tom delmont

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Publications

Genomics-based quantitative biogeography of marine plankton

Margaux Crédeville , Roy El Hourany , Swan Sow , Julie Poulain , Manon Depaty et al.

2025

Pré-publication, Document de travail hal-05363600v1

A new deep-branching environmental lineage of algae

Mahwash Jamy , Thomas Huber , Thibault Antoine , Hans-Joachim Ruscheweyh , Lucas Paoli et al.

2025

Pré-publication, Document de travail hal-05363587v1

Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo

Matthew Schechter , Florian Trigodet , Iva Veseli , Samuel Miller , Matthew Klein et al.

2025

Pré-publication, Document de travail hal-05363596v1
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Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments

Hermine Billard , Maxime Fuster , François Enault , Jean-François Carrias , Léa Fargette et al.

2024

Pré-publication, Document de travail hal-04797458v1
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Closest relatives of poxviruses are spread in the gut of humans and animals worldwide: the egoviruses

Morgan Gaïa , Hans-Joachim Ruscheweyh , A. Murat Eren , Eugene Koonin , Shinichi Sunagawa et al.

2025

Pré-publication, Document de travail hal-05363610v1

Complex genomes of early nucleocytoviruses revealed by ancient origins of viral aminoacyl-tRNA synthetases

Soichiro Kijima , Hiroyuki Hikida , Tom Delmont , Morgan Gaïa , Hiroyuki Ogata

2024

Pré-publication, Document de travail hal-04399845v1
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Mirusviruses provide a missing link in the evolution of giant viruses Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses

Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni et al.

2022

Pré-publication, Document de travail (preprint/prepublication) hal-03876463v1
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Restructuring of genomic provinces of surface ocean plankton under climate change

Paul Frémont , Marion Gehlen , Mathieu Vrac , Jade Leconte , Tom O. Delmont et al.

2021

Pré-publication, Document de travail cea-03166589v2

Equatorial to Polar genomic variability of the microalgae <i>Bathycoccus prasinos</i>

Jade Leconte , Youri Timsit , Tom O Delmont , Magali Lescot , Gwenael Piganeau et al.

2023

Pré-publication, Document de travail (preprint/prepublication) hal-04308022v1

Environmental genomics points to non-diazotrophic $Trichodesmium$ species abundant and widespread in the open ocean

Tom Delmont

2021

Pré-publication, Document de travail hal-03480637v1
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Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments

Hermine Billard , Maxime Fuster , François Enault , Jean-François Carrias , Léa Fargette et al.

ISME Communications, 2025, 5 (1), pp.ycaf098. ⟨10.1093/ismeco/ycaf098⟩

Article dans une revue hal-05351916v1
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Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes

Sofia Medvedeva , Ulysse Guyet , Eric Pelletier , Hans-Joachim Ruscheweyh , Shinichi Sunagawa et al.

Nature Microbiology, 2025, 11 (1), pp.228-239. ⟨10.1038/s41564-025-02190-6⟩

Article dans une revue pasteur-05442839v1

Complex Genomes of Early Nucleocytoviruses Revealed by Ancient Origins of Viral Aminoacyl-tRNA Synthetases

Soichiro Kijima , Hiroyuki Hikida , Tom Delmont , Morgan Gaïa , Hiroyuki Ogata

Molecular Biology and Evolution, 2024, 41 (8), pp.msae149. ⟨10.1093/molbev/msae149⟩

Article dans une revue hal-05363609v1
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Discovery of Eremiobacterota with <i>nifH</i> homologues in tundra soil

Igor S Pessi , Tom O Delmont , Jonathan P Zehr , Jenni Hultman

Environmental Microbiology Reports, 2024, 16 (3), pp.e13277. ⟨10.1111/1758-2229.13277⟩

Article dans une revue hal-04776164v1

Bioprospecting marine microbial genomes to improve biotechnology

A. Murat Eren , Tom Delmont

Nature, 2024, 633 (8029), pp.287-288. ⟨10.1038/d41586-024-02661-6⟩

Article dans une revue hal-05363602v1
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The defensome of complex bacterial communities

Angelina Beavogui , Auriane Lacroix , Nicolas Wiart , Julie Poulain , Tom O Delmont et al.

Nature Communications, 2023, 15, pp.2146. ⟨10.1101/2023.08.12.553040⟩

Article dans une revue hal-04406189v2
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Genomic adaptation of giant viruses in polar oceans

Lingjie Meng , Tom Delmont , Morgan Gaïa , Eric Pelletier , Antonio Fernàndez-Guerra et al.

Nature Communications, 2023, 14 (1), pp.6233. ⟨10.1038/s41467-023-41910-6⟩

Article dans une revue hal-04385851v1
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Mirusviruses link herpesviruses to giant viruses

Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni et al.

Nature, 2023, 616 (7958), pp.783-789. ⟨10.1038/s41586-023-05962-4⟩

Article dans une revue pasteur-04085734v1
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Tracing the invertebrate herpesviruses in the global sequence datasets

Umberto Rosani , Morgan Gaia , Tom O Delmont , Mart Krupovic

Frontiers in Marine Science, 2023, 10, pp.1159754. ⟨10.3389/fmars.2023.1159754⟩

Article dans une revue pasteur-04162270v1

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

Igor Pessi , Sirja Viitamäki , Anna-Maria Virkkala , Eeva Eronen-Rasimus , Tom Delmont et al.

Environmental Microbiome, 2022, 17 (1), pp.30. ⟨10.1186/s40793-022-00424-2⟩

Article dans une revue cea-04425162v1
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Restructuring of plankton genomic biogeography in the surface ocean under climate change

Paul Frémont , Marion Gehlen , Mathieu Vrac , Jade Leconte , Tom O. Delmont et al.

Nature Climate Change, 2022, 12 (4), pp.393-401. ⟨10.1038/s41558-022-01314-8⟩

Article dans une revue insu-03659872v1
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Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Tom Delmont , Morgan Gaia , Damien Hinsinger , Paul Frémont , Chiara Vanni et al.

Cell Genomics, 2022, 2 (5), pp.100123. ⟨10.1016/j.xgen.2022.100123⟩

Article dans une revue hal-03872935v2
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Giant viruses encode actin-related proteins

Violette da Cunha , Morgan Gaia , Hiroyuki Ogata , Olivier Jaillon , Tom O Delmont et al.

Molecular Biology and Evolution, 2022, 39 (2), pp.msac022. ⟨10.1093/molbev/msac022⟩

Article dans une revue cea-04281384v1

Unifying the known and unknown microbial coding sequence space

Chiara Vanni , Matthew Schechter , Silvia Acinas , Albert Barberán , Pier Luigi Buttigieg et al.

eLife, 2022, 11, ⟨10.7554/eLife.67667⟩

Article dans une revue cea-04425144v1
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Priorities for ocean microbiome research

Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas et al.

Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩

Article dans une revue hal-03781942v1
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Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont et al.

eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩

Article dans une revue hal-02399723v2
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The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

Caroline Vernette , Julien Lecubin , Pablo Sánchez , (team) Tara Oceans Coordinators , Shinichi Sunagawa et al.

Nucleic Acids Research, 2022, 11, ⟨10.1093/nar/gkac420⟩

Article dans une revue hal-03696136v1
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Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Tom Delmont , Juan José Pierella Karlusich , Iva Veseli , Jessika Fuessel , A. Murat Eren et al.

The International Society of Microbiologial Ecology Journal, 2021, 16 (4), pp.927-936. ⟨10.1038/s41396-021-01135-1⟩

Article dans une revue hal-03480646v1
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Discovery of viral myosin genes with complex evolutionary history within plankton

Soichiro Kijima , Tom O. Delmont , Urara Miyazaki , Morgan Gaia , Hisashi Endo et al.

Frontiers in Microbiology, 2021, 12, pp.e683294. ⟨10.3389/fmicb.2021.683294⟩

Article dans une revue hal-04288984v1

Community-led, integrated, reproducible multi-omics with anvi'o

A. Murat Eren , Evan Kiefl , Alon Shaiber , Iva Veseli , Samuel E. Miller et al.

Nature Microbiology, 2021, 6 (1), pp.3-6. ⟨10.1038/s41564-020-00834-3⟩

Article dans une revue cea-04284764v1

Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean

Tom O. Delmont

Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (46), pp.e2112355118. ⟨10.1073/pnas.2112355118j1of10⟩

Article dans une revue cea-04284763v1

Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication

Lara Puetz , Tom Delmont , Ostaizka Aizpurua , Chunxue Guo , Guojie Zhang et al.

Advanced Genetics, 2021, 2 (4), ⟨10.1002/ggn2.202100018⟩

Article dans une revue hal-04376251v1
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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

Hiroto Kaneko , Romain Blanc-Mathieu , Hisashi Endo , Samuel Chaffron , Tom Delmont et al.

iScience, 2021, 24 (1), pp.102002. ⟨10.1016/j.isci.2020.102002⟩

Article dans une revue hal-03097258v3

Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms

Petra Bulankova , Mirna Sekulić , Denis Jallet , Charlotte Nef , Cock van Oosterhout et al.

Current Biology, 2021, 31 (15), pp.3221-+. ⟨10.1016/j.cub.2021.05.013⟩

Article dans une revue hal-03333507v1
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Genome-resolved metagenomics suggests a mutualistic relationship between $Mycoplasma$ and salmonid hosts

Jacob A. Rasmussen , Kasper R. Villumsen , David A. Duchene , Lara C. Puetz , Tom O. Delmont et al.

Communications Biology, 2021, 4 (1), pp.e579. ⟨10.1038/s42003-021-02105-1⟩

Article dans une revue hal-04288991v1

Early-life microbial restitution reduces colitis risk promoted by antibiotic-induced gut dysbiosis in interleukin 10(-/-) mice

Jun Miyoshi , Sawako Miyoshi , Tom O. Delmont , Candace Cham , Sonny T. M. Lee et al.

Gastroenterology, 2021, 161 (3), pp.940-952. ⟨10.1053/j.gastro.2021.05.054⟩

Article dans une revue hal-04288988v1
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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Jiarong R. Guo , Ben Bolduc , Ahmed A. Zayed , Arvind Varsani , Guillermo Dominguez-Huerta et al.

Microbiome, 2021, 9 (1), pp.37. ⟨10.1186/s40168-020-00990-y⟩

Article dans une revue cea-04284766v1
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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Alexey Vorobev , Marion Dupouy , Quentin Carradec , Tom O. Delmont , Anita Annamalé et al.

Genome Research, 2020, 30 (4), pp.647-659. ⟨10.1101/gr.253070.119⟩

Article dans une revue hal-02573621v1
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Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Alon Shaiber , Amy D. Willis , Tom O. Delmont , Simon Roux , Lin-Xing Chen et al.

Genome Biology, 2020, 21, pp.292. ⟨10.1186/s13059-020-02195-w⟩

Article dans une revue cea-04300151v1
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Effects of iron and light availability on phytoplankton photosynthetic properties in the Ross Sea

Anne-Carlijn Alderkamp , Gert L. Van Dijken , Kate E. Lowry , Kate M. Lewis , Hannah L. Joy-Warren et al.

Marine Ecology Progress Series, 2019, 621, pp.33-50. ⟨10.3354/meps13000⟩

Article dans une revue cea-04307620v1

Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota

Luke J. Mckay , Mensur Dlakic , Matthew W. Fields , Tom O. Delmont , A. Murat Eren et al.

Nature Microbiology, 2019, 4 (4), pp.614-622. ⟨10.1038/s41564-019-0362-4⟩

Article dans une revue cea-04309464v1
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Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

Rika E. Anderson , Julie Reveillaud , Emily Reddington , Tom O. Delmont , A. Murat Eren et al.

Nature Communications, 2017, 8, ⟨10.1038/s41467-017-01228-6⟩

Article dans une revue hal-02622497v1

Functional Basis of Microorganism Classification

Chengsheng Zhu , Tom O. Delmont , Timothy M. Vogel , Yana Bromberg

PLoS Computational Biology, 2015, 11 (8), ⟨10.1371/journal.pcbi.1004472⟩

Article dans une revue hal-01589154v1
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Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

Tom O. Delmont , A. Murat Eren , Lorrie Maccario , Emmanuel Prestat , Özcan C. Esen et al.

Frontiers in Microbiology, 2015, 6, pp.358. ⟨10.3389/fmicb.2015.00358⟩

Article dans une revue hal-01589179v1

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library

Samuel Jacquiod , Sandrine Demanèche , Laure Franqueville , Luka Ausec , Zhuofei Xu et al.

Journal of Biotechnology, 2014, epub ahead of print. ⟨10.1016/j.jbiotec.2014.03.036⟩

Article dans une revue istex hal-00989480v1

Microbial community development and unseen diversity recovery in inoculated sterile soil

Tom Delmont , Davide Francioli , Sophie Jacquesson , Sandra Laoudi , Alban Mathieu et al.

Biology and Fertility of Soils, 2014, 50 (7), pp.1069 - 1076. ⟨10.1007/s00374-014-0925-8⟩

Article dans une revue hal-01928111v1

Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment

Joseph Nesme , Sébastien Cecillon , Tom Delmont , Jean-Michel Monier , Timothy M. Vogel et al.

Current Biology, 2014, pp.voir DOI. ⟨10.1016/j.cub.2014.03.036⟩

Article dans une revue hal-00988678v1

Life on Human Surfaces: Skin Metagenomics

Alban Mathieu , Tom Delmont , Timothy M. Vogel , Patrick Robe , Renaud Nalin et al.

PLoS ONE, 2013, 8 (6), pp.e65288. ⟨10.1371/journal.pone.0065288⟩

Article dans une revue hal-00846134v1

Mastering methodological pitfalls for surviving the metagenomic jungle.

Tom Delmont , Pascal Simonet , Timothy M. Vogel

BioEssays, 2013, 35 (8), pp.744-54. ⟨10.1002/bies.201200155⟩

Article dans une revue istex hal-00846141v1

Structure, fluctuation and magnitude of a natural grassland soil metagenome.

Tom Delmont , Emmanuel Prestat , Kevin P. Keegan , Michael Faubladier , Patrick Robe et al.

The International Society of Microbiologial Ecology Journal, 2012, 6 (9), pp.1677-87. ⟨10.1038/ismej.2011.197⟩

Article dans une revue hal-00747243v1

Describing microbial communities and performing global comparisons in the 'omic era.

Tom Delmont , Pascal Simonet , Timothy M. Vogel

The International Society of Microbiologial Ecology Journal, 2012, 6 (9), pp.1625-8. ⟨10.1038/ismej.2012.55⟩

Article dans une revue hal-00747239v1

Metagenomic mining for microbiologists

Tom Delmont , Cédric Malandain , Emmanuel Prestat , Catherine Larose , Jean-Michel Monier et al.

The International Society of Microbiologial Ecology Journal, 2011, 5 (12), pp.1837-1843. ⟨10.1038/ismej.2011.61⟩

Article dans une revue hal-00747250v1

Metagenomic comparison of direct and indirect soil DNA extraction approaches

Tom Delmont , Patrick Robe , Ian M. Clark , Pascal Simonet , Timothy M Vogel

Journal of Microbiological Methods, 2011, 86 (3), pp.397-400. ⟨10.1016/j.mimet.2011.06.013⟩

Article dans une revue istex hal-00629399v1

Metagenomic exploration of antibiotic resistance in soil

Jean-Michel Monier , Sandrine Demanèche , Tom Delmont , Alban Mathieu , Timothy M Vogel et al.

Current Opinion in Microbiology, 2011, 14 (3), pp.229-235. ⟨10.1016/j.mib.2011.04.010⟩

Article dans une revue istex hal-00629407v1

Accessing the Soil Metagenome for Studies of Microbial Diversity

Tom Delmont , Patrick Robe , Sébastien Cecillon , Ian M. Clark , Florentin Constancias et al.

Applied and Environmental Microbiology, 2011, 77 (4), pp.1315-1324. ⟨10.1128/AEM.01526-10⟩

Article dans une revue hal-00579312v1

Mirusviruses link herpesviruses to giant viruses

Tom O. Delmont

Ringberg Symposium on Giant Virus Biology, Dec 2023, Ringberg, Germany

Communication dans un congrès hal-04412065v1

A la découverte des génomes du plancton avec TARA Oceans

Tom O. Delmont

AFEM (French national microbial ecology association), Oct 2023, Carqueiranne, France

Communication dans un congrès hal-04423118v1

Plankton genomics with Tara Oceans

Tom O. Delmont

Symposium on Polar Microbes and Viruses, May 2022, Tvärminne Zoological Station, Finland

Communication dans un congrès hal-04423089v1

Plankton genomics with Tara Oceans

Tom O. Delmont

AFEM (French national microbial ecology association), Jun 2022, Clermont - Ferrand, France

Communication dans un congrès hal-04423093v1

Plankton genomics with Tara Oceans

Tom O. Delmont

Plankton genomics with Tara Oceans, Sep 2022, Dijon, France

Communication dans un congrès hal-04423087v1

Diatom environmental genomes

Tom O. Delmont

Molecular Life Of Diatoms, Jul 2021, Online, United States

Communication dans un congrès hal-04423102v1

Plankton genomics with Tara Oceans

Tom O. Delmont

NeLLi Symposium on New Lineages of Life, JGI, Oct 2021, Online, United States

Communication dans un congrès hal-04423098v1

Genome-resolved metagenomics applied to marine microbial ecology

Tom O. Delmont

Nordic meeting in molecular microbial ecology, Sep 2019, Duhrevägen, Sweden

Communication dans un congrès hal-04423108v1

Soil and comparative environmental metagenomics

Timothy M Vogel , Catherine Larose , Pascal Simonet , Tom O. Delmont

Indo-French Workshop on Environmental Biotechnology (Molecular Ecology & Environmental Engineering), Feb 2015, Bhubaneswar, India

Communication dans un congrès hal-01974548v1

Managing microbial communities for sequentially reconstruct genomes from complex metagenomes

Tom Delmont , Timothy M. Vogel , Pascal Simonet

EGU, Apr 2013, Vienne, Austria. pp.1147

Communication dans un congrès hal-00821702v1

Criblage génétique d'une banque fosmidique d'ADN métagénomique d'un sol de référence pour la recherche de gènes fonctionnels d'intérêt industriel

Samuel Jacquiod , Sandrine Demanèche , Tom Delmont , Timothy M. Vogel , Pascal Simonet et al.

VIème Colloque de l'Association Francophone d'Ecologie Microbienne (AFEM), Oct 2013, Parent, France

Communication dans un congrès hal-00925344v1

Managing microbial communities for finding new enzymes and sequentially reconstruct genomes from complex metagenomes

Pascal Simonet , Tom Delmont , Samuel Jacquiod , Laure Franqueville , Timothy M. Vogel

5th Congress of European Microbiologists (FEMS 2013), Jul 2013, Leipzig, Germany. pp.S32, SOIL METAGENOMICS, Hall 5

Communication dans un congrès hal-00932256v1

SOIL METAGENOMIC: WHERE IS THE DIVERSITY?

Tom Delmont , Florentin Constancias , Sébastien Cecillon , Elisabeth Navarro , Pascal Simonet et al.

BAGECO 10 : Bacterial Genetics and Ecology – Coexisting on a Changing Planet, Jun 2009, Uppsala, Sweden

Communication dans un congrès hal-00399234v1

Mirusviruses: a complex evolutionary trajectory beyond realms

Morgan Gaïa , Lingjie Meng , Antonio Fernandez-Guerra , Hiroyuki Ogata , Mart Krupovic et al.

5th Ringberg Symposium on Giant Virus Biology, Dec 2023, Tegernsee, Germany

Poster de conférence hal-04394603v1

Genome Sequence Databases: Types of Data and Bioinformatic Tools

Ana Gutiérrez-Preciado , Philippe Deschamps , Tom Delmont , Claudia Chica , Nathan A.M. Chrismas et al.

Reference Module in Biomedical Sciences, Elsevier, 2019, ⟨10.1016/b978-0-12-801238-3.99223-7⟩

Chapitre d'ouvrage hal-02378810v1

Soil Metagenomic Exploration of the Rare Biosphere

Tom Delmont , Laure Franqueville , Samuel Jacquiod , Pascal Simonet , Timothy M. Vogel

Frans J. de Bruijn. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, Wiley-Blackwell, pp.287-298, 2011, 978-0-470-92418-1

Chapitre d'ouvrage hal-00925266v1