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1. Draft Genome Sequence of Tubulinosema ratisbonensis , a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Author

Adrien Franchet, Ivan Wawrzyniak, Sebastian Niehus, Christine Gaspin, Caroline Belser, Karine Labadie, Arnaud Couloux, Frédéric Delbac, Valérie Polonais, Eric Peyretaillade, Dominique Ferrandon, Matthieu Reichstadt, Abdel Belkorchia, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut für Virologie, Philipps University, Unité de Biométrie et Intelligence Artificielle, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), EA CIDAM - Auvergne IFR Santé, Université d'Auvergne - Clermont-Ferrand I (UdA), Modèles Insectes de l'Immunité Innée (M3I), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Moné, Anne, Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Université d'Auvergne (Clermont Ferrand 1) (UdA)

Subjects
Transposable element, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, ORGANIZATION, ANNOTATION, 03 medical and health sciences, 0302 clinical medicine, Immunology and Microbiology (miscellaneous), Tubulinosema ratisbonensis, Genetic model, Genetics, Melanogaster, Model organism, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, ved/biology, Genome Sequences, biology.organism_classification, [SDV] Life Sciences [q-bio], Drosophila melanogaster, 030217 neurology & neurosurgery
Abstract

We present the draft genome sequence of Tubulinosema ratisbonensis, a microsporidium species infecting Drosophila melanogaster. A total of 3,013 protein-encoding genes and an array of transposable elements were identified. This work represents a necessary step to develop a novel model of host-parasite relationships using the highly tractable genetic model D. melanogaster.

Published
2019

2. Enterohemorrhagic Escherichia coli infection has donor-dependent effect on human gut microbiota and may be antagonized by probiotic yeast during interaction with Peyer’s patches

Author

Sylvain Denis, Jonathan Thévenot, Stéphanie Blanquet-Diot, O. Le Goff, H. T. T. Nguyen, Monique Alric, Amandine Rougeron, Valérie Livrelli, Charlotte Cordonnier, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Centre de Recherche en Nutrition Humaine, CHU Clermont-Ferrand, French Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche, Conseil Régional Auvergne (grant CPER T2ANSH ASTERISK, Auvergne STEC Risque), EA CIDAM, and UMR INSERM/Universite d'Auvergne U1071 USC-INRA 2018

Subjects
Time Factors, Colon, Gene Expression, enterohemorrhagic escherichia coli (ehec), Saccharomyces cerevisiae, Butyrate, Gut flora, medicine.disease_cause, Models, Biological, Applied Microbiology and Biotechnology, Virulence factor, Shiga Toxin, law.invention, Microbiology, Mice, Peyer's Patches, Probiotic, Intestinal mucosa, Ileum, law, Antibiosis, medicine, Animals, Humans, colonic in vitro model, Escherichia coli, Pathogen, Escherichia coli Infections, gut microbiota, biology, Gene Expression Profiling, Probiotics, General Medicine, Fatty Acids, Volatile, biology.organism_classification, Gastrointestinal Microbiome, 3. Good health, Disease Models, Animal, Diarrhea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Treatment Outcome, Enterohemorrhagic Escherichia coli, Immunology, Pre-Exposure Prophylaxis, mice ileal loops, medicine.symptom, probiotic, Biotechnology
Abstract

International audience; Enterohemorrhagic Escherichia coli (EHEC) are major food-borne pathogens responsible for serious infections ranging from mild diarrhea to hemorrhagic colitis and life-threatening complications. Shiga toxins (Stxs) are the main virulence factor of EHEC. The antagonistic effect of a prophylactic treatment with the probiotic strain Saccharomyces cerevisiae against EHEC O157:H7 was investigated using complementary in vitro human colonic model and in vivo murine ileal loop assays. In vitro, the probiotic treatment had no effect on O157:H7 survival but favorably influenced gut microbiota activity through modulation of short-chain fatty acid production, increasing acetate production and decreasing that of butyrate. Both pathogen and probiotic strains had individual-dependent effects on human gut microbiota. For the first time, stx expression was followed in human colonic environment: at 9 and 12 h post EHEC infection, probiotic treatment significantly decreased stx mRNA levels. Besides, in murine ileal loops, the probiotic yeast specifically exerted a trophic effect on intestinal mucosa and inhibited O157:H7 interactions with Peyer's patches and subsequent hemorrhagic lesions. Taken together, the results suggest that S. cerevisiae may be useful in the fight against EHEC infection and that host associated factors such as microbiota could influence clinical evolution of EHEC infection and the effectiveness of probiotics.

Published
2015

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

Author

Pierre Peyret, Monique Alric, Jean-Louis Sébédio, Jean-François Brugère, Nadia Gaci, David Feria-Gervasio, Jean-Michel Cardot, Jean-François Martin, Estelle Pujos, William Tottey, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, EA CIDAM 448, Université d'Auvergne - Clermont-Ferrand I (UdA)-Faculté de Médecine et de Pharmacie, and European Union (UE), Auvergne Council, Auvergne Council

Subjects
Adult, Volunteers, Microbiology (medical), Microarray, Process improvement, Gut microbiota, Computational biology, Biology, Gut flora, Microbiology, Mass Spectrometry, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, Human gut, Humans, Anaerobiosis, Intestine, Large, Molecular Biology, 030304 developmental biology, Fermentation gas, human intestinal bacteria, 0303 health sciences, Three stage, 030306 microbiology, Microbiota, In-vitro simulation of the colon, Metabolism, Models, Theoretical, Microarray Analysis, biology.organism_classification, Biota, chemistry, Female, Distal colon, Xenobiotic, 3S-ECSIM, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Chromatography, Liquid, HuGChip
Abstract

This work was supported by a postdoctoral scholarship support from the European Union (UE) and the Auvergne Council, to D. F.-G. (FEDER), by a PhD Scholarship support from the European Union (UE) and the Auvergne Council to W.T. (FEDER), and to a PhD Scholarship support from the French "Ministere de l'Enseignement Superieur et de la Recherche". We thank Pascal Vandekerckove from Lesaffre SA and Zsolt Popse from Global Process Concept (France) for their support. J.-F.B. thanks Celine Vidal and Claire Ardaens for their technical help.; The technical and ethical difficulties in studying the gut microbiota in vivo warrant the development and improvement of in vitro systems able to simulate and control the physicochemical factors of the gut biology. Moreover, the functional regionalization of this organ implies a model simulating these differences. Here we propose an improved and alternative three-stage continuous bioreactor called 3S-ECSIM (three-stage Environmental Control System for Intestinal Microbiota) to study the human large intestine. Its main feature compared with other in vitro systems is the anaerobic atmosphere originating directly from the microbiota metabolism, leading to different gas ratios of CO2 and H-2 in each compartment Analyses of the metabolic and microbiological profiles (LC-MS and a phylogenetic microarray) show different profiles together with a maintenance of this differentiation between the three compartments, simulating respectively a proximal, a transversal and a distal colon. Moreover, the last reactor presents a high similarity with the initial fecal sample, at the microbiological diversity level. Based on our results, this in-vitro process improvement is a valuable alternative tool to dynamically study the structure and metabolism of gut microbiota, and its response to nutrients, prebiotics, probiotics, drugs or xenobiotics. (C) 2013 Elsevier B.V. All rights reserved.

Published
2014

4. La microbiologie moléculaire au service du diagnostic environnemental. Synthèse de Recherche. Contrat n°1406C0050. Projet de recherche coordonné par : 'Observatoire des sols vivants'

Author

Bouchez , Théodore, Blieux , Anne Laure, Dequiedt , Samuel, Domaizon , Isabelle, Dufresne , Alexis, Ferreira , Stéphanie, Godon , Jean-Jacques, Hellal , Jennifer, Joulian , Catherine, Quaiser , Achim, Martin , Fabrice, Mauffret , Aourell, Monier , Jean Marie, Peyret , Pierre, Schmitt-Koplin , Philippe, Sibourg , Olivier, d’Oiron Verame , Elisabeth, Bispo , Antonio, Deportes , Isabelle, Grand , Cécile, Cuny , Philippe, Maron , Pierre-Alain, Ranjard , Lionel, Hydrosystèmes et bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Welience AgroEnvironnement, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Genoscreen, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), ENOVEO, EA CIDAM, Université Clermont Auvergne (UCA), CRBV, Helmholtz-Zentrum München (HZM), Observatoire Français des Sols Vivants, Unité INFOSOL (ORLEANS INFOSOL), Institut National de la Recherche Agronomique (INRA), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Institut Pythéas (OSU PYTHEAS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut de Recherche pour le Développement (IRD), OCEAMED, n° 1406C0050, Hydrosystèmes et Bioprocédés (UR HBAN), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), InfoSol (InfoSol), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum München = German Research Center for Environmental Health, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS), Hydrosystèmes et bioprocédés ( UR HBAN ), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biotechnologie de l'Environnement [Narbonne] ( LBE ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Bureau de Recherches Géologiques et Minières (BRGM) ( BRGM ), Université Clermont Auvergne ( UCA ), Helmholtz-Zentrum München ( HZM ), Unité INFOSOL ( ORLEANS INFOSOL ), Institut National de la Recherche Agronomique ( INRA ), Agence de l'Environnement et de la Maîtrise de l'Energie ( ADEME ), Institut Pythéas ( OSU PYTHEAS ), and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
[ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

EABIOmEINRA; National audience; L'étude a pour objectif de décrire les différentes techniques relevant de la microbiologie moléculaire en termes d'état d'avancement, de limites techniques et de sensibilité pour étudier l'abondance, la diversité, l'activité et les potentialités fonctionnelles des communautés microbiennes indigènes de diverses matrices environnementales (eau, sol, air, substrats déchets). On trouve dans l'étude neuf fiches de présentation des méthodes, puis vingt-neuf fiches d'application sur les milieux/substrats eau, sol, air et déchets. Des indicateurs de microbiologie moléculaire permettant un diagnostic environnemental ont été recherchés. Une trentaine d'entreprise qui les propose en routine sont données dans le rapport. Ces indicateurs microbiens sont opérationnels pour des prestations de diagnostic de la qualité de différentes matrices environnementales par différents types d'opérateurs (agriculteurs, industriels, gestionnaires de déchets, aménageurs du territoire)

Published
2016

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

Author

Simonetta Gribaldo, Jean-François Brugère, Guillaume Borrel, Paul W. O'Toole, Pierre Peyret, Nadia Gaci, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), EA CIDAM - Auvergne IFR Santé, Natl Univ Ireland Univ Coll Cork, Alimentary Pharmabiot Ctr, Dept Microbiol, Cork, Ireland, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), This work was funded by PhD Scholarship supports from the French 'Ministère de l’Enseignement Supérieur et de la Recherche' to Nadia Gaci Simonetta Gribaldo was supported by the French Agence Nationale de la Recherche (ANR) through Grant ANR-10-BINF-01-01 'Ancestrome.' Paul W. O’Toole was supported by Science Foundation Ireland through a Principal Investigator award and by an FHRI award to the ELDERMET project by the Department of Agriculture, Fisheries and Marine of the Government of Ireland., ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), and Institut Pasteur [Paris]

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, Sequence Homology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Genome, chemistry.chemical_compound, RNA, Transfer, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Phylogeny, chemistry.chemical_classification, Genetics, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic code, QR1-502, Amino acid, Genetic Code, Transfer RNA, Horizontal gene transfer, Corrigendum, Research Article, Gene Transfer, Horizontal, Article Subject, Pyrrolysine, Euryarchaeota, Microbiology, Amino Acyl-tRNA Synthetases, Evolution, Molecular, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Bacteria, 030306 microbiology, Lysine, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biosynthetic Pathways, chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Archaea, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known fromBacteriaandArchaeaand analyzed the phylogeny of each component. This shows unique peculiarities, notably anamber tRNAPylwith an imperfect anticodon stem and a shortenedtRNAPylsynthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.Corrigendum to “Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette”

Published
2014

6. The Human Gut Chip 'HuGChip', an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level

Author

Guillaume Borrel, Hugh M. B. Harris, Jérémie Denonfoux, Ian B. Jeffery, David R.C. Hill, Pierre Peyret, Nicolas Parisot, Marcus J. Claesson, Monique Alric, Jean-François Brugère, William Tottey, Faouzi Jaziri, Eric Peyretaillade, Mohiedine Missaoui, Paul W. O'Toole, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), EA CIDAM - Auvergne IFR Santé, Clermont Université, Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork (UCC), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, Microarray, Microarrays, Applied Microbiology, lcsh:Medicine, mcrA gene, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, law.invention, Feces, Gastrointestinal tract, law, RNA, Ribosomal, 16S, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], lcsh:Science, Polymerase chain reaction, Phylogeny, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Multidisciplinary, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Microbiota, Biodiversity, ARB, Community Ecology, DNA microarray, Research Article, Biotechnology, Molecular Sequence Data, Sequence data, Biology, Environment, Microbiology, Ecosystems, Microbial Ecology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Community Structure, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Analysis of Variance, Bacteria, Base Sequence, 030306 microbiology, Microarray analysis techniques, Human intestinal microbiota, lcsh:R, Communities, Oligonucleotide probes, Computational Biology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Ribosomal RNA, Microarray Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Hypervariable region, Gastrointestinal Tract, Metabolism, Metagenomics, Pyrosequencing, lcsh:Q, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.

Published
2013

7. MetaExploArrays: a large-scale oligonucleotide probe design software for explorative DNA microarrays

Author

Pierre Peyret, Faouzi Jaziri, David R.C. Hill, Eric Peyretaillade, Nicolas Parisot, Jérémie Denonfoux, Eric Dugat-Bony, Clermont Université, Université Blaise Pascal - Clermont-Ferrand 2 (UBP), EA CIDAM - Auvergne IFR Santé, Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), DOREAU, Bastien, Ecole Nationale Supérieure des Mines de St Etienne-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Speedup, Computer science, Distributed computing, [SDV]Life Sciences [q-bio], Multiprocessing, Parallel computing, computer.software_genre, complex environments, 03 medical and health sciences, thermodynamic, Software, parallelization, model driven engineering, 030304 developmental biology, computer.programming_language, 0303 health sciences, 030306 microbiology, business.industry, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, oligonucleotide probe design, meta-programming, Grid computing, Software design, explorative probes, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Model-driven architecture, business, Software architecture, Oligomer restriction, computer
Abstract

The selection of oligonucleotide probes for micro arrays is still very difficult task. With the rapid growth of environmental databases (metagenomics programs coupled to next generation sequencing), the computational capacity requirements of probe design algorithms have hugely increased. The use of parallel and distributed architectures can considerably reduce the complexity and the computational time of these algorithms. In this paper we present a new efficient algorithm of oligonucleotide probe selection for an individual specific nucleic acid sequence or a group of sequences. We used a model driven engineering approach to simultaneous design of thousands of sensitive, specific, isothermal and explorative probes, on both PC, multiprocessor, cluster and grid computing with on the one hand a significant computing speedup and on the other hand an improved quality of the resulting probes when compared to equivalent software.

Published
2012

8. Genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens

Author

William Tottey, Eric Peyretaillade, Hugh M. B. Harris, Guillaume Borrel, Simonetta Gribaldo, Paul W. O'Toole, Agnès Mihajlovski, Nicolas Parisot, Pierre Peyret, Jean-François Brugère, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork (UCC), EA CIDAM - Auvergne IFR Santé, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Candidatus Methanomethylophilus alvus, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Genome, Feces, Genome, Archaeal, RNA, Ribosomal, 16S, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Anaerobiosis, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, Genetics, Human feces, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Methanogen, Genome Announcements, RNA, Ribosomal, 23S, DNA, Archaeal, Methanogenesis, Molecular Sequence Data, Microbiology, 03 medical and health sciences, Human gut, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, Gene, Aged, 030304 developmental biology, Whole genome sequencing, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 030306 microbiology, Methanol, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Methyltransferases, Sequence Analysis, DNA, biology.organism_classification, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gastrointestinal Tract, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

We report the draft genome sequence of “ Candidatus Methanomethylophilus alvus” Mx1201, a methanogen present in the human gut. It was enriched from human feces under anaerobic conditions with methanol as the substrate. Its circular genome, of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from methanol and tri-, di-, and monomethylamine.

9. Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells

Author

Damien Balestrino, Nicolas Charbonnel, Nathalie Gueguen, Christiane Forestier, Nicolas Parisot, Cyril Guilhen, Agnès Iltis, BRICHEUX, Genevieve, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université d'Auvergne - Clermont-Ferrand I (UdA), EA CIDAM - Auvergne IFR Santé, Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Saint-Gobain Cristaux [France], SAINT-GOBAIN, Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, Contrat Quinquennal Recherche [UMR CNRS 6023], Nouveau Chercheur, Region Auvergne, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Balestrino, Damien, and Saint-Gobain

Subjects
0301 basic medicine, Klebsiella pneumoniae, Biofilm, Dispersion, RNAseq, Transcriptional signatures, 030106 microbiology, Computational biology, Klebsiella pneumoniae Biofilm Dispersion RNAseq Transcriptional signatures, Proteomics, DNA sequencing, Bacterial Adhesion, Microbiology, Transcriptome, 03 medical and health sciences, Genetics, Gene, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 2. Zero hunger, biology, Sequence Analysis, RNA, Gene Expression Profiling, Gene Expression Regulation, Bacterial, biology.organism_classification, Non-coding RNA, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biofilms, DNA microarray, Bacteria, Research Article, Biotechnology
Abstract

Background Surface-associated communities of bacteria, known as biofilms, play a critical role in the persistence and dissemination of bacteria in various environments. Biofilm development is a sequential dynamic process from an initial bacterial adhesion to a three-dimensional structure formation, and a subsequent bacterial dispersion. Transitions between these different modes of growth are governed by complex and partially known molecular pathways. Results Using RNA-seq technology, our work provided an exhaustive overview of the transcriptomic behavior of the opportunistic pathogen Klebsiella pneumoniae derived from free-living, biofilm and biofilm-dispersed states. For each of these conditions, the combined use of Z-scores and principal component analysis provided a clear illustration of distinct expression profiles. In particular, biofilm-dispersed cells appeared as a unique stage in the bacteria lifecycle, different from both planktonic and sessile states. The K-means cluster analysis showed clusters of Coding DNA Sequences (CDS) and non-coding RNA (ncRNA) genes differentially transcribed between conditions. Most of them included dominant functional classes, emphasizing the transcriptional changes occurring in the course of K. pneumoniae lifestyle transitions. Furthermore, analysis of the whole transcriptome allowed the selection of an overall of 40 transcriptional signature genes for the five bacterial physiological states. Conclusions This transcriptional study provides additional clues to understand the key molecular mechanisms involved in the transition between biofilm and the free-living lifestyles, which represents an important challenge to control both beneficial and harmful biofilm. Moreover, this exhaustive study identified physiological state specific transcriptomic reference dataset useful for the research community. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2557-x) contains supplementary material, which is available to authorized users.

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10. 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.

Author

Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O'Toole PW, Fardeau ML, Ollivier B, and Brugère JF

Abstract

The methanogenic strain Mx-05 T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales . It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis , the only member of this order previously isolated. The cells of Mx-05 T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H 2 as an electron donor. H 2 /CO 2 , formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05 T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05 T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L -1 NaCl (optimum 0.12 mol.L -1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H 4 MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05 T as being a novel representative of the order Methanomassiliicoccales , within the novel family Methanomethylophilaceae , for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05 T (JCM 31474T).

Published
2023
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11. Molecular and biopharmaceutical investigation of alginate-inulin synbiotic coencapsulation of probiotic to target the colon.

Author

Atia A, Gomma AI, Fliss I, Beyssac E, Garrait G, and Subirade M

Subjects
Colon, Dosage Forms, Alginates pharmacology, Inulin pharmacology, Probiotics, Synbiotics
Abstract

Colon targeting, as a site-specific delivery for oral formulation, remains a major challenge, especially for sensitive bioactive components such as therapeutic forms of phages, live attenuated virus and prebiotics-probiotics association. Synbiotics could be used to protect encapsulated probiotics during the gastrointestinal tract and control their release in the colon. To achieve these goals, effective prebiotics, such as inulin, could be combined with alginate - the most exploited polymer used for probiotic encapsulation - in the form of beads. This work aimed to study the biopharmaceutical behaviour of alginate beads (A) and inulin-alginate beads of different inulin concentrations (5 or 20%) in 2% alginate (AI5, AI20). Beads were loaded with three probiotic strains (Pediococcus acidilactici Ul5, Lactobacillus reuteri and Lactobacillus salivarius). Dissolution of beads was studied by USP4 under conditions simulating the gastrointestinal condition. The survival rates of the bacterial strains were measured by a specific qPCR bacterial count. Mucoadhesiveness of beads was studied by an ex vivo method using intestinal mucosa. To understand the behaviour of each formulation, the ultrastructure of the polymeric network was studied using scanning electron microscopy (SEM). Molecular interactions between alginate and inulin were studied by Fourier transform infra-red spectroscopy (FTIR). Dissolution results suggested that the presence of inulin in beads provided more protection for the tested bacterial strains against the acidic pH. AI5 was the most effective formulation to deliver probiotics to the colon simulation conditions. FTIR and SEM investigations explained the differences in behaviour of each formula. The developed symbiotic form provided a promising matrix for the development of colonic controlled release systems.

Published
2017
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12. Self-assembly of β-lactoglobulin and egg white lysozyme as a potential carrier for nutraceuticals.

Author

Diarrassouba F, Remondetto G, Garrait G, Alvarez P, Beyssac E, and Subirade M

Subjects
Cholecalciferol chemistry, Chromatography, High Pressure Liquid, Hydrogen-Ion Concentration, Microspheres, Dietary Supplements, Drug Carriers, Egg White chemistry, Lactoglobulins chemistry, Muramidase chemistry
Abstract

Self-assembly structures of β-lactoglobulin (βlg) and egg protein lysozyme (Lyso) were developed, using electrostatic interactions between the two oppositely charged proteins. Different βlg/Lyso concentration ratios were essayed at pH 6.8 to select the optimal ratio for the proteins co-precipitation, which behaviour was then studied at varying pH values. Optimal βlg/Lyso concentration ratio, prepared at pH 7.5, was selected for protein co-precipitation. As a result, a structure with a mean diameter of 7.1±2.5 μm was formed, as indicated by static light scattering. Furthermore, the SEM images showed that βlg and Lyso self-assembled to form a microsphere. Vitamin D3, used as a model nutraceutical, was successfully entrapped in the βlg/Lyso microspheres with an encapsulation efficiency of 90.8±4.8%. Therefore, the βlg/Lyso microspheres can serve as a potential food-grade vehicle for bioactives in the formulation of food products and pharmaceuticals., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Published
2015
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13. Food protein-based microspheres for increased uptake of vitamin D3.

Author

Diarrassouba F, Garrait G, Remondetto G, Alvarez P, Beyssac E, and Subirade M

Subjects
Animals, Biological Availability, Cattle, Cholecalciferol administration & dosage, Drug Stability, Drug Storage, Lactoglobulins administration & dosage, Male, Microspheres, Muramidase administration & dosage, Rats, Rats, Wistar, Cholecalciferol chemistry, Cholecalciferol pharmacokinetics, Lactoglobulins chemistry, Muramidase chemistry
Abstract

To protect vitamin D3 during cold storage and exposure to UV-light, vitamin D3 has been entrapped in microspheres formed by bovine protein β-lactoglobulin (βlg) and lysozyme (Lyso) from egg white. The behaviour of the βlg/Lyso microspheres in simulated intestinal fluid and their impact on the kinetic release of D3 were determined. The impact of the D3-loaded βlg/Lyso microspheres on the bioavailability of D3 was evaluated in vivo by force-feeding rats. The data indicate that the βlg/Lyso microspheres effectively improved the stability of D3, which was readily released in the intestines. The release kinetics were accelerated in the presence of proteolytic enzymes. The bioavailability of D3 was improved, as confirmed by the significant increase in the serum levels of 25-hydroxy-D3 in rats. The current work demonstrates that water soluble proteins were used to substantially increase the bioavailability of the lipophilic vitamin, and thus can serve in the oral delivery of D3., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Published
2015
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14. Improved bioavailability of vitamin D3 using a β-lactoglobulin-based coagulum.

Author

Diarrassouba F, Garrait G, Remondetto G, Alvarez P, Beyssac E, and Subirade M

Subjects
Animals, Biological Availability, Cholecalciferol chemistry, Drug Stability, Male, Rats, Rats, Wistar, Solubility, Cholecalciferol pharmacokinetics, Lactoglobulins metabolism
Abstract

Vitamin D3 (D3) was encapsulated within a water-soluble matrix, formed by promoting the βlg/D3 complex by acidification. The capacity of the βlg-based coagulum to increase the long term stability of D3 in cold storage, upon exposure to intensive UV-light, and in the presence and absence of intestinal proteases, was evaluated. Additionally, the impact of the sequestration of D3 within the matrix of βlg-based coagulum on its bioavailability was determined in vivo with force-fed rats. The water solubility, long-term storage and UV-light stability of D3 were significantly increased (p < 0.0001) due to the high encapsulation efficiency (94.5 ± 1.8%). The βlg-based coagulum was not rapidly disrupted by the proteases in the intestines, leading to a slow release of D3, increased uptake of D3 and subsequent enhancement of the bioavailability of D3 in rats., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Published
2015
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15. Liquid anti-solvent recrystallization to enhance dissolution of CRS 74, a new antiretroviral drug.

Author

de Paiva Lacerda S, Espitalier F, Hoffart V, and Ré MI

Subjects
Chemistry, Pharmaceutical methods, Crystallization, Drug Compounding methods, Ethanol chemistry, HIV Protease Inhibitors administration & dosage, Methylurea Compounds administration & dosage, Solubility, Static Electricity, Thiazoles administration & dosage, Excipients chemistry, HIV Protease Inhibitors chemistry, Methylurea Compounds chemistry, Solvents chemistry, Thiazoles chemistry
Abstract

This study concerns a new compound named CRS 74 which has the property of inhibiting Human Immunodeficiency Virus (HIV) protease, an essential enzyme involved in HIV replication process. It is proved in this study that the original CRS 74 exhibits poor aqueous solubility and a very low dissolution rate, which can influence its bioavailability and clinical response. In an attempt to improve the dissolution rate, CRS 74 was recrystallized by liquid anti-solvent (LAS) crystallization. Ethanol was chosen as solvent and water as the anti-solvent. Recrystallized solids were compared with the original drug crystals in terms of physical and dissolution properties. Recrystallization without additives did not modify the CRS 74 dissolution profile compared to the original drug. CRS 74 was then recrystallized using different additives to optimize the process and formulate physicochemical properties. Steric stabilizer in organic phase ensured size-controlling effect, whereas electrostatic stabilizer in aqueous phase decreased particle agglomeration. Cationic additives avoided drug adsorption onto stainless steel T-mixer. In general, additive improved drug dissolution rate due to improvement of wetting properties by specific interactions between the drug and the additives, and ensured continuous production of CRS 74 by electrostatic repulsion.

Published
2015
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16. Development of a novel drug delivery system: chitosan nanoparticles entrapped in alginate microparticles.

Author

Garrait G, Beyssac E, and Subirade M

Subjects
Administration, Oral, Alginates pharmacokinetics, Amaranth Dye chemistry, Amaranth Dye pharmacokinetics, Chitosan pharmacokinetics, Digestive System metabolism, Drug Carriers pharmacokinetics, Gastric Juice chemistry, Glucuronic Acid chemistry, Glucuronic Acid pharmacokinetics, Hexuronic Acids chemistry, Hexuronic Acids pharmacokinetics, Hydrogen-Ion Concentration, Alginates chemistry, Chitosan chemistry, Drug Carriers chemistry, Nanoparticles chemistry
Abstract

A novel carrier using chitosan nanoparticles entrapped into alginate microparticles is proposed for protecting molecules of interest from degradation in the digestive tract. The effects of polymer concentration, sonication, stirring, pH, and processing conditions on the physical characteristics of the carrier were studied. FITC and RBITC were used to localise the polymers within particles using CLSM. Diffusion of amaranth red (AR) from nanoparticles was quantified during dissolution under gastric and intestinal conditions. Under optimal preparation conditions, the size distribution of nanoparticles loaded with AR was uniform (690 nm) with an encapsulation efficacy of 21.9%. Alginate microparticles (285 µm) containing a homogenous distribution of nanoparticles and polymers were obtained. At gastric pH, the carrier released less than 5% of the loaded AR and, at intestinal pH, the release was rapid and complete. The drug carriers developed shows a promising use as a vehicle suitable to protect molecules of interest after oral administration.

Published
2014
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17. Whey protein and alginate hydrogel microparticles for insulin intestinal absorption: evaluation of permeability enhancement properties on Caco-2 cells.

Author

Déat-Lainé E, Hoffart V, Garrait G, and Beyssac E

Subjects
Alginates chemistry, Caco-2 Cells, Drug Carriers chemistry, Glucuronic Acid administration & dosage, Glucuronic Acid chemistry, Hexuronic Acids administration & dosage, Hexuronic Acids chemistry, Humans, Hydrogels, Hypoglycemic Agents chemistry, Insulin chemistry, Intestinal Absorption drug effects, Milk Proteins chemistry, Whey Proteins, Alginates administration & dosage, Drug Carriers administration & dosage, Hypoglycemic Agents administration & dosage, Insulin administration & dosage, Milk Proteins administration & dosage
Abstract

The evaluation of encapsulated insulin intestinal absorption enhancement was investigated by in vitro methods. Insulin-loaded microparticles (INS-MP) made of whey protein (WP) and alginate (ALG) were prepared by a cold gelation technique. Effect of INS encapsulation toward trypsin and chymotrypsin degradation was performed. Permeability studies using in vitro (Caco-2 cells) experiments were conducted. INS was partially protected by encapsulation toward enzymatic degradation. Moreover INS transport experiments showed that WP and, in lesser extent, ALG were able to enhance INS absorption both as MP and as polymeric solutions by opening the tight junctions. These experiments reinforced the interest of encapsulation in WP/ALG hydrogel combination., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Published
2013
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18. The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.

Author

Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HM, Jeffery IB, Claesson MJ, O'Toole PW, Peyret P, and Brugère JF

Subjects
Analysis of Variance, Bacteria classification, Base Sequence, Feces microbiology, Humans, Microarray Analysis, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis instrumentation, RNA, Ribosomal, 16S genetics, Bacteria genetics, Gastrointestinal Tract microbiology, Microbiota genetics, Oligonucleotide Array Sequence Analysis methods, Phylogeny
Abstract

Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.

Published
2013
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