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Publications

2022

Frétin, Marie, Amaury Gérard, Anne Ferlay, Bruno Martin, Solange Buchin, Sébastien Theil, Etienne Rifa, et al. 2022. “Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota.” Microorganisms 10 (2): 334. doi:https://doi.org/10.3390/microorganisms10020334.
Verdier-Metz, Isabelle, Céline Delbès, Matthieu Bouchon, Philippe Pradel, Sébastien Theil, Etienne Rifa, Agnès Corbin, and Christophe Chassard. 2022. “Influence of Post-Milking Treatment on Microbial Diversity on the Cow Teat Skin and in Milk.” Dairy 3 (2): 262–76. doi:https://doi.org/10.3390/dairy3020021.

2021

Defrel, Gilles, Nathalie Marsaud, Etienne Rifa, Frédéric Martins, et Fayza Daboussi. « Identification of Loci Enabling Stable and High-Level Heterologous Gene Expression ». Frontiers in Bioengineering and Biotechnology 9 (2021): 734902. doi:10.3389/fbioe.2021.734902.
Ropers, Delphine, Yohann Couté, Laëtitia Faure, Sabrina Ferré, Delphine Labourdette, Arieta Shabani, Lidwine Trouilh, et al. « Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application ». ACS Synthetic Biology, 5 novembre 2021. doi:10.1021/acssynbio.1c00115.
Piqueras, Justine, Christophe Chassard, Cécile Callon, Etienne Rifa, Sébastien Theil, Annick Lebecque, et Céline Delbès. « Lactic Starter Dose Shapes S. Aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses ». Microorganisms 9, nᵒ 5 (mai 2021): 1081. doi:10.3390/microorganisms9051081.

2019

Öztürk, Sibel, İrem Demir, et Pınar Çalık. « Isolation of High‐Quality RNA from Pichia Pastoris ». Current Protocols in Protein Science 98, nᵒ 1 (décembre 2019). doi:10.1002/cpps.101.
Buvignier, Amaury, Matthieu Peyre-Lavigne, Orlane Robin, Mansour Bounouba, Cédric Patapy, Alexandra Bertron, et Etienne Paul. « Influence of Dissolved-Aluminum Concentration on Sulfur-Oxidizing Bacterial Activity in the Biodeterioration of Concrete ». Applied and Environmental Microbiology 85, nᵒ 15 (s. d.): e00302-19. doi:10.1128/AEM.00302-19.
Peiro, Camille, Pierre Millard, Alessandro de Simone, Edern Cahoreau, Lindsay Peyriga, Brice Enjalbert, et Stéphanie Heux. « Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia Coli ». Applied and Environmental Microbiology 85, nᵒ 15 (1 août 2019). doi:10.1128/AEM.00768-19.
Lecomte, Sylvain, Florence Demay, Thu Ha Pham, Solenn Moulis, Théo Efstathiou, Frédéric Chalmel, et Farzad Pakdel. « Deciphering the Molecular Mechanisms Sustaining the Estrogenic Activity of the Two Major Dietary Compounds Zearalenone and Apigenin in ER-Positive Breast Cancer Cell Lines ». Nutrients 11, nᵒ 2 (février 2019): 237. doi:10.3390/nu11020237.
Pizzolato G, Kaminski H, Tosolini M, Franchini D-M, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, Poupot M, Laurent C, Ysebaert L, Meraviglia S, Dieli F, Merville P, Milpied P, Déchanet-Merville J, Fournié J-J. Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes. PNAS. 2019;116:11906–15. doi:10.1073/pnas.1818488116.
Marsaud N. Séquençage à haut débit - Outils et enjeux pour la santé humaine. Techniques de l’Ingénieur. 2019;:24. https://www.techniques-ingenieur.fr/base-documentaire/biomedical-pharma-th15/nanotechnologies-et-biotechnologies-pour-la-sante-42608210/sequencage-a-haut-debit-bio8205/.

2018

Debaugny RE, Sanchez A, Rech J, Labourdette D, Dorignac J, Geniet F, Palmeri J, Parmeggiani A, Boudsocq F, Anton Leberre V, Walter J, Bouet J. A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids. Mol Syst Biol. 2018;14. doi:10.15252/msb.20188516.
Serif M, Dubois G, Finoux A-L, Teste M-A, Jallet D, Daboussi F. One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing. Nature Communications. 2018;9:3924. doi:10.1038/s41467-018-06378-9.
Lamarre S, Frasse P, Zouine M, Labourdette D, Sainderichin E, Hu G, Le Berre-Anton V, Bouzayen M, Maza E. Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size. Front Plant Sci. 2018;9. doi:10.3389/fpls.2018.00108.
Illikoud N, Klopp C, Roulet A, Bouchez O, Marsaud N, Jaffrès E, Zagorec M. One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. Standards in Genomic Sciences. 2018;13:22. doi:10.1186/s40793-018-0333-z.
Hoareau-Aveilla C, Quelen C, Congras A, Caillet N, Labourdette D, Dozier C, Brousset P, Lamant L, Meggetto F. MiR-497 suppresses cycle progression through an axis involving CDK6 in ALK-positive cells. Haematologica. 2018;:haematol.2018.195131. doi:10.3324/haematol.2018.195131.
Giraud S, Steichen C, Allain G, Couturier P, Labourdette D, Lamarre S, Ameteau V, Tillet S, Hannaert P, Thuillier R, Hauet T. Dynamic transcriptomic analysis of Ischemic Injury in a Porcine Pre-Clinical Model mimicking Donors Deceased after Circulatory Death. Sci Rep. 2018;8. doi:10.1038/s41598-018-24282-6.

2017

Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, Esquerré D, Barbieri J, Klopp C, Philippe R, Blanquet V, Boichard D, Rocha D, Boussaha M. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genetics Selection Evolution. 2017;49:77. doi:10.1186/s12711-017-0352-z.

2016

Naldaiz-Gastesi N, Goicoechea M, Alonso-Martin S, Aiastui A, Lopez-Mayorga M, Garcia-Belda P, Lacalle J, Jose CS, Arauzo-Bravo MJ, Trouilh L, Anton-Leberre V, Herrero D, Matheu A, Bernad A, Garcia-Verdugo JM, Carvajal JJ, Relaix F, Lopez De Munain A, Garcia-Parra P, Izeta A. Identification and characterization of the dermal Panniculus carnosus muscle stem cells. Stem Cell Reports. 2016;7:411–24. doi:10.1016/j.stemcr.2016.08.002.
Chassaing N, Davis EE, McKnight KL, Niederriter AR, Causse A, David V, Desmaison A, LAMARRE S, Vincent-Delorme C, Pasquier L, Coubes C, Lacombe D, Rossi M, Dufier J-L, Dollfus H, Kaplan J, Katsanis N, Etchevers HC, Faguer S, Calvas P. Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network. Genome Research. 2016;26:474–85. doi:10.1101/gr.196048.115.
Barasc H, CONGRAS A, Mary N, Trouilh L, MARQUET V, Ferchaud S, Raymond-Letron I, Calgaro A, Loustau A-M, MOUNEY N, ACLOQUE H, Ducos A, Pinton A. Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation. Chromosome Research. 2016;24:511–27. doi:10.1007/s10577-016-9533-9.
Abot A, Arnal G, Auer L, Lazuka A, Labourdette D, Lamarre S, Trouilh L, Laville E, Lombard V, Potocki-Veronese G, Henrissat B, O’Donohue M, Hernandez-Raquet G, Dumon C, Leberre VA. CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics. 2016;17:1–12. doi:10.1186/s12864-016-2988-4.


Remerciements

Ait-Itto, Fatima-Zahra, James A. Behan, Mathieu Martinez, et Frédéric Barrière. « Development of bioanodes rich in exoelectrogenic bacteria using iron-rich palaeomarine sediment inoculum ». Bioelectrochemistry 156 (avril 2024): 108618. doi:10.1016/j.bioelechem.2023.108618.
Duperray, Maëlle, Mathéo Delvenne, Jean-Marie François, Frank Delvigne, et Jean-Pascal Capp. « Genomic and Metabolic Instability during Long-Term Fermentation of an Industrial Saccharomyces Cerevisiae Strain Engineered for C5 Sugar Utilization ». Frontiers in Bioengineering and Biotechnology 12 (2024). doi:10.3389/fbioe.2024.1357671.
Lutin, Jade, Franck Dufrene, Philippe Guyot, et al. « Microbial composition and viability of natural whey starters used in PDO Comté cheese-making ». Food Microbiology 121 (août 2024): 104521. doi:10.1016/j.fm.2024.104521.
Meyneng, M., H. Lemonnier, R. Le Gendre, et al. « Subtropical Coastal Microbiome Variations Due to Massive River Runoff after a Cyclonic Event ». Environmental Microbiome 19 (1) (2024): 10. doi:10.1186/s40793-024-00554-9.
Naudin, Sarah A., Aude A. Ferran, Pedro Henrique Imazaki, et al. « Development of an in Vitro Biofilm Model for the Study of the Impact of Fluoroquinolones on Sewer Biofilm Microbiota ». Frontiers in Microbiology 15 (2024). doi:10.3389/fmicb.2024.1377047.
Roux, Charlotte, Marvin Ramos-Hue, Marjorie Audonnet, et al. « RNA stability is regulated by both RNA polyadenylation and ATP levels, linking RNA and energy metabolisms in Escherichia coli ». mBio (2024): e02680-24. doi:10.1128/mbio.02680-24.
Veillat, Loïs, Stéphane Boyer, Marina Querejeta, et al. « Benchmarking Three DNA Metabarcoding Technologies for Efficient Detection of Non-Native Cerambycid Beetles in Trapping Collections ». NeoBiota 96 (novembre 2024): 237-59. doi:10.3897/neobiota.96.130195.
Fournier, Elora, Jeremy Ratel, Sylvain Denis, et al. « Exposure to Polyethylene Microplastics Alters Immature Gut Microbiome in an Infant in Vitro Gut Model ». Journal of Hazardous Materials 443 (février 2023): 130383. doi:10.1016/j.jhazmat.2022.130383.
Gomes, Pedro, Valérie Laroute, Catherine Beaufrand, et al. « Lactococcus Lactis CNCM I-5388 versus NCDO2118 by Its GABA Hyperproduction Ability, Counteracts Faster Stress-Induced Intestinal Hypersensitivity in Rats ». The FASEB Journal 37 (11) (2023): e23264. doi:10.1096/fj.202301588R.
Guéraud, Françoise, Charline Buisson, Aurélie Promeyrat, et al. « Effects of Sodium Nitrite Reduction, Removal or Replacement on Cured and Cooked Meat for Microbiological Growth, Food Safety, Colon Ecosystem, and Colorectal Carcinogenesis in Fischer 344 Rats ». Npj Science of Food 7 (1) (2023): 1. doi:10.1038/s41538-023-00228-9.
Letenneur, Vivien, Magali Monnoye, Catherine Philippe, et al. « Effects of a Lacticaseibacillus Mix on Behavioural, Biochemical, and Gut Microbial Outcomes of Male Mice Following Chronic Restraint Stress ». Nutrients 15 (21) (2023): 21. doi:10.3390/nu15214635.
Methou, Pierre, Valérie Cueff-Gauchard, Loïc N. Michel, Nicolas Gayet, Florence Pradillon, et Marie-Anne Cambon-Bonavita. « Symbioses of Alvinocaridid Shrimps from the South West Pacific: No Chemosymbiotic Diets but Partially Conserved Gut Microbiomes ». Prépublication, bioRxiv, 8 février 2023. doi:10.1101/2023.02.08.527621.
Naudet, Jeanne, Emmanuelle Roque d’Orbcastel, Thierry Bouvier, et al. « Identifying macroplastic pathobiomes and antibiotic resistance in a subtropical fish farm ». Marine Pollution Bulletin 194 (septembre 2023): 115267. doi:10.1016/j.marpolbul.2023.115267.
Park, Soyoung, Amine M. Belfoul, Marialetizia Rastelli, et al. « Maternal Low-Calorie Sweetener Consumption Rewires Hypothalamic Melanocortin Circuits via a Gut Microbial Co-Metabolite Pathway ». JCI Insight 8 (10) (2023). doi:10.1172/jci.insight.156397.
Philippon, Timothé, Fatima-Zahra Ait-Itto, Alicia Monfort, Frédéric Barrière, et James A. Behan. « Fe(III) Oxide Microparticles Modulate Extracellular Electron Transfer in Anodic Biofilms Dominated by Bacteria of the Pelobacter Genus ». Bioelectrochemistry 151 (juin 2023): 108394. doi:10.1016/j.bioelechem.2023.108394.
Aboulela, Amr, Matthieu Peyre Lavigne, Tony Pons, et al. “The Fate of Tetrathionate during the Development of a Biofilm in Biogenic Sulfuric Acid Attack on Different Cementitious Materials.” Science of The Total Environment 850 (2022): 158031. doi:10.1016/j.scitotenv.2022.158031.
Fournier, Elora, Sylvain Denis, Alessandra Dominicis, et al. “A Child Is Not an Adult: Development of a New in Vitro Model of the Toddler Colon.” Applied Microbiology and Biotechnology 106 (21) (2022): 7315–36. doi:10.1007/s00253-022-12199-0.
Laguillaumie, Léa, Yan Rafrafi, Elisabeth Moya-Leclair, et al. “Stability of Ex Situ Biological Methanation of H2/CO2 with a Mixed Microbial Culture in a Pilot Scale Bubble Column Reactor.” Bioresource Technology 354 (2022): 127180. doi:10.1016/j.biortech.2022.127180.
Laroute, Valérie, Catherine Beaufrand, Pedro Gomes, et al. “Lactococcus Lactis NCDO2118 Exerts Visceral Antinociceptive Properties in Rat via GABA Production in the Gastro-Intestinal Tract.” eLife 11 (2022): e77100. doi:10.7554/eLife.77100.
Nguyen, Huong Le, Marie-Pierre Duviau, Sandrine Laguerre, et al. “Synergistic Regulation of Transcription and Translation in Escherichia Coli Revealed by Codirectional Increases in MRNA Concentration and Translation Efficiency.” Microbiology Spectrum 10 (1) (2022). doi:10.1128/spectrum.02041-21.
Pregnon, Guillaume, Nigel P. Minton, et Philippe Soucaille. “Genome Sequence of Eubacterium Limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources.” Microorganisms 10 (9) (2022): 1790. doi:10.3390/microorganisms10091790.
Arnould, Coline, Vincent Rocher, Anne-Laure Finoux, et al. « Loop Extrusion as a Mechanism for Formation of DNA Damage Repair Foci ». Nature 590 (2021): 660-65. doi:10.1038/s41586-021-03193-z.
Courtot, Lilas, Elodie Bournique, Chrystelle Maric, et al. « Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing ». International Journal of Molecular Sciences 22 (9) (2021): 4959. doi:10.3390/ijms22094959.
Millard, Pierre, Brice Enjalbert, Sandrine Uttenweiler-Joseph, et al. « Control and regulation of acetate overflow in Escherichia coli ». eLife 10 (2021): e63661. doi:10.7554/eLife.63661.
Paccoud, Romain, Céline Saint-Laurent, Enzo Piccolo, et al. « SHP2 Drives Inflammation-Triggered Insulin Resistance by Reshaping Tissue Macrophage Populations ». Science Translational Medicine 13 (2021). doi:10.1126/scitranslmed.abe2587.
Bertorello, Juliette, Julie Sesen, Julia Gilhodes, et al. « Translation Reprogramming by EIF3 Linked to Glioblastoma Resistance ». NAR Cancer 2 (3) (2020): zcaa020. doi:10.1093/narcan/zcaa020.
De Simone, A., C. M. Vicente, C. Peiro, et al. « Mixing and Matching Methylotrophic Enzymes to Design a Novel Methanol Utilization Pathway in E. Coli ». Metabolic Engineering 61 (2020): 315-25. doi:10.1016/j.ymben.2020.07.005.
Morin, Manon, Brice Enjalbert, Delphine Ropers, et al. « Genomewide Stabilization of MRNA during a “Feast-to-Famine” Growth Transition in Escherichia Coli ». MSphere 5 (3) (2020). doi:10.1128/mSphere.00276-20.
Pavlovic, Marion, Christelle Gross, Chahinaize Chili, et al. « MAIT Cells Display a Specific Response to Type 1 IFN Underlying the Adjuvant Effect of TLR7/8 Ligands ». Frontiers in Immunology 11 (2020): 2097. doi:10.3389/fimmu.2020.02097.
Tauzin, Alexandra S., Mariana Rangel Pereira, Liisa D. Van Vliet, et al. « Investigating Host-Microbiome Interactions by Droplet Based Microfluidics ». Microbiome 8 (1) (2020): 141. doi:10.1186/s40168-020-00911-z.
Wang, Zhi, Alexandra S. Tauzin, Elisabeth Laville, et al. « Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria ». MSphere 5 (1) (2020). doi:10.1128/mSphere.00771-19.
Öztürk, Sibel, İrem Demir, and Pınar Çalık. “Isolation of High‐Quality RNA from Pichia Pastoris.” Current Protocols in Protein Science 98 (1) (2019). doi:10.1002/cpps.101.