Simon Dittami

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Publications

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A Practical Comparison of Short‐ and Long‐Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples

Coralie Rousseau , Nicolas Henry , Sylvie Rousvoal , Gwenn Tanguy , Erwan Legeay et al.

Molecular Ecology Resources, 2025, 25 (7), ⟨10.1111/1755-0998.14129⟩

Article dans une revue hal-05273465v1
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Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria

Catherine A. Pfister , Johanna Berlinghof , Maximiliana Bogan , Ulisse Cardini , Angelique Gobet et al.

MSphere, 2025, 10 (6), pp.e00996--24. ⟨10.1128/msphere.00996-24⟩

Article dans une revue hal-05195842v1
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A duo of fungi and complex and dynamic bacterial community networks contribute to shape the Ascophyllum nodosum holobiont

Coralie Rousseau , Gwenn Tanguy , Erwan Legeay , Samuel Blanquart , Arnaud Belcour et al.

Environmental Microbiome, 2025, pp.1-53. ⟨10.1186/s40793-025-00825-z⟩

Article dans une revue hal-05413201v1
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Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

France Denoeud , Olivier Godfroy , Corinne Cruaud , Svenja Heesch , Zofia Nehr et al.

Cell, 2024, 187 (24), pp.6943-6965. ⟨10.1016/j.cell.2024.10.049⟩

Article dans une revue hal-04794231v1
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Progress and future directions for seaweed holobiont research

Mahasweta Saha , Simon M Dittami , Cheong Xin Chan , Jean‐baptiste Raina , Willem Stock et al.

New Phytologist, 2024, 244 (2), pp.364-376. ⟨10.1111/nph.20018⟩

Article dans une revue hal-04740366v1
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A review on the chemical ecology of the Fucaceae holobionts: from fundamental knowledge to applications

Coralie Rousseau , Gautier Demoulinger , Sylvie Rousvoal , Delphine Champeval , Maurane Dolly et al.

Comptes Rendus. Chimie, 2024, 26 (S2), pp.1-25. ⟨10.5802/crchim.271⟩

Article dans une revue hal-04740350v1
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Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains

Elham Karimi , Simon Dittami

FEMS Microbiology Ecology, 2023, 99 (12), pp.fiad130. ⟨10.1093/femsec/fiad130⟩

Article dans une revue hal-04254487v1
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Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation

Hetty Kleinjan , Clémence Frioux , Gianmaria Califano , Méziane Aite , Enora Fremy et al.

Molecular Ecology, In press, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩

Article dans une revue hal-03868898v1
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The Saccharina latissima microbiome: Effects of region, season, and physiology

Bertille Burgunter-Delamare , Sylvie Rousvoal , Erwan Legeay , Gwenn Tanguy , Stein Fredriksen et al.

Frontiers in Microbiology, 2023, 13, ⟨10.3389/fmicb.2022.1050939⟩

Article dans une revue hal-03951625v1
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The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species

Agnieszka P Lipinska , Stacy A Krueger-Hadfield , Olivier Godfroy , Simon M Dittami , Lígia Ayres-Ostrock et al.

Genome Biology and Evolution, 2023, 15 (7), pp.evad124. ⟨10.1093/gbe/evad124⟩

Article dans une revue hal-04190579v1
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Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén et al.

Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩

Article dans une revue hal-04192851v3
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Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

Bertille Burgunter-Delamare , Gwenn Tanguy , Erwan Legeay , Catherine Boyen , Simon M. Dittami

Marine Genomics, 2022, 63, pp.100944. ⟨10.1016/j.margen.2022.100944⟩

Article dans une revue hal-03618853v1
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Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea

Charlotte Nef , Simon M. Dittami , Raymond Kaas , Enora Briand , Cyril Noël et al.

Microorganisms, 2022, 10, ⟨10.3390/microorganisms10071337⟩

Article dans une revue hal-03845772v1
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Effect of essential oil-and iodine treatments on the bacterial microbiota of the brown alga Ectocarpus siliculosus

Bertille Burgunter-Delamare , Catherine Boyen , Simon M Dittami

Journal of Applied Phycology, 2021, 33, pp.459-470. ⟨10.1007/s10811-020-02286-y⟩

Article dans une revue hal-03030933v1
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A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Simon M. Dittami , Enrique Arboleda , J.-C. Auguet , Arite Bigalke , Enora Briand et al.

PeerJ, 2021, 9, pp.e10911. ⟨10.7717/peerj.10911⟩

Article dans une revue hal-03166872v2
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Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae

Jean Girard , Goulven Lanneau , Ludovic Delage , Cédric Leroux , Arnaud Belcour et al.

Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩

Article dans une revue hal-03222505v1
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Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters

J. Robla , J. García-Hierrro , F. J Alguacil , Simon M. Dittami , D. Marie et al.

Environmental Science : Water Research and Technology, 2021, 7 (7), pp.1230-1239. ⟨10.1039/D0EW00927J⟩

Article dans une revue hal-03428933v1
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Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Elham Karimi , Enora Geslain , Arnaud Belcour , Clémence Frioux , Méziane Aite et al.

PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩

Article dans une revue hal-03223662v1
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Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions

Bertille Burgunter-Delamare , Hetty Kleinjan , Clémence Frioux , Enora Fremy , Margot Wagner et al.

Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩

Article dans une revue hal-02866101v2
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Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Clémence Frioux , Simon Dittami , Anne Siegel

Biochemical Society Transactions, 2020, 48 (3), pp.901-913. ⟨10.1042/BST20190667⟩

Article dans une revue hal-02569935v1
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The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga

Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Noé Pontoizeau et al.

Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩

Article dans une revue hal-02866117v1
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Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: distribution, abiotic environment, and associated microbiota

Simon M. Dittami , Akira F Peters , John West , Thierry Cariou , Hetty Kleinjan et al.

Journal of Phycology, 2020, 56 (3), pp.719-729. ⟨10.1111/jpy.12970⟩

Article dans une revue hal-02340942v2
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Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology

Elham Karimi , Enora Geslain , Hetty Kleinjan , Gwenn Tanguy , Erwan Legeay et al.

Genome Biology and Evolution, 2020, 12 (1), pp.3647-3655. ⟨10.1093/gbe/evz278⟩

Article dans une revue hal-02553731v1
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Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Arnaud Belcour , Jean Girard , Méziane Aite , Ludovic Delage , Camille Trottier et al.

iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩

Article dans une revue hal-01943880v2
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Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga‐associated bacterial communities

François Thomas , Simon Dittami , Maéva Brunet , Nolwen Le Duff , Gwenn Tanguy et al.

Environmental Microbiology Reports, 2019, 12 (1), pp.30-37. ⟨10.1111/1758-2229.12806⟩

Article dans une revue hal-02404303v1
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Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Delphine Nègre , Méziane Aite , Arnaud Belcour , Clémence Frioux , Loraine Brillet-Guéguen et al.

Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩

Article dans une revue hal-02395080v1
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Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

Angélique Gobet , Laëtitia Mest , Morgan Perennou , Simon M. Dittami , Claire Caralp et al.

Microbiome, 2018, 6, pp.60. ⟨10.1186/s40168-018-0430-7⟩

Article dans une revue hal-01774836v1
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Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

Simon Dittami , Erwan Corre

PeerJ, 2017, 5, pp.e4073. ⟨10.7717/peerj.4073⟩

Article dans une revue hal-01654700v1

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

Susan Brawley , Nicolas Blouin , Elizabeth Ficko-Blean , Glen Wheeler , Martin Lohr et al.

Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (31), pp.E6361-E6370. ⟨10.1073/pnas.1703088114⟩

Article dans une revue hal-02950557v1
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Exploring the Cultivable Ectocarpus Microbiome

Hetty Kleinjan , Christian Jeanthon , Catherine Boyen , Simon M. Dittami

Frontiers in Microbiology, 2017, 8, pp.2456. ⟨10.3389/fmicb.2017.02456⟩

Article dans une revue hal-03940941v1
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Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae

Simon M Dittami , Svenja Heesch , Jeanine L. Olsen , Jonas Collén

Journal of Phycology, 2017, ⟨10.1111/jpy.12547⟩

Article dans une revue hal-01528781v1
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Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica

Linhong Teng , Wentao Han , Xiao Fan , Dong Xu , Xiaowen Zhang et al.

Frontiers in Plant Science, 2017, 8, pp.2018. ⟨10.3389/fpls.2017.02018⟩

Article dans une revue hal-03940964v1
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Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Sylvain Prigent , Clémence Frioux , Simon M Dittami , Sven Thiele , Abdelhalim Larhlimi et al.

PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩

Article dans une revue hal-01449100v1
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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Jeanine L. Olsen , Pierre Rouzé , Bram Verhelst , Yao-Cheng Y.-C. Lin , Till Bayer et al.

Nature, 2016, 530 (7590), pp.331-335. ⟨10.1038/nature16548⟩

Article dans une revue hal-01289099v1
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A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp.

Sophia S. Ahmed , J. Mark Cock , Eugenie Pessia , Remy Luthringer , Alexandre Cormier et al.

Current Biology, 2014, 24 (17), pp.1945-1957. ⟨10.1016/j.cub.2014.07.042⟩

Article dans une revue hal-01132642v1

A metabolic approach to study algal-bacterial interactions in changing environments.

Simon M. Dittami , Damien Eveillard , Thierry Tonon

Molecular Ecology, 2014, 23 (7), pp.1656-60. ⟨10.1111/mec.12670⟩

Article dans une revue hal-00936195v1
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Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

Simon M Dittami , Tristan Barbeyron , Catherine Boyen , Jeanne Cambefort , Guillaume Collet et al.

Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩

Article dans une revue hal-01079739v1
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Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae

Andrés Ritter , Simon M Dittami , Sophie Goulitquer , Juan A Correa , Catherine Boyen et al.

BMC Plant Biology, 2014, 14, pp.116. ⟨10.1186/1471-2229-14-116⟩

Article dans une revue hal-01311060v1

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.

Sylvain Prigent , Guillaume Collet , Simon M Dittami , Ludovic Delage , Floriane Ethis de Corny et al.

The Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩

Article dans une revue hal-01057153v1
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Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae.

Andrés Ritter , Simon M Dittami , Sophie Goulitquer , Juan A Correa , Catherine Boyen et al.

BMC Plant Biology, 2013, 14, pp.116

Article dans une revue hal-01113858v1
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Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

Jonas Collén , Betina Porcel , Wilfrid Carré , Steven G Ball , Cristian Chaparro et al.

Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (13), pp.5247-52. ⟨10.1073/pnas.1221259110⟩

Article dans une revue hal-01073830v1

Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae)

Simon M. Dittami , Antoine Gravot , Sophie Goulitquer , Sylvie Rousvoal , Akira F. Peters et al.

The Plant Journal, 2012, 71 (3), pp.366 - 377. ⟨10.1111/j.1365-313X.2012.04982.x⟩

Article dans une revue hal-01208656v1

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias et al.

Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩

Article dans une revue hal-02649287v1
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Genomes of extremophile crucifers: new platforms for comparative genomics and beyond.

Simon M Dittami , Thierry Tonon

Genome Biology, 2012, 13 (8), pp.166. ⟨10.1186/gb-2012-13-8-166⟩

Article dans une revue hal-00925419v1
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Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

Simon M Dittami , Caroline Proux , Sylvie Rousvoal , Akira F Peters , J Mark Cock et al.

BMC Molecular Biology, 2011, 12, pp.2. ⟨10.1186/1471-2199-12-2⟩

Article dans une revue hal-00925432v1

Integrative analysis of metabolite and transcript abundance during the short-term response to saline and oxidative stress in the brown alga Ectocarpus siliculosus.

Simon M. Dittami , Antoine Gravot , David Renault , Sophie Goulitquer , Anja Eggert et al.

Plant, Cell and Environment, 2011, 34 (4), pp.629-642. ⟨10.1111/j.1365-3040.2010.02268.x⟩

Article dans une revue hal-00597335v1

Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus

Antoine Gravot , Simon Dittami , Sylvie Rousvoal , Raphaël Lugan , Anja Eggert et al.

New Phytologist, 2010, 188 (4), pp.98-110. ⟨10.1111/j.1469-8137.2010.03400.x⟩

Article dans une revue hal-02661518v1
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The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen et al.

Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩

Article dans une revue cea-00906990v1
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Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

Simon M Dittami , Delphine Scornet , Jean-Louis Petit , Béatrice Segurens , Corinne da Silva et al.

Genome Biology, 2009, 10, pp.R66. ⟨10.1186/gb-2009-10-6-r66⟩

Article dans une revue hal-01806423v1
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Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus

Aude Le Bail , Simon Dittami , Pierre-Olivier de Franco , Sylvie Rousvoal , J. Mark Cock et al.

BMC Molecular Biology, 2008, 9, pp.75. ⟨10.1186/1471-2199-9-75⟩

Article dans une revue hal-01806432v1
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Methods for a species-specific genome-scale metabolic model designed for eukaryotes and applied to the Ascophyllum nodosum macroalga

Pauline Hamon-Giraud , Benoît Bergk Pinto , Jeanne Got , Coralie Rousseau , Erwan Corre et al.

JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.109-117

Communication dans un congrès hal-05374724v1

Toward the study of metabolic functions in algal holobionts

Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami et al.

4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France

Communication dans un congrès hal-01576484v1