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2. Hepatic microbiome in healthy lean and obese humans

Author

Malte Palm Suppli, Jonatan Ising Bagger, Benjamin Lelouvier, Amandine Broha, Mia Demant, Merete Juhl Kønig, Charlotte Strandberg, Asger Lund, Tina Vilsbøll, and Filip Krag Knop

Subjects
Non-alcoholic fatty liver disease, Obesity, Metabolic syndrome, Microbiome, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Background & Aims: Dysbiosis of the gut microbiota in response to an energy-rich Western diet and the potential leak of bacteria and/or bacterial products from the intestine to the liver is perceived as a potential risk factor for the development of non-alcoholic fatty liver disease (NAFLD). We investigated the microbiome in liver biopsies from healthy lean and obese individuals and compared it with their blood microbiome. Methods: We examined liver biopsies from 15 healthy lean and 14 obese individuals (BMI of 18.5–25 and 30–40 kg/m2, respectively). Bacterial 16S ribosomal DNA (rDNA) was analysed by quantitative polymerase chain reaction (qPCR) and 16S metagenomic sequencing targeting the hypervariable V3–V4 region. Metagenomic analysis was performed using the linear discriminant analysis effect size (LEfSe) algorithm. Data are medians with IQRs in brackets. Results: Histology revealed hepatic steatosis in 13 obese individuals and in 2 lean individuals. A robust signal from qPCR revealed significantly higher amounts of bacterial rDNA copies in liver samples from obese individuals compared with those from lean individuals (148 [118–167] vs. 77 [62–122] 16S copies/ng DNA, p

Published
2021
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3. Hepatic microbiome in healthy lean and obese humans

Author

Jonatan I. Bagger, Tina Vilsbøll, Filip K. Knop, Benjamin Lelouvier, Malte P. Suppli, Charlotte Strandberg, Amandine Broha, Mia Demant, Merete J Kønig, and Asger Lund

Subjects
NAFLD, non-alcoholic fatty liver disease, NASH, non-alcoholic steatohepatitis, Physiology, RC799-869, Gut flora, rDNA, ribosomal DNA, Liver disease, Internal Medicine, medicine, OTU, operational taxonomic unit, Immunology and Allergy, Microbiome, Obesity, Hepatology, biology, business.industry, Fatty liver, Gastroenterology, Diseases of the digestive system. Gastroenterology, medicine.disease, biology.organism_classification, LEfSe, linear discriminant analysis effect size, Metabolic syndrome, Real-time polymerase chain reaction, qPCR, quantitative polymerase chain reaction, HbA1c, glycated haemoglobin, Steatosis, business, Dysbiosis, FLI, fatty liver index, Research Article, Non-alcoholic fatty liver disease
Abstract

Background & Aims Dysbiosis of the gut microbiota in response to an energy-rich Western diet and the potential leak of bacteria and/or bacterial products from the intestine to the liver is perceived as a potential risk factor for the development of non-alcoholic fatty liver disease (NAFLD). We investigated the microbiome in liver biopsies from healthy lean and obese individuals and compared it with their blood microbiome. Methods We examined liver biopsies from 15 healthy lean and 14 obese individuals (BMI of 18.5–25 and 30–40 kg/m2, respectively). Bacterial 16S ribosomal DNA (rDNA) was analysed by quantitative polymerase chain reaction (qPCR) and 16S metagenomic sequencing targeting the hypervariable V3–V4 region. Metagenomic analysis was performed using the linear discriminant analysis effect size (LEfSe) algorithm. Data are medians with IQRs in brackets. Results Histology revealed hepatic steatosis in 13 obese individuals and in 2 lean individuals. A robust signal from qPCR revealed significantly higher amounts of bacterial rDNA copies in liver samples from obese individuals compared with those from lean individuals (148 [118–167] vs. 77 [62–122] 16S copies/ng DNA, p, Graphical abstract, Highlights • Liver tissue from healthy lean and obese individuals contains bacterial rDNA. • Significantly higher amounts of bacterial rDNA and lower alpha diversity were found in liver samples from obese individuals. • Proteobacteria-enriched metataxonomic signature was found in liver samples from obese individuals. • There is strong correlation between the amount of bacterial rDNA in liver samples and the fatty liver index. • Differences in the liver microbiome between lean and obese individuals are not reflected in the blood microbiome.

Published
2021
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4. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis

Author

Iampietro, Carole, Eché, Camille, Castinel, Adrien, Serre, Rémy-Félix, Klopp, Christophe, Denis, Erwan, Bouchez, Olivier, Kuchly, Claire, Vandecasteele, Céline, BROHA, Amandine, THERVILLE, Romain, Di Franco, Arnaud, Djebali Quelen, Sarah, DREAU, Andreea, Hoede, Claire, KOROVINA, Oleksandra, BIRBES, CLEMENT, Laborie, Didier, Mainguy, Jean, Noirot, Céline, Salin, Gerald, Terzian, Paul, Trotard, Marie-Stéphane, Boichard, Didier, Boussaha, Mekki, Grohs, Cécile, Charcosset, Alain, Belcram, Harry, Joets, Johann, Combes, Sylvie, Pascal, Géraldine, Pitel, Frederique, Leroux, Sophie, Riquet, Juliette, Demars, Julie, Tosser-Klopp, Gwenola, Vitte, Clémentine, Iannuccelli, Nathalie, Lluch, Jérôme, Lopez-Roques, Celine, Faraut, Thomas, Zytnicki, Matthias, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FEDER-Région Occitanie, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

8. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis

Author

IAMPIETRO, Carole, Castinel, Adrien, SERRE, Rémy-Félix, Klopp, Christophe, Denis, Erwan, Bouchez, Olivier, Kuchly, Claire, Vandecasteele, Céline, BROHA, Amandine, THERVILLE, Romain, Di Franco, Arnaud, Djebali Quelen, Sarah, DREAU, Andreea, Hoede, Claire, KOROVINA, Oleksandra, BIRBES, CLEMENT, Laborie, Didier, Mainguy, Jean, Noirot, Céline, Salin, Gerald, Terzian, Paul, Trotard, Marie-Stéphane, Boichard, Didier, Boussaha, Mekki, Grohs, Cécile, Charcosset, Alain, Belcram, Harry, Joets, Johann, Combes, Sylvie, Pascal, Géraldine, Pitel, Frédérique, Leroux, Sophie, Riquet, Juliette, Tosser, Gwenola, Vitte, Clémentine, Iannuccelli, Nathalie, Lopez-Roques, Céline, Faraut, Thomas, Zytnicki, Matthias, Gaspin, Christine, Milan, Denis, Donnadieu, Cecile, Génome et Transcriptome - Plateforme Génomique, Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and FEDER-Région Occitanie

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs]

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