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1. Title: Region-specific microRNA alterations in marmosets carrying SLC6A4 polymorphisms are associated with anxiety-like behavior

Author

Popa, Natalia, Dipankar, Bachar, Roberts, Angela, Santangelo, Andrea, Gascon, Eduardo, Aix Marseille Université (AMU), University of Cambridge [UK] (CAM), and Gascon, Eduardo

Subjects
[SDV] Life Sciences [q-bio], anxiety and region-specific miRNAs, Marmoset SLC6A4 polymorphisms, [SDV]Life Sciences [q-bio]
Abstract

Psychiatric diseases such as depression and anxiety are multifactorial conditions,highly prevalent in western societies. Human studies have identified a number ofhigh-risk genetic variants for these diseases. Among them, polymorphisms in thepromoter region of the serotonin transporter gene (SLC6A4) have attracted muchattention. However, due to the paucity of experimental models, molecular alterationsinduced by these genetic variants and how they correlate to behavioral deficits havenot been examined. Marmosets have emerged as a powerful model in translationalneuroscience to investigate molecular underpinnings of complex behaviors. Here, wetook advantage of naturally occurring genetic polymorphisms inmarmoset SLC6A4 gene that have been linked to anxiety-like behaviors. UsingFACS-sorted cells from different brain regions, we revealed that marmosets bearingdifferent SLC6A4 variants exhibit distinct microRNAs signatures in a region of theprefrontal cortex whose activity has been consistently altered in patients withdepression/anxiety. We also identified DCC, a gene previously linked to thesediseases, as a downstream target of the dysregulated microRNAs. Significantly, weshowed that levels of both microRNAs and DCC in this region were highly correlatedto anxiety-like behaviors as well as to the response to citalopram, a selectiveserotonin re-uptake inhibitor and widely prescribed anti-depressant. Our findingsestablish links between genetic variants, molecular modifications in specific corticalregions and complex behavioral/pharmacological responses, providing new insightsinto gene-behavior relationships underlying human psychopathology.

Published
2022

2. Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study

Author

Abdalla Ahmed, Sulaiman M. Alfadul, Ahmed M. Al-Hejin, Ahmed A. Mirza, Steve Harakeh, Suhad Bahijri, Suha A. Farraj, Emmanouil Angelakis, Dipankar Bachar, Turki Al Amri, Esam I. Azhar, Ghada Ajabnoor, Timokratis Karamitros, Raoult Didier, King Abdulaziz University, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Laboratoire de microbiologie médicale = Laboratory of Medical Microbiology [Athènes], Institut Pasteur Hellénique, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Bioinformatics and Applied Genomics Unit [Athens], King Abdulaziz City for Science and Technology [Riyadh] (KACST), Umm Al-Qura University, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), The authors express their sincere gratitude and gratefulness to King Abdulaziz City for Science and Technology, Saudi Arabia, for funding this work under Grant #AR-34-191 to SH., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and King Abdulaziz City for Science and Technology [Riyadh]

Subjects
0301 basic medicine, Male, Physiology, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Social Sciences, Gut flora, Pathology and Laboratory Medicine, Biochemistry, Coffee, Habits, Lactobacillus, Medicine and Health Sciences, Smoking Habits, Psychology, Food science, Gut bacteria, 2. Zero hunger, Aged, 80 and over, Multidisciplinary, biology, Genomics, Bread, Middle Aged, 3. Good health, Bacterial Pathogens, Nucleic acids, Physiological Parameters, Ribosomal RNA, Medical Microbiology, Medicine, Female, Pathogens, Bacteroides thetaiotaomicron, Research Article, Adult, Cell biology, Cellular structures and organelles, Adolescent, Science, 030106 microbiology, Saudi Arabia, Microbial Genomics, Microbiology, digestive system, Fusobacteria, Beverages, 03 medical and health sciences, Young Adult, medicine, Genetics, Humans, Microbiome, Obesity, Non-coding RNA, Microbial Pathogens, Feces, Nutrition, Aged, Behavior, Bacteria, Organisms, Biology and Life Sciences, Body weight, biology.organism_classification, medicine.disease, Gastrointestinal Microbiome, Diet, 030104 developmental biology, Cross-Sectional Studies, Food, Smoking cessation, RNA, Smoking Cessation, Ribosomes
Abstract

International audience; The gut microbiota is often affected by the dietary and lifestyle habits of the host, resulting in a better efficacy that favors energy harvesting from the consumed food. Our objective was to characterize the composition of gut microbiota in adult Saudis and investigate possible association with lifestyle and dietary practices. Feces from 104 Saudi volunteers (48% males) were tested for microbiota by sequencing the V3-V4 region of bacterial 16S ribosomal RNA (rRNA). For all participants, data were collected related to their lifestyle habits and dietary practices. The relative abundance (RA) of Fusobacteria was significantly higher in normal weight Saudis (P = 0.005, false discovery rate-FDR = 0.014). Individuals who consumed more coffee presented marginally significant more RA of Fusobacteria (P = 0.02, FDR = 0.20) in their gut microbiota compared to those reporting low or no coffee intake, but the RA of Fusobacteria was significantly higher in smokers compared to nonsmokers (P = 0.009, FDR = 0.027). The RA of Fusobacteria was also significantly higher in those reporting daily consumption of bread (P = 0.005, FDR = 0.015). At the species level, the gut microbiota of people who consumed coffee was dominated by Bacteroides thetaiotaomicron followed by Phascolarctobacterium faecium and Eubacterium rectale. Similarly, the gut microbiota of smokers was also enriched by B. thetaiotaomicron and Lactobacillus amylovorus. Smoking cessation, bread and coffee consumption induce changes in the intestinal microbial composition of Saudis. This indicates the significance of diet and lifestyle practices in the determination of the composition of the gut microbiota, which could possibly lead later to changes in metabolic profile and weight.

Published
2020

3. The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens

Author

Didier Raoult, Rémi N. Charrel, Grégory Dubourg, Caroline Michelle, Matthieu Million, Dipankar Bachar, Laetitia Ninove, Sophie Edouard, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité des Virus Emergents (UVE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Male, medicine.disease_cause, Moraxella catarrhalis, Medical microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Nasopharynx, RNA, Ribosomal, 16S, Child, Respiratory Tract Infections, Aged, 80 and over, biology, Respiratory tract infections, Coinfection, Microbiota, Respiratory infection, High-Throughput Nucleotide Sequencing, General Medicine, Middle Aged, 3. Good health, Infectious Diseases, medicine.anatomical_structure, Streptococcus pneumoniae, Virus Diseases, Child, Preschool, Acute Disease, Female, Disease Susceptibility, Microbiology (medical), Adult, medicine.medical_specialty, Staphylococcus aureus, Adolescent, Microbiology, 03 medical and health sciences, Young Adult, medicine, Humans, Microbiome, Aged, Bacterial disease, Bacteria, business.industry, Infant, Newborn, Infant, biology.organism_classification, Haemophilus influenzae, 030104 developmental biology, Case-Control Studies, Metagenomics, business, Respiratory tract
Abstract

International audience; The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.

Published
2018

4. Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

Author

Didier Raoult, Emmanouil Angelakis, Jeremy Delerce, Frédéric Cadoret, Pierre-Edouard Fournier, Catherine Robert, Jean-Michel Gonzalez, Jean-Christophe Lagier, M. Mailhe, Dipankar Bachar, Véronique Vitton, Anthony Levasseur, D. Ricaboni, Grégory Dubourg, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Male, Colony Count, Microbial, lcsh:QR1-502, Gut flora, Gastroenterology, lcsh:Microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, Endoscopy, Digestive System, Aged, 80 and over, Gastrointestinal tract, Culturomics, Stomach, digestive, oral, and skin physiology, Human microbiome, High-Throughput Nucleotide Sequencing, Colonoscopy, Hydrogen-Ion Concentration, Middle Aged, 3. Good health, New species, medicine.anatomical_structure, Female, Research Article, Microbiology (medical), Adult, DNA, Bacterial, medicine.medical_specialty, Colon, Gut microbiota, Biology, Microbiology, digestive system, 03 medical and health sciences, Young Adult, Internal medicine, medicine, Humans, Aged, Bacteria, Proton Pump Inhibitors, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, Gastrointestinal Microbiome, 030104 developmental biology, Metagenomics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Duodenum
Abstract

Background Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene. Results Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p

Published
2018

5. Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis

Author

Didier Raoult, Dipankar Bachar, Sophie Amrane, Jean-Christophe Lagier, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), biology, 030106 microbiology, Gut flora, Clostridium difficile, biology.organism_classification, 3. Good health, Microbiology, 03 medical and health sciences, 030104 developmental biology, [Clostridium] scindens, Metagenomics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Letter to the Editor, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

6. Culture of previously uncultured members of the human gut microbiota by culturomics

Author

Félix Djossou, Ndeye Mery Dia Badiane, M. Mailhe, Sory Ibrahima Traore, Donia Mouelhi, Sara Bellali, Camille Valles, Muhammad Yasir, Didier Raoult, Aurelia Caputo, Bernard La Scola, Frédéric Cadoret, Jean-Marc Rolain, Matthieu Million, Jônatas Santos Abrahão, Esam I. Azhar, Dipankar Bachar, Grégory Dubourg, El hadji Seck, Jeremy Delerce, Khoudia Diop, Aldiouma Diallo, Fehmida Bibi, E. Guilhot, Guillaume André Durand, Cheikh Sokhna, S. Ndongo, Melhem Bilen, Amadou Hamidou Togo, Perrine Hugon, D. Ricaboni, Fadi Bittar, Véronique Vitton, Catherine Robert, Anthony Levasseur, Jean-Christophe Lagier, Saber Khelaifia, Didier Musso, Niokhor Dione, Gaël Mourembou, Nadim Cassir, Maryam Tidjani Alou, Pierre-Edouard Fournier, Nicole Prisca Makaya Dangui Nieko, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Assistance Publique - Hôpitaux de Marseille (APHM), Centre de recherche en éducation de Nantes (CREN), Le Mans Université (UM)-Université de Nantes - UFR Lettres et Langages (UFRLL), Université de Nantes (UN)-Université de Nantes (UN), Ecole Doctorale Régionale d’Afrique Centrale, Université Bordeaux Segalen - Bordeaux 2, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Unité des Maladies Infectieuses et Tropicales (UMIT), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Gastroentérologie, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital Nord [CHU - APHM], INSB-INSB-Centre National de la Recherche Scientifique (CNRS), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Université de Nantes - UFR Lettres et Langages (UFRLL), and Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)

Subjects
0301 basic medicine, Microbiology (medical), DNA, Bacterial, Microbiological Techniques, 030106 microbiology, Immunology, Computational biology, Applied Microbiology and Biotechnology, Microbiology, DNA, Ribosomal, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, Genetics, Humans, Microbiome, biology, Bacteria, Microbiota, Gastrointestinal Microbiome, Human microbiome, Cell Biology, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, Archaea, Gastrointestinal Tract, DNA, Archaeal, Culturomics, Metagenomics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Proteobacteria
Abstract

Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism1. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms2. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization–time of flight and 16S rRNA for identification2. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies3–5. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut. Optimization of culturing techniques has allowed the identification of 1,057 prokaryotic species within the human gut microbiome repertoire, doubling the previous number of isolated species from the human gut.

Published
2016

7. Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies

Author

Didier Raoult, Fabrice Armougom, Bernard Henrissat, Gilles Audoly, Emmanouil Angelakis, Jean-Christophe Lagier, Catherine Robert, Dipankar Bachar, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, DNA, Bacterial, Glycan, Lysis, 030106 microbiology, Protein-Energy Malnutrition, Deep sequencing, Article, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Feces, Polysaccharides, Humans, Obesity, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, biology, Bacteria, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Extraction (chemistry), Polysaccharides, Bacterial, High-Throughput Nucleotide Sequencing, biology.organism_classification, DNA extraction, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gastrointestinal Microbiome, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Biochemistry, chemistry, Metagenomics, Kwashiorkor, biology.protein, Female, DNA
Abstract

Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.

Published
2016

8. Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Niokhor Dione, Fabrice Armougom, Souleymane Brah, Dipankar Bachar, Philippe Parola, Matthieu Million, Régis Guieu, Saber Khelaifia, Maryam Tidjani Alou, Julien Fromonot, Alexandre Fabre, Bernard Henrissat, Caroline Michelle, Catherine Robert, Perrine Hugon, Aldiouma Diallo, Didier Raoult, Jean-Christophe Lagier, Cheikh Sokhna, Vincent Lombard, Bourne, Yves, Instituts Hospitalo-Universitaires - I.H.U. Méditerranée Infection - - Méditerranée Infection2010 - ANR-10-IAHU-0003 - IAHU - VALID, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Hôpital National de Niamey, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Dysoxie, suractivité : aspects cellulaires et intégratifs thérapeutiques (DS-ACI / UMR MD2), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de pédiatrie multidisciplinaire [Hôpital de la Timone Enfants - APHM], Hôpital de la Timone [CHU - APHM] (TIMONE), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, ANR-10-IAHU-0003/10-IAHU-0003,Méditerranée Infection,Méditerranée Infection(2010), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Asia, Severe Acute Malnutrition, Gut flora, Article, Microbiology, 03 medical and health sciences, [SDV.MHEP.PED] Life Sciences [q-bio]/Human health and pathology/Pediatrics, medicine, Humans, Niger, Microbiome, Child, Bacteroidaceae, 2. Zero hunger, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, Multidisciplinary, Bacteria, biology, Lachnospiraceae, Malnutrition, Methanobrevibacter smithii, Obligate anaerobe, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Bacterial Load, Senegal, Gastrointestinal Microbiome, 3. Good health, Gastrointestinal Tract, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, 030104 developmental biology, Child, Preschool, Dysbiosis, Metagenomics, Oxidation-Reduction, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Severe acute malnutrition (SAM) is associated with inadequate diet, low levels of plasma antioxidants and gut microbiota alterations. The link between gut redox and microbial alterations, however, remains unexplored. By sequencing the gut microbiomes of 79 children of varying nutritional status from three centers in Senegal and Niger, we found a dramatic depletion of obligate anaerobes in malnutrition. This was confirmed in an individual patient data meta-analysis including 107 cases and 77 controls from 5 different African and Asian countries. Specifically, several species of the Bacteroidaceae, Eubacteriaceae, Lachnospiraceae and Ruminococceae families were consistently depleted while Enterococcus faecalis, Escherichia coli and Staphylococcus aureus were consistently enriched. Further analyses on our samples revealed increased fecal redox potential, decreased total bacterial number and dramatic Methanobrevibacter smithii depletion. Indeed, M. smithii was detected in more than half of the controls but in none of the cases. No causality was demonstrated but, based on our results, we propose a unifying theory linking microbiota specificity, lacking anaerobes and archaea, to low antioxidant nutrients, and lower food conversion.

Published
2016

9. Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers

Author

Richard Christen, Karine Alain, Virginie Chapon, Nicolas Theodorakopoulos, Dipankar Bachar, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Interactions Protéine Métal (IPM), Laboratoire de Biogéochimie, Biodisponibilité et Transfert des Radionucléides (IRSN/PRP-ENV/SERIS/L2BT), Service de Recherche et d'Expertise sur les Risques environnementaux (IRSN/PRP-ENV/SERIS), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), CEA - Toxicology programme, 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), IRSN, PRP-ENV, SERIS, L2BT, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
DNA, Bacterial, molecular diversity, Hot Temperature, Tunisia, [SDV]Life Sciences [q-bio], information science, group-specific primers, Microbiology, Polymerase Chain Reaction, Sensitivity and Specificity, law.invention, 03 medical and health sciences, Phylogenetics, law, RNA, Ribosomal, 16S, Deinococcus-Thermus, Extreme environment, Deinococcus, Thermus, Polymerase chain reaction, Phylogeny, 030304 developmental biology, Original Research, DNA Primers, Genetics, 0303 health sciences, biology, 030306 microbiology, Phylum, Genetic Variation, biology.organism_classification, 16S ribosomal RNA, bacteria
Abstract

International audience; The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly , Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deino-coccus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.

Published
2013

10. Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect

Author

Séverine Boiry, Lionel Ranjard, Christophe Mougel, Sébastien Terrat, Noémie Pascault, Pierre-Alain Maron, Jean Lévêque, Richard Christen, Michel Pean, Aurore Kaisermann, Olivier Mathieu, Dipankar Bachar, Catherine Hénault, Sébastien Fontaine, Philippe Lemanceau, 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 Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut de signalisation, biologie du développement et cancer (ISBDC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Groupe de Recherches Appliquées en Phytotechnologie (GRAP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Unité de recherche sur l'Ecosystème Prairial (UREP), Institut National de la Recherche Agronomique (INRA), Study financially supported by the Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME) and the Burgundy region., European Project: 264465,EC:FP7:ENV,FP7-ENV-2010,ECOFINDERS(2011), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), and 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)

Subjects
Firmicutes, [SDE.MCG]Environmental Sciences/Global Changes, Stable-isotope probing, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Decomposer, soil, 03 medical and health sciences, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, soil organic matter, Botany, carbon cycle, Environmental Chemistry, Gemmatimonadetes, Organic matter, stable isotope probing, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, Soil organic matter, Verrucomicrobia, bacterial diversity, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, pyrosequencing, Agronomy, chemistry, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Acidobacteria
Abstract

13 pages; International audience; The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOMdegrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOMdegrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.

Published
2013

11. Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil

Author

Virginie Chapon, Dipankar Bachar, Laure Mondani, Richard Christen, Laurie Piette, Catherine Berthomieu, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Interactions Protéine Métal (IPM), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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 des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, type strain, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Peptidoglycan, Biology, medicine.disease_cause, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Soil, RNA, Ribosomal, 16S, Actinomycetales, medicine, Ecology, Evolution, Behavior and Systematics, Phospholipids, Phylogeny, Soil Microbiology, 030304 developmental biology, 0303 health sciences, Base Composition, Strain (chemistry), 030306 microbiology, Fatty Acids, Nucleic Acid Hybridization, Vitamin K 2, General Medicine, Sequence Analysis, DNA, Microbacterium lemovicicum, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, Bacterial Typing Techniques, chemistry, Uranium, Microbacterium binotii, France, Soil microbiology, Bacteria
Abstract

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).

Published
2013

12. Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Author

Charles G Howes, David VanInsberghe, Rolf Henrik Nilsson, Richard Christen, William W. Mohn, Martin Hartmann, Steven J. Hallam, Dipankar Bachar, Hang Yu, Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Genome British Columbia, Canadian Institute for Advanced Research, Tula Foundation, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
DNA, Bacterial, Genetic Markers, massively parallel pyrosequencing, Sustainable forest management, organic matter removal, Biodiversity, Biology, Microbiology, Trees, soil compaction, 03 medical and health sciences, Forest ecology, Soil ecology, Cluster Analysis, DNA, Fungal, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, geography, 0303 health sciences, geography.geographical_feature_category, Bacteria, British Columbia, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Logging, Fungi, Forestry, bacteria and fungi, Sequence Analysis, DNA, 04 agricultural and veterinary sciences, 15. Life on land, Old-growth forest, Tracheophyta, 13. Climate action, microbial community structure, Soil compaction, Multivariate Analysis, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Original Article, timber harvesting, Corrigendum, Soil microbiology
Abstract

International audience; Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting. The ISME Journal (2012) 6, 2199-2218; doi:10.1038/ismej.2012.84; published online 2 August 2012

Published
2012

13. LODE: A distance-based classifier built on ensembles of positive and negative observations

Author

Dipankar Bachar, Dino Ienco, Rosa Meo, Dipartimento di Informatica [Torino], Università degli studi di Torino = University of Turin (UNITO), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Fouille de données environnementales (TATOO), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Torino (UNITO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
FEATURE SELECTION, Association rule learning, itemsets, Computation, negative observations, Feature selection, 02 engineering and technology, delta measure, ASSOCIATIVE CLASSIFIER, computer.software_genre, DATA MINING, MODELE, SUPERVISED LEARNING, classifier, ensemble, ranking, dependencies, Artificial Intelligence, 020204 information systems, Concept learning, 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], ANALYSE DE DONNEES, Mathematics, Lode, business.industry, Supervised learning, Pattern recognition, Ensemble learning, MODELISATION, ENSEMBLE LEARNING, CONCEPT LEARNING, INFORMATIQUE, Signal Processing, 020201 artificial intelligence & image processing, Computer Vision and Pattern Recognition, Data mining, Artificial intelligence, business, computer, Classifier (UML), Software
Abstract

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SYNERGIE; International audience; Current work on assembling a set of local patterns such as rules and class association rules into a global model for the prediction of a target usually focuses on the identification of the minimal set of patterns that cover the training data. In this paper we present a different point of view: the model of a class has been built with the purpose to emphasise the typical features of the examples of the class. Typical features are modelled by frequent itemsets extracted from the examples and constitute a new representation space of the examples of the class. Prediction of the target class of test examples occurs by computation of the distance between the vector representing the example in the space of the itemsets of each class and the vectors representing the classes. It is interesting to observe that in the distance computation the critical contribution to the discrimination between classes is given not only by the itemsets of the class model that match the example but also by itemsets that do not match the example. These absent features constitute some pieces of information on the examples that can be considered for the prediction and should not be disregarded. Second, absent features are more abundant in the wrong classes than in the correct ones and their number increases the distance between the example vector and the negative class vectors. Furthermore, since absent features are frequent features in their respective classes, they make the prediction more robust against over-fitting and noise. The usage of features absent in the test example is a novel issue in classification: existing learners usually tend to select the best local pattern that matches the example - and do not consider the abundance of other patterns that do not match it. We demonstrate the validity of our observations and the effectiveness of LODE, our learner, by means of extensive empirical experiments in which we compare the prediction accuracy ofLODE with a consistent set of classifiers of the state of the art. In this paper we also report the methodology that we adopted in order to determine automatically the setting of the learner and of its parameters.

Published
2012

14. Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

Author

Linda A. Amaral-Zettler, Richard Christen, Laure Guillou, Jan Pawlowski, Béatrice Lecroq, Dipankar Bachar, Hamid Reza Shahbazkia, Department of genetics and evolution, University of Geneva [Switzerland], Laboratoire de Biologie Virtuelle, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Departamento de Engenharia Electronica e Informatica [Faro], Faculdade de Ciências e Tecnologia [Faro] (FCT), Universidade do Algarve (UAlg)-Universidade do Algarve (UAlg), Brown University, Marine Biological Laboratory (MBL), University of Chicago, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Rare biosphere, Geologic Sediments, Biodiversity, lcsh:Medicine, Cold-seep, Protozoology, 01 natural sciences, 18S ribosomal RNA, ddc:590, Environmental DNA, lcsh:Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 0303 health sciences, Diversity, Multidisciplinary, Ecology, Marine Ecology, Eukaryota, High-Throughput Nucleotide Sequencing, Genomics, respiratory system, Arctic-ocean, Research Article, Ecological Metrics, Sequence analysis, Oceans and Seas, Marine Biology, Biology, Microbiology, 010603 evolutionary biology, 03 medical and health sciences, Eastern mediterranean sea, RNA, Ribosomal, 18S, Animals, 14. Life underwater, Gene, 030304 developmental biology, Cercozoa Protozoa, Microbial Eukaryotes, Sequence Analysis, RNA, lcsh:R, Deep-sea, Computational Biology, Dna, Ribosomal RNA, Marine Environments, Hypervariable region, 13. Climate action, Evolutionary biology, lcsh:Q, Metagenomics, Species Richness, Species richness, human activities, Ecological Environments
Abstract

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundation SNSF /Project funding info:eu-repo/semantics/publishedVersion

Published
2011

15. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

Author

Magne Osteras, Laurent Farinelli, Jan Pawlowski, Loïc Baerlocher, Richard Christen, Philippe Esling, Franck Lejzerowicz, Dipankar Bachar, Béatrice Lecroq, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Genetics and Evolution [Genève], University of Geneva [Switzerland], Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Fasteris SA, Sciences et Technologies de la Musique et du Son (STMS), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), and Fasteris SA [Plan-les-Ouates, Switzerland]

Subjects
0106 biological sciences, Geologic Sediments, Oceans and Seas, Meiobenthos, Biodiversity, Foraminifera, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 01 natural sciences, Deep sea, 03 medical and health sciences, DNA Barcoding, Taxonomic, 14. Life underwater, Phylogeny, Illumina dye sequencing, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Base Sequence, Geography, biology, Ecology, 010604 marine biology & hydrobiology, High-Throughput Nucleotide Sequencing, Biological Sciences, biology.organism_classification, Taxon, Benthic zone, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile , and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribo-somal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational tax-onomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) fora-minifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology , the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.

Published
2011

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