , Julian Zaugg , Sarah Chisholm , Richard Linedale , Nancy Lachner , Siok Min Teoh , Zewen K Tuong , Samuel W Lukowski , Mark Morrison , H Peter Soyer , Michelle M Hill , Ian H Frazer

Effects of laboratory domestication on the rodent gut microbiome.

ISME communications

Avec: Kate L Bowerman , Sarah C L Knowles , Janette E Bradley , Laima Baltrūnaitė , Michael D J Lynch , Kathryn M Jones ,

Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.

ISME communications

Avec: Jiarui Sun , Paul N Evans , Emma J Gagen , Ben J Woodcroft , Brian P Hedlund , Tanja Woyke , Christian Rinke

The koala gut microbiome is largely unaffected by host translocation but rather influences host diet.

Frontiers in microbiology

Avec: Michaela D J Blyton , Jack Pascoe , Emily Hynes , Rochelle M Soo , Ben D Moore

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes.

FEMS microbiology letters

Avec: Maria Chuvochina , Aaron J Mussig , Pierre-Alain Chaumeil , Adam Skarshewski , Christian Rinke , Donovan H Parks ,

Microvolume DNA extraction methods for microscale amplicon and metagenomic studies.

ISME communications

Avec: Anna R Bramucci , Amaranta Focardi , Christian Rinke , Gene W Tyson , Justin R Seymour , Jean-Baptiste Raina

Putative genome contamination has minimal impact on the GTDB taxonomy.

Microbial genomics

Avec: Aaron J Mussig , Pierre-Alain Chaumeil , Maria Chuvochina , Christian Rinke , Donovan H Parks ,

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era.

National science review

Avec: Jian-Yu Jiao , Rashidin Abdugheni , Dao-Feng Zhang , Iftikhar Ahmed , Mukhtiar Ali , Maria Chuvochina , Svetlana N Dedysh , Xiuzhu Dong , Markus Göker , Brian P Hedlund , Kamlesh Jangid , Shuang-Jiang Liu , Edward R B Moore , Manik Prabhu Narsing Rao , Aharon Oren , Ramon Rossello-Mora , Bhagwan Narayan Rekadwad , Nimaichand Salam , Wensheng Shu , Iain C Sutcliffe , Wee Fei Aaron Teo , Martha E Trujillo , Stephanus N Venter , William B Whitman , Guoping Zhao , Wen-Jun Li

Options and considerations for validation of prokaryotic names under the SeqCode.

Systematic and applied microbiology

Avec: Stephanus N Venter , Luis M Rodriguez-R , Maria Chuvochina , Marike Palmer , Emma T Steenkamp

Prokaryotic taxonomy and nomenclature in the age of big sequence data.

The ISME journal

Avec: Maria Chuvochina , Aharon Oren , Donovan H Parks , Rochelle M Soo

The importance of designating type material for uncultured taxa.

Systematic and applied microbiology

Avec: Maria Chuvochina , Christian Rinke , Donovan H Parks , Michael S Rappé , Gene W Tyson , Pelin Yilmaz , William B Whitman ,

Evolution of photosynthesis and aerobic respiration in the cyanobacteria.

Free radical biology & medicine

Avec: Rochelle M Soo , James Hemp ,

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.

The Science of the total environment

Avec: Warish Ahmed , Nicola Angel , Janette Edson , Kyle Bibby , Aaron Bivins , Jake W O'Brien , Phil M Choi , Masaaki Kitajima , Stuart L Simpson , Jiaying Li , Ben Tscharke , Rory Verhagen , Wendy J M Smith , Julian Zaugg , Leanne Dierens , Kevin V Thomas , Jochen F Mueller

Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea.

Nature biotechnology

Avec: Donovan H Parks , Maria Chuvochina , Pierre-Alain Chaumeil , Christian Rinke , Aaron J Mussig ,

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.

Microbiome

Avec: Yulin Wang , Jun Ye , Feng Ju , Lei Liu , Joel A Boyd , Yu Deng , Donovan H Parks , Xiaotao Jiang , Xiaole Yin , Ben J Woodcroft , Gene W Tyson , Martin F Polz , Tong Zhang

Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Eleonora Chiri , Philipp A Nauer , Rachael Lappan , Thanavit Jirapanjawat , David W Waite , Kim M Handley , Perran L M Cook , Stefan K Arndt , Chris Greening

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development.

Environmental microbiology

Avec: Michaela D J Blyton , Rochelle M Soo , Ben D Moore

A genome and gene catalog of glacier microbiomes.

Nature biotechnology

Avec: Yongqin Liu , Mukan Ji , Tao Yu , Julian Zaugg , Alexandre M Anesio , Zhihao Zhang , Songnian Hu , Keshao Liu , Pengfei Liu , Yuying Chen , Yingfeng Luo , Tandong Yao

Skin Cancer-Associated

Cancers

Avec: Annika Krueger , Ahmed Mohamed , Cathryn M Kolka , Thomas Stoll , Julian Zaugg , Richard Linedale , Mark Morrison , H Peter Soyer , Ian H Frazer , Michelle M Hill

Critical evaluation of faecal microbiome preservation using metagenomic analysis.

ISME communications

Avec: Alena L Pribyl , Donovan H Parks , Nicola Z Angel , Joel A Boyd , Alexander G Hasson , Liang Fang , Samantha L MacDonald , Blake A Wills , David L A Wood , Lutz Krause , Gene W Tyson ,

Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients.

ISME communications

Avec: Annika Krueger , Julian Zaugg , Nancy Lachner , Seweryn Bialasiewicz , Lynlee L Lin , Sharon Gabizon , Priyamvada Sobarun , Mark Morrison , H Peter Soyer , Ian H Frazer

Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts.

The ISME journal

Avec: Angelique E Ray , Julian Zaugg , Nicole Benaud , Devan S Chelliah , Sean Bay , Hon Lun Wong , Pok Man Leung , Mukan Ji , Aleks Terauds , Kate Montgomery , Chris Greening , Don A Cowan , Weidong Kong , Timothy J Williams , Belinda C Ferrari

Réseau de co-auteurs

Donovan H Parks 23 collaborations

Maria Chuvochina 16 collaborations

Christian Rinke 13 collaborations

Gene W Tyson 11 collaborations

Julian Zaugg 10 collaborations

Rochelle M Soo 9 collaborations

Pierre-Alain Chaumeil 8 collaborations

Aaron J Mussig 7 collaborations

Kate L Bowerman 7 collaborations

David W Waite 7 collaborations

William B Whitman 6 collaborations

Nancy Lachner 6 collaborations

Justin R Seymour 5 collaborations

Mark Morrison 5 collaborations

Chris Greening 5 collaborations

Michaela D J Blyton 4 collaborations

Ben D Moore 4 collaborations

Adrián A Davín 4 collaborations

Tom A Williams 4 collaborations

Gergely J Szöllősi 4 collaborations

Anja Spang 4 collaborations

Annika Krueger 4 collaborations

Ian H Frazer 4 collaborations

David L A Wood 4 collaborations

Brian P Hedlund 4 collaborations

Stephanus N Venter 4 collaborations

Ben J Woodcroft 4 collaborations

Kurtis F Budden 3 collaborations

Shakti D Shukla 3 collaborations

Saima Firdous Rehman 3 collaborations

Philip M Hansbro 3 collaborations

Francesco Rubino 3 collaborations

Pelin Yilmaz 3 collaborations

Lénárd L Szánthó 3 collaborations

Soo Jen Low 3 collaborations

Nikos C Kyrpides 3 collaborations

Mukan Ji 3 collaborations

Timothy J Williams 3 collaborations

Kate Montgomery 3 collaborations

Belinda C Ferrari 3 collaborations

Marike Palmer 3 collaborations

Ramon Rossello-Mora 3 collaborations

Iain C Sutcliffe 3 collaborations

Paul N Evans 3 collaborations

Joel A Boyd 3 collaborations

Perran L M Cook 3 collaborations

Jean-Baptiste Raina 3 collaborations

H Peter Soyer 3 collaborations

Simon Keely 2 collaborations

Sanjay H Chotirmall 2 collaborations

Lauren F Messer 2 collaborations

Noha Youssef 2 collaborations

Mark Brown 2 collaborations

Thomas Jeffries 2 collaborations

Michael Wagner 2 collaborations

Alexandros Stamatakis 2 collaborations

Mária Džunková 2 collaborations

Natalia N Ivanova 2 collaborations

David Páez-Espino 2 collaborations

Tanja Woyke 2 collaborations

Antiopi Varelias 2 collaborations

Rachel D Kuns 2 collaborations

Geoffrey R Hill 2 collaborations

P Hugenholtz 2 collaborations

Jack Pascoe 2 collaborations

Hon Lun Wong 2 collaborations

Jonathan F Berengut 2 collaborations

Annalicia Vaughan 2 collaborations

Shaan L Gellatly 2 collaborations

Ian A Yang 2 collaborations

Konstantinos T Konstantinidis 2 collaborations

Alison E Murray 2 collaborations

Alexander J Probst 2 collaborations

Anna-Louise Reysenbach 2 collaborations

Luis M Rodriguez-R 2 collaborations

Adam J Kessler 2 collaborations

Ya-Jou Chen 2 collaborations

Pok Man Leung 2 collaborations

Sean K Bay 2 collaborations

Martin Ostrowski 2 collaborations

Roman Stocker 2 collaborations

Stephen Nayfach 2 collaborations

Angelique E Ray 2 collaborations

Xiaole Yin 2 collaborations

James M Tiedje 2 collaborations

Tong Zhang 2 collaborations

Warish Ahmed 2 collaborations

Nicola Angel 2 collaborations

Kyle Bibby 2 collaborations

Aaron Bivins 2 collaborations

Leanne Dierens 2 collaborations

Janette Edson 2 collaborations

Masaaki Kitajima 2 collaborations

Stuart L Simpson 2 collaborations

Wendy J M Smith 2 collaborations

Kevin V Thomas 2 collaborations

Rory Verhagen 2 collaborations

Jochen F Mueller 2 collaborations

Ranjeny Thomas 2 collaborations

Wen-Jun Li 2 collaborations

Emma T Steenkamp 2 collaborations

Lutz Krause 2 collaborations

Richard Linedale 2 collaborations

Michelle M Hill 2 collaborations

Aharon Oren 2 collaborations

Darius P H Armstrong-James 1 collaboration

Ian M Adcock 1 collaboration

Kian Fan Chung 1 collaboration

Claus Pelikan 1 collaboration

Alexander Loy 1 collaboration

Takeshi Naganuma 1 collaboration

Ryosuke Nakai 1 collaboration

Martin W Hahn 1 collaboration

Jan Kuever 1 collaboration

Dominik Schrempf 1 collaboration

Benoit Morel 1 collaboration

Simon Roux 1 collaboration

Evelien M Adriaenssens 1 collaboration

Bas E Dutilh 1 collaboration

Eugene V Koonin 1 collaboration

Andrew M Kropinski 1 collaboration

Mart Krupovic 1 collaboration

Jens H Kuhn 1 collaboration

Rob Lavigne 1 collaboration

J Rodney Brister 1 collaboration

Arvind Varsani 1 collaboration

Clara Amid 1 collaboration

Ramy K Aziz 1 collaboration

Seth R Bordenstein 1 collaboration

Peer Bork 1 collaboration

Mya Breitbart 1 collaboration

Guy R Cochrane 1 collaboration

Rebecca A Daly 1 collaboration

Christelle Desnues 1 collaboration

Melissa B Duhaime 1 collaboration

Joanne B Emerson 1 collaboration

François Enault 1 collaboration

Jed A Fuhrman 1 collaboration

Pascal Hingamp 1 collaboration

Bonnie L Hurwitz 1 collaboration

Jessica M Labonté 1 collaboration

Kyung-Bum Lee 1 collaboration

Rex R Malmstrom 1 collaboration

Manuel Martinez-Garcia 1 collaboration

Ilene Karsch Mizrachi 1 collaboration

Hiroyuki Ogata 1 collaboration

Marie-Agnès Petit 1 collaboration

Catherine Putonti 1 collaboration

Thomas Rattei 1 collaboration

Alejandro Reyes 1 collaboration

Francisco Rodriguez-Valera 1 collaboration

Karyna Rosario 1 collaboration

Lynn Schriml 1 collaboration

Frederik Schulz 1 collaboration

Grieg F Steward 1 collaboration

Matthew B Sullivan 1 collaboration

Shinichi Sunagawa 1 collaboration

Curtis A Suttle 1 collaboration

Ben Temperton 1 collaboration

Susannah G Tringe 1 collaboration

Rebecca Vega Thurber 1 collaboration

Nicole S Webster 1 collaboration

Katrine L Whiteson 1 collaboration

Steven W Wilhelm 1 collaboration

K Eric Wommack 1 collaboration

Kelly C Wrighton 1 collaboration

Takashi Yoshida 1 collaboration

Mark J Young 1 collaboration

Natalya Yutin 1 collaboration

Lisa Zeigler Allen 1 collaboration

Emiley A Eloe-Fadrosh 1 collaboration

B C Campbell 1 collaboration

J Al Kouba 1 collaboration

V Timbrell 1 collaboration

M J Noor 1 collaboration

K Massel 1 collaboration

E K Gilding 1 collaboration

N Angel 1 collaboration

B Kemish 1 collaboration

I D Godwin 1 collaboration

J M Davies 1 collaboration

Desley Whisson 1 collaboration

Karen J Marsh 1 collaboration

Mark Le Pla 1 collaboration

William Foley 1 collaboration

Gareth A Coleman 1 collaboration

Tara A Mahendrarajah 1 collaboration

Andrew Bissett 1 collaboration

Liam A Wilson 1 collaboration

Esmée G Knaven 1 collaboration

Marc T Morris 1 collaboration

Marcelo Monteiro Pedroso 1 collaboration

Christopher J Schofield 1 collaboration

Thomas B Brück 1 collaboration

Mikael Boden 1 collaboration

Luke Guddat 1 collaboration

Gerhard Schenk 1 collaboration

Adrienne L Jones 1 collaboration

Carrie J Pratt 1 collaboration

Casey H Meili 1 collaboration

Mostafa S Elshahed 1 collaboration

Noha H Youssef 1 collaboration

Lex E X Leong 1 collaboration

Stuart E Denman 1 collaboration

Seungha Kang 1 collaboration

Stanislas Mondot 1 collaboration

Chris S McSweeney 1 collaboration

Jacoba I Bromfield 1 collaboration

Rodney C Straw 1 collaboration

Julia Cathie 1 collaboration

Debottam Sinha 1 collaboration

Janin Chandra 1 collaboration

Sobia Idrees 1 collaboration

Alen Faiz 1 collaboration

Vyoma K Patel 1 collaboration

Chantal Donovan 1 collaboration

Charlotte A Alemao 1 collaboration

Sj Shen 1 collaboration

Nadia Amorim 1 collaboration

Rajib Majumder 1 collaboration

Kanth S Vanka 1 collaboration

Jazz Mason 1 collaboration

Tatt Jhong Haw 1 collaboration

Bree Tillet 1 collaboration

Michael Fricker 1 collaboration

Nicole Hansbro 1 collaboration

Gabrielle T Belz 1 collaboration

Jay Horvat 1 collaboration

Thomas Ashhurst 1 collaboration

Caryn van Vreden 1 collaboration

Helen McGuire 1 collaboration

Barbara Fazekas de St Groth 1 collaboration

Nicholas J C King 1 collaboration

Ben Crossett 1 collaboration

Stuart J Cordwell 1 collaboration

Lorenzo Bonaguro 1 collaboration

Joachim L Schultze 1 collaboration

Emma E Hamilton-Williams 1 collaboration

Elizabeth Mann 1 collaboration

Samuel C Forster 1 collaboration

Matthew A Cooper 1 collaboration

Leopoldo N Segal 1 collaboration

Peter Collins 1 collaboration

Rayleen Bowman 1 collaboration

Kwun M Fong 1 collaboration

Peter A B Wark 1 collaboration

Paul G Dennis 1 collaboration

James G Volmer 1 collaboration

Emily C Hoedt 1 collaboration

Ana L Astorga Alsina 1 collaboration

Benjamin J Woodcroft 1 collaboration

Rafael R de la Haba 1 collaboration

David R Arahal 1 collaboration

Cristina Sánchez-Porro 1 collaboration

Stijn Wittouck 1 collaboration

Antonio Ventosa 1 collaboration

Adrian A Davin 1 collaboration

Noah A Wahl 1 collaboration

Laura Eme 1 collaboration

Paul O Sheridan 1 collaboration

Cecile Gubry-Rangin 1 collaboration

H M H N Bandara 1 collaboration

D L A Wood 1 collaboration

I Vanwonterghem 1 collaboration

B P K Cheung 1 collaboration

L P Samaranayake 1 collaboration

Andy O Leu 1 collaboration

Tess Hutchinson 1 collaboration

Sharlynn Koh 1 collaboration

M Elena Popa 1 collaboration

John Beardall 1 collaboration

Andrea S Henden 1 collaboration

Motoko Koyama 1 collaboration

Renee J Robb 1 collaboration

Adriana Forero 1 collaboration

Karshing Chang 1 collaboration

Kathleen S Ensbey 1 collaboration

Stephen H Kazakoff 1 collaboration

Nicole Waddell 1 collaboration

Andrew D Clouston 1 collaboration

Rabina Giri 1 collaboration

Jakob Begun 1 collaboration

Bruce R Blazar 1 collaboration

Mariapia A Degli-Esposti 1 collaboration

Sergei V Kotenko 1 collaboration

Steven W Lane 1 collaboration

Ram Savan 1 collaboration

Kate H Gartlan 1 collaboration

Jennifer L Wood 1 collaboration

Guy Shelley 1 collaboration

Ashley E Franks 1 collaboration

Bennett S Lambert 1 collaboration

Nachshon Siboni 1 collaboration

Anna Bramucci 1 collaboration

Brandon Signal 1 collaboration

Adrian Lutz 1 collaboration

Himasha Mendis 1 collaboration

Vicente I Fernandez 1 collaboration

Lee Call 1 collaboration

Hila Sberro 1 collaboration

Amy D Proal 1 collaboration

Michael A Fischbach 1 collaboration

Ami S Bhatt 1 collaboration

Merryn Brettle 1 collaboration

Eden Zhang 1 collaboration

Xiyang Dong 1 collaboration

Osnat Gillor 1 collaboration

Steven L Chown 1 collaboration

Søren Hallstrøm 1 collaboration

Lasse Riemann 1 collaboration

Xi Chen 1 collaboration

Xiao-Tao Jiang 1 collaboration

Ying Yang 1 collaboration

Bing Li 1 collaboration

Marcus Ho-Hin Shum 1 collaboration

Tommy T Y Lam 1 collaboration

Gabriel M Leung 1 collaboration

Joan Rose 1 collaboration

Concepcion Sanchez-Cid 1 collaboration

Timothy M Vogel 1 collaboration

Fiona Walsh 1 collaboration

Thomas U Berendonk 1 collaboration

Janet Midega 1 collaboration

Chibuzor Uchea 1 collaboration

Dominic Frigon 1 collaboration

Gerard D Wright 1 collaboration

Carlos Bezuidenhout 1 collaboration

Renata C Picão 1 collaboration

Shaikh Z Ahammad 1 collaboration

Per Halkjær Nielsen 1 collaboration

Nicholas J Ashbolt 1 collaboration

Gianluca Corno 1 collaboration

Despo Fatta-Kassinos 1 collaboration

Helmut Bürgmann 1 collaboration

Heike Schmitt 1 collaboration

Chang-Jun Cha 1 collaboration

Amy Pruden 1 collaboration

Kornelia Smalla 1 collaboration

Eddie Cytryn 1 collaboration

Yu Zhang 1 collaboration

Min Yang 1 collaboration

Yong-Guan Zhu 1 collaboration

Arnaud Dechesne 1 collaboration

Barth F Smets 1 collaboration

David W Graham 1 collaboration

Michael R Gillings 1 collaboration

William H Gaze 1 collaboration

Célia M Manaia 1 collaboration

Mark C M van Loosdrecht 1 collaboration

Pedro J J Alvarez 1 collaboration

Martin J Blaser 1 collaboration

Edward Topp 1 collaboration

Daniel McDonald 1 collaboration

Yueyu Jiang 1 collaboration

Metin Balaban 1 collaboration

Kalen Cantrell 1 collaboration

Qiyun Zhu 1 collaboration

Antonio Gonzalez 1 collaboration

James T Morton 1 collaboration

Giorgia Nicolaou 1 collaboration

Søren M Karst 1 collaboration

Mads Albertsen 1 collaboration

Todd DeSantis 1 collaboration

Se Jin Song 1 collaboration

Andrew Bartko 1 collaboration

Aki S Havulinna 1 collaboration

Pekka Jousilahti 1 collaboration

Susan Cheng 1 collaboration

Michael Inouye 1 collaboration

Teemu Niiranen 1 collaboration

Mohit Jain 1 collaboration

Veikko Salomaa 1 collaboration

Leo Lahti 1 collaboration

Siavash Mirarab 1 collaboration

Rob Knight 1 collaboration

Alexandre Almeida 1 collaboration

Miguel Boland 1 collaboration

Francesco Strozzi 1 collaboration

Martin Beracochea 1 collaboration

Zhou Jason Shi 1 collaboration

Katherine S Pollard 1 collaboration

Ekaterina Sakharova 1 collaboration

Nicola Segata 1 collaboration

Robert D Finn 1 collaboration

Paul M Bertsch 1 collaboration

John Ehret 1 collaboration

Pradip Gyawali 1 collaboration

Kerry A Hamilton 1 collaboration

Ian Hosegood 1 collaboration

Guangming Jiang 1 collaboration

Homa T Sichani 1 collaboration

Jiahua Shi 1 collaboration

Katja M Shimko 1 collaboration

Erin M Symonds 1 collaboration

Joshua N Daly 1 collaboration

Li Deng 1 collaboration

Linda M Rehaume 1 collaboration

Nicholas Matigian 1 collaboration

Ahmed M Mehdi 1 collaboration

Joshua Daly 1 collaboration

Kim-Anh Lê Cao 1 collaboration

Rabia Moentadj 1 collaboration

Yiwen Wang 1 collaboration

Kate Bowerman 1 collaboration

Linda Rehaume 1 collaboration

Hendrik Nel 1 collaboration

Paraic O Cuiv 1 collaboration

Juliette Stephens 1 collaboration

Amalina Baharom 1 collaboration

Muralidhara Maradana 1 collaboration

Vanessa Lakis 1 collaboration

Timothy Wells 1 collaboration

Helen Benham 1 collaboration

Kim-Anh Le Cao 1 collaboration

Richard Y Kim 1 collaboration

Lisa G Wood 1 collaboration

Peter A Wark 1 collaboration

John Freudenstein 1 collaboration

Simonetta Gribaldo 1 collaboration

Roland Hatzenpichler 1 collaboration

Peter Kämpfer 1 collaboration

Christopher E Lane 1 collaboration

R Thane Papke 1 collaboration

Matthew B Stott 1 collaboration

J Cameron Thrash 1 collaboration

Silvia G Acinas 1 collaboration

Rudolf I Amann 1 collaboration

Karthik Anantharaman 1 collaboration

Jean Armengaud 1 collaboration

Brett J Baker 1 collaboration

Roman A Barco 1 collaboration

Helge B Bode 1 collaboration

Eric S Boyd 1 collaboration

Carrie L Brady 1 collaboration

Paul Carini 1 collaboration

Patrick S G Chain 1 collaboration

Daniel R Colman 1 collaboration

Kristen M DeAngelis 1 collaboration

Maria Asuncion de Los Rios 1 collaboration

Paulina Estrada-de Los Santos 1 collaboration

Christopher A Dunlap 1 collaboration

Jonathan A Eisen 1 collaboration

David Emerson 1 collaboration

Thijs J G Ettema 1 collaboration

Damien Eveillard 1 collaboration

Peter R Girguis 1 collaboration

Ute Hentschel 1 collaboration

James T Hollibaugh 1 collaboration

Laura A Hug 1 collaboration

William P Inskeep 1 collaboration

Elena P Ivanova 1 collaboration

Hans-Peter Klenk 1 collaboration

Karen G Lloyd 1 collaboration

Frank E Löffler 1 collaboration

Thulani P Makhalanyane 1 collaboration

Duane P Moser 1 collaboration

Takuro Nunoura 1 collaboration

Victor Parro 1 collaboration

Carlos Pedrós-Alió 1 collaboration

Theo H M Smits 1 collaboration

Andrew D Steen 1 collaboration

Frank J Stewart 1 collaboration

Peter Vandamme 1 collaboration

Feng-Ping Wang 1 collaboration

Pablo Yarza 1 collaboration

Fabio Rigato 1 collaboration

Patricia Vera-Wolf 1 collaboration

Sarah Chisholm 1 collaboration

Siok Min Teoh 1 collaboration

Zewen K Tuong 1 collaboration

Samuel W Lukowski 1 collaboration

Sarah C L Knowles 1 collaboration

Janette E Bradley 1 collaboration

Laima Baltrūnaitė 1 collaboration

Michael D J Lynch 1 collaboration

Kathryn M Jones 1 collaboration

Jiarui Sun 1 collaboration

Emma J Gagen 1 collaboration

Emily Hynes 1 collaboration

Adam Skarshewski 1 collaboration

Anna R Bramucci 1 collaboration

Amaranta Focardi 1 collaboration

Jian-Yu Jiao 1 collaboration

Rashidin Abdugheni 1 collaboration

Dao-Feng Zhang 1 collaboration

Iftikhar Ahmed 1 collaboration

Mukhtiar Ali 1 collaboration

Svetlana N Dedysh 1 collaboration

Xiuzhu Dong 1 collaboration

Markus Göker 1 collaboration

Kamlesh Jangid 1 collaboration

Shuang-Jiang Liu 1 collaboration

Edward R B Moore 1 collaboration

Manik Prabhu Narsing Rao 1 collaboration

Bhagwan Narayan Rekadwad 1 collaboration

Nimaichand Salam 1 collaboration

Wensheng Shu 1 collaboration

Wee Fei Aaron Teo 1 collaboration

Martha E Trujillo 1 collaboration

Guoping Zhao 1 collaboration

Michael S Rappé 1 collaboration

James Hemp 1 collaboration

Jake W O'Brien 1 collaboration

Phil M Choi 1 collaboration

Jiaying Li 1 collaboration

Ben Tscharke 1 collaboration

Yulin Wang 1 collaboration

Jun Ye 1 collaboration

Feng Ju 1 collaboration

Lei Liu 1 collaboration

Yu Deng 1 collaboration

Xiaotao Jiang 1 collaboration

Martin F Polz 1 collaboration

Eleonora Chiri 1 collaboration

Philipp A Nauer 1 collaboration

Rachael Lappan 1 collaboration

Thanavit Jirapanjawat 1 collaboration

Kim M Handley 1 collaboration

Stefan K Arndt 1 collaboration

Yongqin Liu 1 collaboration

Tao Yu 1 collaboration

Alexandre M Anesio 1 collaboration

Zhihao Zhang 1 collaboration

Songnian Hu 1 collaboration

Keshao Liu 1 collaboration

Pengfei Liu 1 collaboration

Yuying Chen 1 collaboration

Yingfeng Luo 1 collaboration

Tandong Yao 1 collaboration

Ahmed Mohamed 1 collaboration

Cathryn M Kolka 1 collaboration

Thomas Stoll 1 collaboration

Alena L Pribyl 1 collaboration

Nicola Z Angel 1 collaboration

Alexander G Hasson 1 collaboration

Liang Fang 1 collaboration

Samantha L MacDonald 1 collaboration

Blake A Wills 1 collaboration

Seweryn Bialasiewicz 1 collaboration

Lynlee L Lin 1 collaboration

Sharon Gabizon 1 collaboration

Priyamvada Sobarun 1 collaboration

Nicole Benaud 1 collaboration

Devan S Chelliah 1 collaboration

Sean Bay 1 collaboration

Aleks Terauds 1 collaboration

Don A Cowan 1 collaboration

Weidong Kong 1 collaboration