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  1. Fast and sensitive multiplexed diagnostic system enabled by real-time solid-phase PCR assay

    Article • July 2025, openRxiv

    Dr Jean-François Brugère

  2. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.

    Article • Microorganisms, November 2023, MDPI AG

    Dr Jean-François Brugère

  3. Growth temperature and chromatinization in archaea

    Article • Nature Microbiology, October 2022, Springer Science + Business Media

    Dr Jean-François Brugère

  4. Publisher Correction: A catalogue of 1,167 genomes from the human gut archaeome

    Article • Nature Microbiology, January 2022, Springer Science + Business Media

    Dr Jean-François Brugère

  5. A catalogue of 1,167 genomes from the human gut archaeome

    Article • Nature Microbiology, December 2021, Springer Science + Business Media

    Dr Jean-François Brugère

  6. The host-associated archaeome

    Article • Nature Reviews Microbiology, July 2020, Springer Science + Business Media

    Dr Jean-François Brugère

  7. Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics

    Article • Applied Microbiology and Biotechnology, April 2020, Springer Science + Business Media

    Dr Jean-François Brugère

  8. Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion

    Article • Emerging Topics in Life Sciences, November 2018, Portland Press Ltd.

    Dr Jean-François Brugère

  9. ASaiM: a Galaxy-based framework to analyze microbiota data

    Article • GigaScience, May 2018, Oxford University Press (OUP)

    Dr Jean-François Brugère

  10. Archaea

    Article • Journal of Clinical Gastroenterology, April 2018, Wolters Kluwer Health

    Dr Jean-François Brugère

  11. Archaebiotics: Archaea as Pharmabiotics for Treating Chronic Disease in Humans?

    Article • October 2017, IntechOpen

    Dr Jean-François Brugère

  12. ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Dr Jean-François Brugère

  13. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

    Article • The ISME Journal, June 2017, Nature

    Dr Jean-François Brugère

  14. Fecal microbiota variation across the lifespan of the healthy laboratory rat

    Article • Gut Microbes, June 2017, Taylor & Francis

    Dr Jean-François Brugère

  15. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

    Article • DNA Research, February 2017, Oxford University Press (OUP)

    Dr Jean-François Pombert, Dr Jean-François Brugère

  16. Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

    Article • Journal of Neurogastroenterology and Motility, January 2017, The Korean Society of Neurogastroenterology and Motility

    Dr Jean-François Brugère

  17. Functional amplification and preservation of human gut microbiota

    Article • Microbial Ecology in Health and Disease, January 2017, Taylor & Francis

    Dr Jean-François Brugère

  18. Whole Rye Consumption Improves Blood and Liver n-3 Fatty Acid Profile and Gut Microbiota Composition in Rats

    Article • PLOS One, February 2016, PLOS

    Dr Jean-François Brugère

  19. In-vitro model for studying methanogens in human gut microbiota

    Article • Anaerobe, August 2015, Elsevier

    Dr Jean-François Brugère

  20. Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

    Article • Applied Microbiology and Biotechnology, June 2015, Springer Science + Business Media

    Dr Jean-François Brugère

  21. Corrigendum to “Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette”

    Article • Archaea, February 2015, Wiley

    Dr Jean-François Brugère

  22. P153: Les acides gras omega-3 A longue chaîne reduisent la lipotoxicite induite par le palmitate en modifiant son metabolisme et son stockage dans la cellule musculaire C2C12

    Article • Nutrition Clinique et Métabolisme, December 2014, Elsevier

    Dr Jean-François Brugère

  23. P191: La consommation de seigle complet augmente les acides gras à chaine longue oméga-3 et modifie le profil du microbiote intestinal chez le rat

    Article • Nutrition Clinique et Métabolisme, December 2014, Elsevier

    Dr Jean-François Brugère

  24. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

    Article • BMC Genomics, August 2014, Springer Science + Business Media

    Dr Jean-François Brugère

  25. PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

    Article • Database, April 2014, Oxford University Press (OUP)

    Dr Jean-François Brugère

  26. Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette

    Article • Archaea, January 2014, Hindawi Publishing Corporation

    Dr Jean-François Brugère

  27. Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota

    Article • Journal of Microbiological Methods, January 2014, Elsevier

    Dr Jean-François Brugère

  28. Archaea and the human gut: New beginning of an old story

    Article • World Journal of Gastroenterology, January 2014, Baishideng Publishing Group Co., Limited (formerly WJG Press)

    Dr Jean-François Brugère

  29. Archaebiotics

    Article • Gut Microbes, October 2013, Taylor & Francis

    Dr Jean-François Brugère

  30. Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis

    Article • Genome Biology and Evolution, August 2013, Oxford University Press (OUP)

    Dr Jean-François Brugère

  31. Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces

    Article • Genome Announcements, July 2013, ASM Journals

    Dr Jean-François Brugère

  32. The Human Gut Chip “HuGChip”, an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level

    Article • PLOS One, May 2013, PLOS

    Dr Jean-François Brugère

  33. Design and Validation of a Colorimetric Test for the Genetic Diagnosis of Hemochromatosis Using α-Phosphorothioate Nucleotides

    Article • Biochemical Genetics, May 2013, Springer Science + Business Media

    Dr Jean-François Brugère

  34. Genome Sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens

    Article • Journal of Bacteriology, December 2012, ASM Journals

    Dr Jean-François Brugère

  35. P063 Le temps de transit colique simulé en modèle tri-étagé de fermentation continue (3s-ecsim) influence la structure et le métabolisme d’un microbiote humain

    Article • Nutrition Clinique et Métabolisme, December 2011, Elsevier

    Dr Jean-François Brugère

  36. P064 Influence segment-dépendante d’une souche probiotique de Lactobacillus plantarum sur le microbiote colique humain analysé en système in vitro 3S-ECSIM

    Article • Nutrition Clinique et Métabolisme, December 2011, Elsevier

    Dr Jean-François Brugère

  37. P064 Influence segment-dépendante d’une souche probiotique de Lactobacillus plantarum sur le microbiote colique humain analysé en système in vitro 3S-ECSIM

    Article • Cahiers de Nutrition et de Diététique, December 2011, Elsevier

    Dr Jean-François Brugère

  38. P063 Le temps de transit colique simulé en modèle tri-étagé de fermentation continue (3s-ecsim) influence la structure et le métabolisme d’un microbiote humain

    Article • Cahiers de Nutrition et de Diététique, December 2011, Elsevier

    Dr Jean-François Brugère

  39. The ECSIM Concept (Environmental Control System for Intestinal Microbiota) and Its Derivative Versions to Help Better Understand Human Gut Biology

    Article • August 2011, IntechOpen

    Dr Jean-François Brugère

  40. In vitro maintenance of a human proximal colon microbiota using the continuous fermentation system P-ECSIM

    Article • Applied Microbiology and Biotechnology, July 2011, Springer Science + Business Media

    Dr Jean-François Brugère

  41. Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age‐associated increase of the diversity

    Article • Environmental Microbiology Reports, March 2010, Wiley

    Dr Jean-François Brugère

  42. Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics

    Article • Expert Review of Molecular Diagnostics, May 2009, Taylor & Francis

    Dr Jean-François Brugère

  43. Single-tube genotyping using a solid-phase method that combines α-phosphorothioate-mediated primer extension and ExoIII: Proof of concept with the F508del cystic fibrosis diagnosis

    Article • Molecular and Cellular Probes, October 2008, Elsevier

    Dr Jean-François Brugère

  44. A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

    Article • Research in Microbiology, September 2008, Elsevier

    Dr Jean-François Brugère

  45. Characterisation and expression of phospholipases B from the opportunistic fungusAspergillus fumigatus

    Article • FEMS Microbiology Letters, October 2004, Oxford University Press (OUP)

    Dr Jean-François Brugère

  46. In vitro susceptibility of Aspergillus spp. clinical isolates to albendazole

    Article • Journal of Antimicrobial Chemotherapy, April 2003, Oxford University Press (OUP)

    Dr Jean-François Brugère

  47. Inter-Strain Variability of Insertion/Deletion Events in the Encephalitozoon cuniculi Genome: A Comparative KARD-PFGE Analysis

    Article • Journal of Eukaryotic Microbiology, June 2001, Wiley

    Dr Jean-François Brugère

  48. Occurence of subtelomeric rearrangements in the genome of the microsporidian parasite Encephalitozoon cuniculi, as revealed by a new fingerprinting procedure based on two-dimensional pulsed field gel electrophoresis

    Article • Electrophoresis, July 2000, Wiley

    Dr Jean-François Brugère

  49. Occurence of subtelomeric rearrangements in the genome of the microsporidian parasiteEncephalitozoon cuniculi, as revealed by a new fingerprinting procedure based on two-dimensional pulsed field gel electrophoresis

    Article • Electrophoresis, July 2000, Wiley

    Dr Jean-François Brugère

  50. Encephalitozoon cuniculi (Microspora) genome: physical map and evidence for telomere-associated rDNA units on all chromosomes

    Article • Nucleic Acids Research, May 2000, Oxford University Press (OUP)

    Dr Jean-François Brugère

  51. In-gel DNA radiolabelling and two-dimensional pulsed field gel electrophoresis procedures suitable for fingerprinting and mapping small eukaryotic genomes

    Article • Nucleic Acids Research, May 2000, Oxford University Press (OUP)

    Dr Jean-François Brugère

  52. Article • PLOS

    Dr Jean-François Brugère