Simon Dittami

Publications

Article dans une revue (53)

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 Legeayet al. Molecular Ecology Resources, 2025, 25 (7), ⟨10.1111/1755-0998.14129⟩ Article dans une revue hal-05273465v1
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 Legeayet al. Molecular Ecology Resources, 2025, 25 (7), pp.e14129. ⟨10.1111/1755-0998.14129⟩ Article dans une revue hal-05557625v1
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria Catherine A. Pfister,Johanna Berlinghof,Maximiliana Bogan,Ulisse Cardini,Angelique Gobetet al. MSphere, 2025, 10 (6), pp.e00996--24. ⟨10.1128/msphere.00996-24⟩ Article dans une revue hal-05195842v1
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 Legeayet al. Molecular Ecology Resources, 2025, 25 (7), pp.e14129. ⟨10.1111/1755-0998.14129⟩ Article dans une revue hal-05557567v1
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 Belcouret al. Environmental Microbiome, 2025, pp.1-53. ⟨10.1186/s40793-025-00825-z⟩ Article dans une revue hal-05413201v1
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria Catherine Pfister,Johanna Berlinghof,Maximiliana Bogan,Ulisse Cardini,Angélique Gobetet al. MSphere, 2025, 10 (6), ⟨10.1128/msphere.00996-24⟩ Article dans une revue hal-05557791v1
Progress and future directions for seaweed holobiont research Mahasweta Saha,Simon M Dittami,Cheong Xin Chan,Jean‐baptiste Raina,Willem Stocket al. New Phytologist, 2024, 244 (2), pp.364-376. ⟨10.1111/nph.20018⟩ Article dans une revue hal-04740366v1
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems France Denoeud,Olivier Godfroy,Corinne Cruaud,Svenja Heesch,Zofia Nehret al. Cell, 2024, 187 (24), pp.6943-6965. ⟨10.1016/j.cell.2024.10.049⟩ Article dans une revue hal-04794231v1
A review on the chemical ecology of the Fucaceae holobionts: from fundamental knowledge to applications Coralie Rousseau,Gautier Demoulinger,Sylvie Rousvoal,Delphine Champeval,Maurane Dollyet al. Comptes Rendus. Chimie, 2024, 26 (S2), pp.1-25. ⟨10.5802/crchim.271⟩ Article dans une revue hal-04740350v1
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
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 Fremyet al. Molecular Ecology, In press, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩ Article dans une revue hal-03868898v1
The Saccharina latissima microbiome: Effects of region, season, and physiology Bertille Burgunter-Delamare,Sylvie Rousvoal,Erwan Legeay,Gwenn Tanguy,Stein Fredriksenet al. Frontiers in Microbiology, 2023, 13, ⟨10.3389/fmicb.2022.1050939⟩ Article dans une revue hal-03951625v1
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-Ostrocket al. Genome Biology and Evolution, 2023, 15 (7), pp.evad124. ⟨10.1093/gbe/evad124⟩ Article dans une revue hal-04190579v1
Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe Arnaud Belcour,Jeanne Got,Méziane Aite,Ludovic Delage,Jonas Collénet al. Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩ Article dans une revue hal-04192851v3
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
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 Noëlet al. Microorganisms, 2022, 10, ⟨10.3390/microorganisms10071337⟩ Article dans une revue hal-03845772v1
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
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 Briandet al. PeerJ, 2021, 9, pp.e10911. ⟨10.7717/peerj.10911⟩ Article dans une revue hal-03166872v2
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 Belcouret al. Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩ Article dans une revue hal-03222505v1
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. Marieet al. Environmental Science : Water Research and Technology, 2021, 7 (7), pp.1230-1239. ⟨10.1039/D0EW00927J⟩ Article dans une revue hal-03428933v1
Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines Elham Karimi,Enora Geslain,Arnaud Belcour,Clémence Frioux,Méziane Aiteet al. PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩ Article dans une revue hal-03223662v1
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 Wagneret al. Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩ Article dans une revue hal-02866101v2
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
The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga Simon M. Dittami,Erwan Corre,Loraine Brillet-Guéguen,Agnieszka Lipinska,Noé Pontoizeauet al. Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩ Article dans une revue hal-02866117v1
Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology Elham Karimi,Enora Geslain,Hetty Kleinjan,Gwenn Tanguy,Erwan Legeayet al. Genome Biology and Evolution, 2020, 12 (1), pp.3647-3655. ⟨10.1093/gbe/evz278⟩ Article dans une revue hal-02553731v1
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift Arnaud Belcour,Jean Girard,Méziane Aite,Ludovic Delage,Camille Trottieret al. iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩ Article dans une revue hal-01943880v2
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 Kleinjanet al. Journal of Phycology, 2020, 56 (3), pp.719-729. ⟨10.1111/jpy.12970⟩ Article dans une revue hal-02340942v2
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 Tanguyet al. Environmental Microbiology Reports, 2019, 12 (1), pp.30-37. ⟨10.1111/1758-2229.12806⟩ Article dans une revue hal-02404303v1
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-Guéguenet al. Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩ Article dans une revue hal-02395080v1
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 Caralpet al. Microbiome, 2018, 6, pp.60. ⟨10.1186/s40168-018-0430-7⟩ Article dans une revue hal-01774836v1
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 Lohret 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
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
Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica Linhong Teng,Wentao Han,Xiao Fan,Dong Xu,Xiaowen Zhanget al. Frontiers in Plant Science, 2017, 8, pp.2018. ⟨10.3389/fpls.2017.02018⟩ Article dans une revue hal-03940964v1
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
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks Sylvain Prigent,Clémence Frioux,Simon M Dittami,Sven Thiele,Abdelhalim Larhlimiet al. PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Article dans une revue hal-01449100v1
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 Bayeret al. Nature, 2016, 530 (7590), pp.331-335. ⟨10.1038/nature16548⟩ Article dans une revue hal-01289099v1
A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. Sophia S. Ahmed,J. Mark Cock,Eugenie Pessia,Remy Luthringer,Alexandre Cormieret al. Current Biology, 2014, 24 (17), pp.1945-1957. ⟨10.1016/j.cub.2014.07.042⟩ Article dans une revue hal-01132642v1
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 Boyenet al. BMC Plant Biology, 2014, 14, pp.116. ⟨10.1186/1471-2229-14-116⟩ Article dans une revue hal-01311060v1
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
Genome and metabolic network of &quot;Candidatus Phaeomarinobacter ectocarpi&quot; Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae Simon M Dittami,Tristan Barbeyron,Catherine Boyen,Jeanne Cambefort,Guillaume Colletet al. Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩ Article dans une revue hal-01079739v1
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 Cornyet al. The Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩ Article dans une revue hal-01057153v1
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 Boyenet al. BMC Plant Biology, 2013, 14, pp.116 Article dans une revue hal-01113858v1
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 Chaparroet 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. Peterset 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 Amoutziaset 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
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
Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae) Simon M Dittami,Caroline Proux,Sylvie Rousvoal,Akira F Peters,J Mark Cocket 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 Eggertet 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 Eggertet al. New Phytologist, 2010, 188 (4), pp.98-110. ⟨10.1111/j.1469-8137.2010.03400.x⟩ Article dans une revue hal-02661518v1
The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae J. Mark Cock,Lieven Sterck,Pierre Rouzé,Delphine Scornet,Andrew E. Allenet al. Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩ Article dans une revue cea-00906990v1
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 Silvaet al. Genome Biology, 2009, 10, pp.R66. ⟨10.1186/gb-2009-10-6-r66⟩ Article dans une revue hal-01806423v1
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 Cocket al. BMC Molecular Biology, 2008, 9, pp.75. ⟨10.1186/1471-2199-9-75⟩ Article dans une revue hal-01806432v1

Communication dans un congrès (2)

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 Correet 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 Dittamiet al. 4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France Communication dans un congrès hal-01576484v1

Pré-publication, Document de travail (5)

Estimating consensus proteomes and metabolic functions from taxonomic affiliations Arnaud Belcour,Pauline Hamon-Giraud,Alice Mataigne,Baptiste Ruiz,Yann Le Cunffet al. 2025 Pré-publication, Document de travail hal-03697249v2
The JEDI marker as a universal measure of planetary biodiversity Taylor Priest,Nicolas Henry,Thomas Weber,Laurine Planat,Coralie Rousseauet al. 2026 Pré-publication, Document de travail hal-05507468v1
The &lt;i&gt;Saccharina latissima&lt;/i&gt; microbiome: algal tissue matters more than region, season, and physiology Bertille Burgunter-Delamare,Sylvie Rousvoal,Erwan Legeay,Gwenn Tanguy,Stein Fredriksenet al. 2022 Pré-publication, Document de travail hal-03705545v1
Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus Hetty Kleinjan,Gianmaria Caliafano,Méziane Aite,Enora Fremy,Clémence Friouxet al. 2021 Pré-publication, Document de travail hal-03429533v1
The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga Simon M. Dittami,Erwan Corre,Loraine Brillet-Guéguen,Agnieszka Lipinska,Méziane Aiteet al. 2019 Pré-publication, Document de travail hal-02333021v1

Thèse (1)

Abiotic stress response in Ectocarpus siliculosis : a global approach Simon M. Dittami Genomics [q-bio.GN]. Rennes 1, 2009. English. ⟨NNT : ⟩ Thèse tel-01110364v1

HDR (1)

Metabolic interactions between algae and bacteria in changing conditions Simon M. Dittami Biodiversity and Ecology. Sorbonne Université, 2022 HDR tel-04093436v1