Search

Your search keyword '"Dipankar Bachar"' showing total 44 results
Start Over Author "Dipankar Bachar"
44 results on '"Dipankar Bachar"'

2. Retraction Note: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Matthieu Million, Maryam Tidjani Alou, Saber Khelaifia, Dipankar Bachar, Jean-Christophe Lagier, Niokhor Dione, Souleymane Brah, Perrine Hugon, Vincent Lombard, Fabrice Armougom, Julien Fromonot, Catherine Robert, Caroline Michelle, Aldiouma Diallo, Alexandre Fabre, Régis Guieu, Cheikh Sokhna, Bernard Henrissat, Philippe Parola, and Didier Raoult

Subjects
Medicine, Science
Published
2023
Full Text
View/download PDF

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

Author

Natalia Popa, Dipankar Bachar, Angela C. Roberts, Andrea M. Santangelo, and Eduardo Gascon

Subjects
Anxiety, Depression, Non-human primates, Marmoset, microRNA, Ventro-medial prefrontal cortex, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: Psychiatric diseases such as depression and anxiety are multifactorial conditions, highly prevalent in western societies. Human studies have identified a number of high-risk genetic variants for these diseases. Among them, polymorphisms in the promoter region of the serotonin transporter gene (SLC6A4) have attracted much attention. However, due to the paucity of experimental models, molecular alterations induced by these genetic variants and how they correlate to behavioral deficits have not been examined. In this regard, marmosets have emerged as a powerful model in translational neuroscience to investigate molecular underpinnings of complex behaviors. Methods: Here, we took advantage of naturally occurring genetic polymorphisms in marmoset SLC6A4 gene that have been linked to anxiety-like behaviors. Using FACS-sorting, we profiled microRNA contents in different brain regions of genotyped and behaviorally-phenotyped marmosets. Findings: We revealed that marmosets bearing different SLC6A4 variants exhibit distinct microRNAs signatures in a region of the prefrontal cortex whose activity has been consistently altered in patients with depression/anxiety. We also identified Deleted in Colorectal Cancer (DCC), a gene previously linked to these diseases, as a downstream target of the differently expressed microRNAs. Significantly, we showed that levels of both microRNAs and DCC in this region were highly correlated to anxiety-like behaviors. Interpretation: Our findings establish links between genetic variants, molecular modifications in specific cortical regions and complex behavioral responses, providing new insights into gene-behavior relationships underlying human psychopathology. Funding: This work was supported by France National Agency, NRJ Foundation, Celphedia and Fondation de France as well as the Wellcome Trust.

Published
2022
Full Text
View/download PDF

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

Author

Steve Harakeh, Emmanouil Angelakis, Timokratis Karamitros, Dipankar Bachar, Suhad Bahijri, Ghada Ajabnoor, Sulaiman M Alfadul, Suha A Farraj, Turki Al Amri, Ahmed Al-Hejin, Abdalla Ahmed, Ahmed A Mirza, Raoult Didier, and Esam I Azhar

Subjects
Medicine, Science
Abstract

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 non-smokers (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
Full Text
View/download PDF

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

Author

Morgane Mailhe, Davide Ricaboni, Véronique Vitton, Jean-Michel Gonzalez, Dipankar Bachar, Grégory Dubourg, Frédéric Cadoret, Catherine Robert, Jérémy Delerce, Anthony Levasseur, Pierre-Edouard Fournier, Emmanouil Angelakis, Jean-Christophe Lagier, and Didier Raoult

Subjects
Gut microbiota, Culturomics, Metagenomics, New species, Microbiology, QR1-502
Abstract

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
Full Text
View/download PDF

7. RETRACTED ARTICLE: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Matthieu Million, Maryam Tidjani Alou, Saber Khelaifia, Dipankar Bachar, Jean-Christophe Lagier, Niokhor Dione, Souleymane Brah, Perrine Hugon, Vincent Lombard, Fabrice Armougom, Julien Fromonot, Catherine Robert, Caroline Michelle, Aldiouma Diallo, Alexandre Fabre, Régis Guieu, Cheikh Sokhna, Bernard Henrissat, Philippe Parola, and Didier Raoult

Subjects
Medicine, Science
Abstract

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
Full Text
View/download PDF

8. Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Author

Maryam Tidjani Alou, Matthieu Million, Sory I. Traore, Donia Mouelhi, Saber Khelaifia, Dipankar Bachar, Aurelia Caputo, Jeremy Delerce, Souleymane Brah, Daouda Alhousseini, Cheikh Sokhna, Catherine Robert, Bouli A. Diallo, Aldiouma Diallo, Philippe Parola, Michael Golden, Jean-Christophe Lagier, and Didier Raoult

Subjects
severe acute malnutrition, kwashiorkor, gut microbiota, culturomics, metagenomics, probiotics, Microbiology, QR1-502
Abstract

Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host) to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation), a depletion in oxygen-sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.

Published
2017
Full Text
View/download PDF

9. A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity.

Author

Emmanouil Angelakis, Fabrice Armougom, Frédéric Carrière, Dipankar Bachar, René Laugier, Jean-Christophe Lagier, Catherine Robert, Caroline Michelle, Bernard Henrissat, and Didier Raoult

Subjects
Medicine, Science
Abstract

Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05).The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.

Published
2015
Full Text
View/download PDF

10. Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection.

Author

Anne Boissière, Majoline T Tchioffo, Dipankar Bachar, Luc Abate, Alexandra Marie, Sandrine E Nsango, Hamid R Shahbazkia, Parfait H Awono-Ambene, Elena A Levashina, Richard Christen, and Isabelle Morlais

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

The susceptibility of Anopheles mosquitoes to Plasmodium infections relies on complex interactions between the insect vector and the malaria parasite. A number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite clearance is under genetic control, but little is known about the influence of environmental factors on the transmission success. We present here evidence that the composition of the vector gut microbiota is one of the major components that determine the outcome of mosquito infections. A. gambiae mosquitoes collected in natural breeding sites from Cameroon were experimentally challenged with a wild P. falciparum isolate, and their gut bacterial content was submitted for pyrosequencing analysis. The meta-taxogenomic approach revealed a broader richness of the midgut bacterial flora than previously described. Unexpectedly, the majority of bacterial species were found in only a small proportion of mosquitoes, and only 20 genera were shared by 80% of individuals. We show that observed differences in gut bacterial flora of adult mosquitoes is a result of breeding in distinct sites, suggesting that the native aquatic source where larvae were grown determines the composition of the midgut microbiota. Importantly, the abundance of Enterobacteriaceae in the mosquito midgut correlates significantly with the Plasmodium infection status. This striking relationship highlights the role of natural gut environment in parasite transmission. Deciphering microbe-pathogen interactions offers new perspectives to control disease transmission.

Published
2012
Full Text
View/download PDF

11. Eukaryotic richness in the abyss: insights from pyrotag sequencing.

Author

Jan Pawlowski, Richard Christen, Béatrice Lecroq, Dipankar Bachar, Hamid Reza Shahbazkia, Linda Amaral-Zettler, and Laure Guillou

Subjects
Medicine, Science
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.

Published
2011
Full Text
View/download PDF

13. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy.

Author

Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cédric Berney, Lucie Bittner, Christophe Boutte, Gaétan Burgaud, Colomban de Vargas, Johan Decelle, Javier del Campo, John R. Dolan, Micah Dunthorn, Bente Edvardsen, Maria Holzmann, Wiebe H. C. F. Kooistra, Enrique Lara, Noan Le Bescot, Ramiro Logares, Frédéric Mahé, Ramon Massana, Marina Montresor, Raphael Morard, Fabrice Not, Jan Pawlowski, Ian Probert, Anne-Laure Sauvadet, Raffaele Siano, Thorsten Stoeck, Daniel Vaulot, Pascal Zimmermann, and Richard Christen

Published
2013
Full Text
View/download PDF

14. 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

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

Author

Natalia Popa, Dipankar Bachar, Angela C. Roberts, Andrea M. Santangelo, Eduardo Gascon, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK, Aix Marseille Université (AMU), University of Cambridge [UK] (CAM), ANR-18-CE37-0017,Marmobrain,Un nouveau modèle primate non-humain pour la recherche translationnelle sur le cerveau(2018), Gascon, Eduardo [0000-0002-2625-5509], and Apollo - University of Cambridge Repository

Subjects
[SDV]Life Sciences [q-bio], Ventromedial prefrontal cortex, Context (language use), 03 medical and health sciences, 0302 clinical medicine, Region specific, biology.animal, microRNA, medicine, Animals, Humans, Gene, DCC, 030304 developmental biology, Serotonin Plasma Membrane Transport Proteins, marmoset, 0303 health sciences, Polymorphism, Genetic, biology, Marmoset, Callithrix, anxiety, 3. Good health, MicroRNAs, medicine.anatomical_structure, depression, Anxiety, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], non-human primates, medicine.symptom, ventro-medial prefrontal cortex, Neuroscience, 030217 neurology & neurosurgery, Psychopathology
Abstract

BACKGROUND: Psychiatric diseases such as depression and anxiety are multifactorial conditions, highly prevalent in western societies. Human studies have identified a number of high-risk genetic variants for these diseases. Among them, polymorphisms in the promoter region of the serotonin transporter gene (SLC6A4) have attracted much attention. However, due to the paucity of experimental models, molecular alterations induced by these genetic variants and how they correlate to behavioral deficits have not been examined. In this regard, marmosets have emerged as a powerful model in translational neuroscience to investigate molecular underpinnings of complex behaviors. METHODS: Here, we took advantage of naturally occurring genetic polymorphisms in marmoset SLC6A4 gene that have been linked to anxiety-like behaviors. Using FACS-sorting, we profiled microRNA contents in different brain regions of genotyped and behaviorally-phenotyped marmosets. FINDINGS: We revealed that marmosets bearing different SLC6A4 variants exhibit distinct microRNAs signatures in a region of the prefrontal cortex whose activity has been consistently altered in patients with depression/anxiety. We also identified Deleted in Colorectal Cancer (DCC), a gene previously linked to these diseases, as a downstream target of the differently expressed microRNAs. Significantly, we showed that levels of both microRNAs and DCC in this region were highly correlated to anxiety-like behaviors. INTERPRETATION: Our findings establish links between genetic variants, molecular modifications in specific cortical regions and complex behavioral responses, providing new insights into gene-behavior relationships underlying human psychopathology. FUNDING: This work was supported by France National Agency, NRJ Foundation, Celphedia and Fondation de France as well as the Wellcome Trust.

Published
2021

17. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Author

Selim Melvin Atay, Iska Moxon-Emre, Anders Eklund, Paula P. Brooks, Nandita Vijayakumar, Anibal Sólon Heinsfeld, Jean-Baptiste Poline, Yaroslav O. Halchenko, David Meunier, Daniela M. Hohmann, Martin Szinte, Arshitha Basavaraj, Andrija Štajduhar, Link Tejavibulya, Michael Dayan, Anisha Keshavan, Chao Jiang, Felix Hoffstaedter, Michael P. Milham, Davide Momi, Hua Xie, Ai Wern Chung, Georg Langs, Hao-Ting Wang, Xenia Kobeleva, Robert Oostenveld, Thomas G. Close, Lena Dorfschmidt, Jesse A. Brown, Serge Koudoro, J.P. Manzano-Patron, Isil P. Bilgin, Shreyas Fadnavis, Sylvain Takerkart, R. Cameron Craddock, Stephan Heunis, Scott Peltier, Kathryn Berluti, Hayli Spence, Pablo F. Damasceno, David H. O’Connor, Eleftherios Garyfallidis, Eugene P. Duff, Rudolph Pienaar, Nicolas Traut, AmanPreet Badhwar, Ali R. Khan, Marissa Laws, Abigail S. Greene, Richard A. I. Bethlehem, Angela R. Laird, Krista DeStasio, Ina Thome, Camille Maumet, Alexandru D. Iordan, P. Christiaan Klink, Damion V. Demeter, John A. Onofrey, Cassandra D. Gould van Praag, Jakub Vohryzek, Suzanne T. Witt, Aysha Motala, Valerie Hayot-Sasson, Geetika Gupta, Alexandre Rosa Franco, John W. VanMeter, Michel Thiebaut de Schotten, James M. Shine, Lucina Q. Uddin, Thomas S. Hartmann, Guillaume Flandin, Clara Moreau, Tomislav Lipic, Claire Bradley, Fernando A. Barrios, Daniel S. Margulies, R. Austin Benn, Sofie Van Den Bossche, Lydia Riedl, Xihe Xie, Christopher R. Madan, Roberto Toro, Viviana Siless, Fabrizio De Vico Fallani, Nikoloz Sirmpilatze, Emily Olafson, Anqi Qiu, Theresa W. Cheng, Valentina Borghesani, Sidhant Chopra, Claire Cury, Giorgio Marinato, Horea-Ioan Ioanas, Giorgia Cona, Michael Joseph, Angela Tam, Mathias Scharinger, Daniel A. Handwerker, Katherine L. Bottenhorn, Sina Mansour L, Kathryn L. Mills, Christopher J. Markiewicz, Elizabeth Levitis, Cyril Pernet, Stephanie J. Forkel, Agah Karakuzu, Edwina R Orchard, Sarah L. Dziura, Saige Rutherford, Kamalaker Dadi, Enrico Glerean, Desiree Lussier, Davide Poggiali, Molly Simmonite, Jason Kai, Jessica Flannery, Ting Xu, Jon Haitz Legarreta, Nasim Anousheh, Marco Bedini, Tristan Glatard, Thomas E. Nichols, Joscelin Rocha-Hidalgo, Erin W. Dickie, Dipankar Bachar, Malin Sandström, Xi-Nian Zuo, Pedro Pinheiro-Chagas, Laura C. Rice, Jakša Vukojević, Javier Gonzalez-Castillo, José C. García Alanis, Lorenzo Pasquini, Yu-Fang Yang, Matteo Mancini, Deena Shariq, Chao-Gan Yan, Laura Tomaz da Silva, César Caballero-Gaudes, Yasmine Bassil, Aurina Arnatkeviciute, Dustin Scheinost, Satrajit S. Ghosh, Gaël Varoquaux, Etienne Combrisson, Bramsh Qamar Chandio, Kelly Garner, Tiago Quendera, Patrick Friedrich, Shawn A. Rhoads, Roxane Licandro, Elizabeth DuPre, Aki Nikolaidis, Simon Schwab, Stephanie Noble, Guillaume Auzias, Daniel J. Lurie, Mahboobeh Parsapoor, Eneko Uruñuela, Andrew Doyle, Peer Herholz, Saampras Ganesan, Vincent Koppelmans, Corey Horien, Samir Das, Junaid S. Merchant, Siyuan Gao, Matheus Marcon, Nathalia Bianchini Esper, B.T. Thomas Yeo, Katja Heuer, Caroline O’Brien, Micaela Y. Chan, Sook-Lei Liew, Lindsay D. Oliver, Kirstie Whitaker, Christoph Vogelbacher, Dylan M. Nielson, Krisanne Litinas, Dorien C. Huijser, Pierre Bellec, R. Todd Constable, David N. Kennedy, Julia Sprenger, Lea-Theresa Mais, Oscar Esteban, Patrick J. Park, Patrick Callahan, Christopher R. Nolan, Johanna Bayer, Guillaume Dumas, Elise Bannier, Elizabeth A. McDevitt, Ariel Rokem, Samuel A. Nastase, Olivia W. Stanley, Ruggero Basanisi, Daniele Marinazzo, Gregory Kiar, Lisa Novello, Samuel Guay, John C. Flournoy, Stefano Moia, Kendra Oudyk, Fang-Cheng Yeh, Gustav Nilsonne, Thomas B. Shaw, Steve Wideman, Saskia Bollmann, Steffen Bollmann, Julia M. Huntenburg, Augusto Buchweitz, Matteo Visconti di Oleggio Castello, Dimitra Maoutsa, Lucy B. Whitmore, Catherine Alice Hahn, Antonino Vallesi, Remi Gau, Felipe Meneguzzi, Université Catholique de Louvain = Catholic University of Louvain (UCL), Yale University [New Haven], Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Florida International University [Miami] (FIU), University of Reading (UOR), University of Würzburg, Champalimaud Centre for the Unknown [Lisbon], University of Melbourne, University of Cambridge [UK] (CAM), Georgetown University [Washington] (GU), Philipps Universität Marburg = Philipps University of Marburg, Université de Montréal (UdeM), University College of London [London] (UCL), University of Sussex, Universiteit Gent = Ghent University (UGENT), German Research Center for Neurodegenerative Diseases - Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Université de Sherbrooke (UdeS), Middle East Technical University [Ankara] (METU), McGill University = Université McGill [Montréal, Canada], Modelling brain structure, function and variability based on high-field MRI data (PARIETAL), Service NEUROSPIN (NEUROSPIN), 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)-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)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universiteit Leiden, Karolinska Institutet [Stockholm], Princeton University, Universität Zürich [Zürich] = University of Zurich (UZH), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), University medical center and campus biotech Geneva, Emory University [Atlanta, GA], Cardiff University's Brain Research Imaging Centre [Cardiff] (CUBRIC), School of Psychology [Cardiff University], Cardiff University-Cardiff University, The University of Sydney, Weill Cornell Medicine [Cornell University], Cornell University [New York], Università degli Studi di Padova = University of Padua (Unipd), Jülich Research Centre, University of Texas at Austin [Austin], Institut Pasteur [Paris] (IP), Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Basque Center on Cognition Brain and Language [Gipuzkoa, Espagne] (BCBL), Linköping University (LIU), University of Queensland [Brisbane], University of New South Wales [Sydney] (UNSW), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), University of Maryland [College Park], University of Maryland System, University of Washington [Seattle], Harvard Medical School [Boston] (HMS), Child Mind Institute, University of Western Ontario (UWO), Indiana University [Bloomington], Indiana University System, Monash university, Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Neuroimagerie: méthodes et applications (Empenn), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), National Institute of Mental Health (NIMH), Università degli Studi di Trento (UNITN), Centro Nacional de Investigaciones Cardiovasculares Carlos III [Madrid, Spain] (CNIC), Instituto de Salud Carlos III [Madrid] (ISC), Queensland University of Technology [Brisbane] (QUT), University of California [San Francisco] (UC San Francisco), University of California (UC), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), University of Texas at Dallas [Richardson] (UT Dallas), University of Oregon [Eugene], Monash University [Melbourne], Boston Children's Hospital, Algorithms, models and methods for images and signals of the human brain (ARAMIS), Sorbonne Université (SU)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Neuroimagerie: méthodes et applications (EMPENN), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAL, IMAGE ET LANGAGE (IRISA-D6), Chinese Academy of Sciences [Beijing] (CAS), Beijing Normal University (BNU), This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 867458 awarded to Julia M. Huntenburg, from ANR-19-DATA-0025 NeuroWebLab for Katja Heuer, Roberto Toro, and Nicholas Traut, and from NIH K00MH122372 for Stephanie Noble., Brainhack Community: Nasim Anousheh, Aurina Arnatkeviciute, Guillaume Auzias, Dipankar Bachar, Elise Bannier, Ruggero Basanisi, Arshitha Basavaraj, Marco Bedini, Pierre Bellec, R Austin Benn, Kathryn Berluti, Steffen Bollmann, Saskia Bollmann, Claire Bradley, Jesse Brown, Augusto Buchweitz, Patrick Callahan, Micaela Y Chan, Bramsh Q Chandio, Theresa Cheng, Sidhant Chopra, Ai Wern Chung, Thomas G Close, Etienne Combrisson, Giorgia Cona, R Todd Constable, Claire Cury, Kamalaker Dadi, Pablo F Damasceno, Samir Das, Fabrizio De Vico Fallani, Krista DeStasio, Erin W Dickie, Lena Dorfschmidt, Eugene P Duff, Elizabeth DuPre, Sarah Dziura, Nathalia B Esper, Oscar Esteban, Shreyas Fadnavis, Guillaume Flandin, Jessica E Flannery, John Flournoy, Stephanie J Forkel, Alexandre R Franco, Saampras Ganesan, Siyuan Gao, José C García Alanis, Eleftherios Garyfallidis, Tristan Glatard, Enrico Glerean, Javier Gonzalez-Castillo, Cassandra D Gould van Praag, Abigail S Greene, Geetika Gupta, Catherine Alice Hahn, Yaroslav O Halchenko, Daniel Handwerker, Thomas S Hartmann, Valérie Hayot-Sasson, Stephan Heunis, Felix Hoffstaedter, Daniela M Hohmann, Corey Horien, Horea-Ioan Ioanas, Alexandru Iordan, Chao Jiang, Michael Joseph, Jason Kai, Agah Karakuzu, David N Kennedy, Anisha Keshavan, Ali R Khan, Gregory Kiar, P Christiaan Klink, Vincent Koppelmans, Serge Koudoro, Angela R Laird, Georg Langs, Marissa Laws, Roxane Licandro, Sook-Lei Liew, Tomislav Lipic, Krisanne Litinas, Daniel J Lurie, Désirée Lussier, Christopher R Madan, Lea-Theresa Mais, Sina Mansour L, J P Manzano-Patron, Dimitra Maoutsa, Matheus Marcon, Daniel S Margulies, Giorgio Marinato, Daniele Marinazzo, Christopher J Markiewicz, Camille Maumet, Felipe Meneguzzi, David Meunier, Michael P Milham, Kathryn L Mills, Davide Momi, Clara A Moreau, Aysha Motala, Iska Moxon-Emre, Thomas E Nichols, Dylan M Nielson, Gustav Nilsonne, Lisa Novello, Caroline O'Brien, Emily Olafson, Lindsay D Oliver, John A Onofrey, Edwina R Orchard, Kendra Oudyk, Patrick J Park, Mahboobeh Parsapoor, Lorenzo Pasquini, Scott Peltier, Cyril R Pernet, Rudolph Pienaar, Pedro Pinheiro-Chagas, Jean-Baptiste Poline, Anqi Qiu, Tiago Quendera, Laura C Rice, Joscelin Rocha-Hidalgo, Saige Rutherford, Mathias Scharinger, Dustin Scheinost, Deena Shariq, Thomas B Shaw, Viviana Siless, Molly Simmonite, Nikoloz Sirmpilatze, Hayli Spence, Julia Sprenger, Andrija Stajduhar, Martin Szinte, Sylvain Takerkart, Angela Tam, Link Tejavibulya, Michel Thiebaut de Schotten, Ina Thome, Laura Tomaz da Silva, Nicolas Traut, Lucina Q Uddin, Antonino Vallesi, John W VanMeter, Nandita Vijayakumar, Matteo Visconti di Oleggio Castello, Jakub Vohryzek, Jakša Vukojević, Kirstie Jane Whitaker, Lucy Whitmore, Steve Wideman, Suzanne T Witt, Hua Xie, Ting Xu, Chao-Gan Yan, Fang-Cheng Yeh, B T Thomas Yeo, Xi-Nian Zuo, ANR-19-DATA-0025,NeuroWebLab,Un laboratoire de neuroscience collectif: Au delà de FAIR(2019), European Project: 867458,LC-FMR, Maumet, Camille, Un laboratoire de neuroscience collectif: Au delà de FAIR - - NeuroWebLab2019 - ANR-19-DATA-0025 - DONNEES - VALID, Brainhack: Developing a culture of open, inclusive, community-driven neuroscience - LC-FMR - 867458 - INCOMING, Leiden University, Weill Cornell Medicine [New York], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Universiteit Gent = Ghent University [Belgium] (UGENT), University Hospital Bonn, Sherbrooke Connectivity Imaging Lab [Sherbrooke] (SCIL), Département d'informatique [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS)-Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Videos and Images Theory and Analytics Laboratory (VITAL), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Service NEUROSPIN (NEUROSPIN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Erasmus University Rotterdam, Origami (Origami), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2), Princeton Neuroscience Institute [Princeton], Human Neuroscience Platform, Brighton and Sussex Medical School (BSMS), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), Institute of Neuroscience and Medicine [Jülich] (INM-1), Département de Neuroscience - Department of Neuroscience, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Queensland Brain Institute, Universidad Nacional Autónoma de México (UNAM), Radboud university [Nijmegen], McGovern Institute for Brain Research [Cambridge], Massachusetts Institute of Technology (MIT), The Brainhack Community - https://pubmed.ncbi.nlm.nih.gov/33932337, Philipps University of Marburg, University of the Basque Country [Bizkaia] (UPV/EHU), Universita degli Studi di Padova, Philipps Universität Marburg, Institut Pasteur [Paris], Empenn, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), University of California [San Francisco] (UCSF), University of California, Geochemistry, and University of Padova [Padova, Italy]

Subjects
0301 basic medicine, Open science, Community building, Best practice, Neuroscience(all), Brainhack, Article, neuroscience, 03 medical and health sciences, 0302 clinical medicine, best practices, collaboration, community building, hackathon, inclusivity, open science, reproducibility, training, Congresses as Topic, Neurosciences, Practice Guidelines as Topic, Communication, Internet, Research community, Medical Bioscience, Psychology, ddc:610, Sociology, Brainhack Community, Training, Neurology & Neurosurgery, Scientific progress, organization & administration [Neurosciences], General Neuroscience, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, Medicinsk biovetenskap, 030104 developmental biology, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Cognitive Sciences, Engineering ethics, 030217 neurology & neurosurgery
Abstract

Available online 30 April 2021. Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress. The present manuscript is part of a growing community effort to collate Brainhack-related insights and expertise into a Jupyter Book (http://brainhack.org/brainhack_jupyter_book/) that will serve as a centralized set of resources for the community; we acknowledge all the individuals who contributed and will make ongoing contributions to these resources. A pre-print version of the present manuscript is available as part of the Jupyter Book. Moreover, we would like to acknowledge all Brainhack organizers, supporters, presenters, and participants for their contribution to growing and maintaining this community. The benefits described in this manuscript would not be possible without them. We also thank all institutions, labs, and organizations who have helped this community grow, meet in stimulating environments, and add an excellent educational resource pool and agenda. With an expanding community, Brainhack’s support network keeps growing, and we thank all labs and individual researchers for their dedication and expertise offered to this community (see http://brainhack.org/brainhack_jupyter_book/acknowledgments.html for a full list of individual acknowledgments; an updated list will be maintained in the Jupyter Book). Grants and funding bodies: This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 867458 awarded to Julia M. Huntenburg; from ANR-19-DATA-0025 NeuroWebLab for Katja Heuer, Roberto Toro, and Nicholas Traut; and from NIH K00MH122372 for Stephanie Noble. The Brainhack Community member list and contributions of the different authors are detailed at http://brainhack.org/brainhack_jupyter_book/contributors.html. Our crediting system is described here: http://brainhack.org/brainhack_jupyter_book/neuroview_authorship-agreement.html.

Published
2021

18. Characterisation of the Vaginal Microbiota Using Culturomics and Metagenomics Suggests Transplantation of Gut Microbiota Into the Vagina During Bacterial Vaginosis

Author

Florence Bretelle, Anthony Levasseur, Dipankar Bachar, Didier Raoult, Ndeye Safietou Fall, Cheikh Sokhna, Khoudia Diop, Jean-Christophe Lagier, Florence Fenollar, and Nafissatou Diagne

Subjects
Transplantation, medicine.anatomical_structure, biology, Culturomics, Metagenomics, medicine, Vagina, Gut flora, Bacterial vaginosis, biology.organism_classification, medicine.disease, Microbiology
Abstract

Background: Bacterial vaginosis is a very common vaginal disorder, with a gynaeco-obstetrical impact, but remains poorly understood. Current antibiotic treatment most often fails. Our objective was to exhaustively map the bacterial community present in bacterial vaginosis and normal flora, using not only a molecular approach but also a highly efficient culture approach, culturomics. Vaginal bacterial diversity was evaluated using both strategies for 24 Caucasian French women, including 7 cases of bacterial vaginosis, and 10 rural Senegalese women, including 5 cases of bacterial vaginosis. An additional 16 specimens (three cases of bacterial vaginosis and 13 normal flora) obtained during the follow-up visits of five French women with bacterial vaginosis were analysed using metagenomics.Results: The combination of culturomics and metagenomics reveals the richness and diversity of vaginal microbiota. Our data demonstrated that compared to healthy women, those with bacterial vaginosis present a shift in vaginal flora. The microbiota of the bacterial vaginosis group can be easily distinguished from that of healthy group by their increased bacterial diversity, abundance of Bacteroidales and Leptotrichiaeceae, and depletion of Proteobacteria and Lactobacillaceae species. In addition, a complex of 10 genera was associated with bacterial vaginosis: Gardnerella, Atopobium, Snethia, Aerococcus, Prevotella, Gemella, Facklamia, Porphyromonas, Mycoplasma, and Urinacoccus. Overall, the microbial population detected in bacterial vaginosis flora was largely similar to the bacterial communities found in gut microbiota. The two approaches showed a diverse vaginal microbiota that was largely non-overlapping, with only 146 common species. Furthermore, culturomics extends the repertoire of human-associated bacteria with the isolation of 27 new bacterial species.Conclusions: This study provides the most representative topology of the vaginal microbiota of normal flora and bacterial vaginosis and suggests the transplantation of gut microbiota into the vagina during bacterial vaginosis. Several sets of clinically relevant anaerobic bacteria and new species were also isolated from the human vagina, confirming that some previously “uncultivated” species may be cultivated using an appropriate strategy. Exhaustive characterisation of vaginal microbiota will enable a better understanding and management of bacterial vaginosis. Obtaining isolates will allow us to explore the bacterial interactions of the vaginal microbiota and will serve as a basis for the potential development of bacteriotherapy to prevent or treat vaginal dysbiosis.

Published
2020

19. 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

20. Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus

Author

Frank T. Wieringa, Didier Raoult, Cheikh Sokhna, Anthony Levasseur, T.-P.-T. Pham, Dipankar Bachar, Aldiouma Diallo, Souleymane Brah, Maryam Tidjani Alou, Daouda Alhousseini, Matthieu Million, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Service des Maladies Infectieuses et Tropicales [CHU Hôpital Nord - Marseille] (M.I.T), Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital Nord [CHU - APHM], Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), 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, medicine.drug_class, Antibiotics, Physiology, lcsh:Medicine, Gut flora, Protein-Energy Malnutrition, Article, Fusobacteria, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Proteobacteria, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Nutrition, 2. Zero hunger, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, biology, Bacteroidetes, lcsh:R, Kwashiorkor, Biodiversity, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Gastrointestinal Microbiome, Malnutrition, 030104 developmental biology, Fusobacterium, Case-Control Studies, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Marasmus, lcsh:Q, Female, Microbiome, 030217 neurology & neurosurgery
Abstract

Kwashiorkor and marasmus are considered to be two different clinical diseases resulting from severe malnutrition, but this distinction has been questioned. In a previous study comparing children with kwashiorkor and healthy children from Niger and Senegal, we found a dramatic gut microbiota alteration with a predominant depletion of anaerobes and enrichment in Proteobacteria and Fusobacteria in kwashiorkor. However, it remained unknown whether this association was related to malnutrition or was a specific feature of kwashiorkor. In this continuation study, we added 7 new marasmus subjects and 71,162 new colonies from the same countries. Our results showed that, compared to marasmus, the kwashiorkor gut microbiota was characterized by an increased proportion of Proteobacteria (culturomics, Marasmus 5.0%, Kwashiorkor 16.7%, p p = 0.001), but there was a decreased proportion of Bacteroidetes in marasmus (culturomics, Marasmus 0.8%, Kwashiorkor 6.5%, p = 0.001; metagenomics, Marasmus 5.4%, Kwashiorkor 7.0%, p = 0.03). Fusobacterium was more frequently cultured from kwashiorkor. All detected potential pathogenic species were enriched in the kwashiorkor gut microbiota. These results provide a biological basis to support the usage of an antibiotic therapy more effective in suppressing the overgrowth of bacterial communities resistant to penicillin, combined with antioxidants and probiotics for nutritional recovery therapies, particularly for kwashiorkor.

Published
2019

21. Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection

Author

Camille Valles, T.-P.-T. Pham, Sophie Amrane, Dipankar Bachar, Issa Isaac Ngom, Didier Raoult, Pamela Afouda, Marie Hocquart, Niokhor Dione, Edmond Kuete, Jean-Christophe Lagier, Aix-Marseille Université - Faculté de médecine (AMU MED), Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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, Male, Bifidobacterium longum, genetic structures, lcsh:Medicine, Gut flora, Feces, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Bacteroides, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, biology, High-throughput screening, Clostridium difficile, Middle Aged, Diarrhoea, 3. Good health, Biological Therapy, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Adult, Article, Microbiology, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Aged, Bacteria, lcsh:R, Bacteroidetes, Bacteriology, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gastrointestinal Microbiome, Molecular Typing, 030104 developmental biology, Metagenomics, Clostridium Infections, lcsh:Q, Bifidobacterium, Dysbiosis, 030217 neurology & neurosurgery
Abstract

Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.

Published
2019

22. Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans

Author

M. Million, Anthony Levasseur, Muhammad Yasir, E.I. Azhar, Cheikh Sokhna, Dipankar Bachar, Didier Raoult, D Musso, Bruno Senghor, Saber Khelaifia, Frédéric Cadoret, D S Konate, Vicky Merhej, El hadji Seck, J.-C. Lagier, Fehmida Bibi, Catherine Robert, Ogobara K. Doumbo, Asif A. Jiman-Fatani, 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 pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Adult, Male, Endocrinology, Diabetes and Metabolism, Medicine (miscellaneous), Zoology, 030209 endocrinology & metabolism, Gut flora, Global Health, Feces, 03 medical and health sciences, 0302 clinical medicine, fluids and secretions, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Obesity, 030212 general & internal medicine, Sodium Chloride, Dietary, Bifidobacterium, Inflammation, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Nutrition and Dietetics, biology, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Halophile, Gastrointestinal Microbiome, 3. Good health, Salinity, Refractometry, Metagenomics, Case-Control Studies, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Akkermansia muciniphila
Abstract

International audience; Background/objectives High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. Methods/subjects We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by tax-onogenomics and their genome sequenced. Results Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. Conclusions High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Published
2019

23. 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

24. 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

25. 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

26. 16S Metagenomic Comparison of Plasmodium falciparum–Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal

Author

Bassene, Hubert, primary, Niang, El Hadji Amadou, additional, Fenollar, Florence, additional, Dipankar, Bachar, additional, Doucouré, Souleymane, additional, Ali, Essoham, additional, Michelle, Caroline, additional, Raoult, Didier, additional, Sokhna, Cheikh, additional, and Mediannikov, Oleg, additional

Published
2018
Full Text
View/download PDF

27. 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

28. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences

Author

Dipankar Bachar, Richard Christen, and Laure Guillou

Subjects
Genetics, biology, Phylogenetic tree, GenBank, Ribosomal rna gene, Intron, Taxonomy (biology), biology.organism_classification, Gene, Bacteria, Archaea
Abstract

The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank.

Published
2013

29. Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Author

Maryam, Tidjani Alou, Matthieu, Million, Sory I, Traore, Donia, Mouelhi, Saber, Khelaifia, Dipankar, Bachar, Aurelia, Caputo, Jeremy, Delerce, Souleymane, Brah, Daouda, Alhousseini, Cheikh, Sokhna, Catherine, Robert, Bouli A, Diallo, Aldiouma, Diallo, Philippe, Parola, Michael, Golden, Jean-Christophe, Lagier, and Didier, Raoult

Subjects
metagenomics, gut microbiota, probiotics, Streptococcus gallolyticus, Methanobrevibacter smithii, severe acute malnutrition, culturomics, digestive system, Microbiology, Original Research, kwashiorkor
Abstract

Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host) to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation), a depletion in oxygen-sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.

Published
2016

30. Gut microbiome and dietary patterns in different Saudi populations and monkeys

Author

Catherine Robert, Dipankar Bachar, Marwan A. Bakarman, Didier Raoult, Emmanouil Angelakis, Maha Alawi, Fehmida Bibi, Asif A. Jiman-Fatani, Esam I. Azhar, Jean-Christophe Lagier, Muhammad Yasir, 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), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, DNA, Bacterial, Male, 030106 microbiology, Population, Saudi Arabia, Zoology, Gut flora, DNA, Ribosomal, digestive system, Article, 03 medical and health sciences, Food Preferences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, Animals, Humans, Microbiome, education, Collinsella, Close contact, Feces, 2. Zero hunger, education.field_of_study, Multidisciplinary, biology, Bacteria, Ecology, Gastrointestinal Microbiome, digestive, oral, and skin physiology, biology.organism_classification, Gut microbiome, Arabs, 030104 developmental biology, Female, Papio
Abstract

Host genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. To investigate the association of dietary variables with the gut microbiota, we used 16S rDNA sequencing to test the fecal microbiome of Bedouins and urban Saudis and we compared it to the gut microbiome of baboons living in close contact with Bedouins and eating their leftovers. We also analyzed fermented dairy products commonly consumed by Bedouins in order to investigate their impact on the gut microbiome of this population. We found that the gut microbiomes of westernized urban Saudis had significantly lower richness and biodiversity than the traditional Bedouin population. The gut microbiomes of baboons were more similar to that of Bedouins compared to urban Saudis, probably due the dietary overlap between baboons and Bedouins. Moreover, we found clusters that were compositionally similar to clusters identified in humans and baboons, characterized by differences in Acinetobacter, Turicibacter and Collinsella. The fermented food presented significantly more bacteria genera common to the gut microbiome of Bedouins compared to urban Saudis. These results support the hypothesis that dietary habits influence the composition of the gut microbiome.

Published
2016
Full Text
View/download PDF

31. 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

32. Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen

Author

Grégory, Dubourg, Jean-Christophe, Lagier, Sophie, Hüe, Mathieu, Surenaud, Dipankar, Bachar, Catherine, Robert, Caroline, Michelle, Isabelle, Ravaux, Saadia, Mokhtari, Matthieu, Million, Andreas, Stein, Philippe, Brouqui, Yves, Levy, and Didier, Raoult

Subjects
INFLAMMATION, INTESTINAL BACTERIA, HIV/AIDS, Intestinal Microflora, OXIDATIVE STRESS
Abstract

Objectives Gut microbiota modifications occurring during HIV infection have recently been associated with inflammation and microbial translocation. However, discrepancies between studies justified a comprehensive analysis performed on a large sample size. Design and methods In a case–control study, next-generation sequencing of the 16S rRNA gene was applied to the faecal microbiota of 31 HIV-infected patients, of whom 18 were treated with antiretroviral treatment (ART), compared with 27 healthy controls. 21 sera samples from HIV-infected patients and 7 sera samples from control participants were used to test the presence of 25 markers of inflammation and/or immune activation. Results Diversity was significantly reduced in HIV individuals when compared with controls and was not restored in the ART group. The relative abundance of several members of Ruminococcaceae such as Faecalibacterium prausnitzii was critically less abundant in the HIV-infected group and inversely correlated with inflammation/immune activation markers. Members of Enterobacteriaceae and Enterococcaceae were found to be enriched and positively correlated with these markers. There were significantly more aerotolerant species enriched in HIV samples (42/52 species, 80.8%) when compared with the control group (14/87 species, 16.1%; χ2 test, p

Published
2016

33. 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

34. Patho-Genes.org: a website dedicated to gene sequences of potential bioterror bacteria and PCR primers used to amplify them

Author

Olivier Croce, Richard Christen, Dipankar Bachar, and Julien Gardès

Subjects
Genetics, 0303 health sciences, Melting temperature, 030302 biochemistry & molecular biology, Bioengineering, Biology, MOLECULAR BIOLOGY METHODS, biology.organism_classification, Applied Microbiology and Biotechnology, Biochemistry, 3. Good health, law.invention, 03 medical and health sciences, Functional annotation, law, Target gene, Primer (molecular biology), Gene, Polymerase chain reaction, Bacteria, 030304 developmental biology, Biotechnology
Abstract

Pathogenic agents can be very hard to detect, and usually they do not cause illness for several hours or days. To improve the speed and the accuracy of detection tests and satisfy the needs of early diagnosis, molecular biology methods such as PCR are now used. However, selecting a proper target gene and designing good primers is often not easy. We present a dedicated website, http://patho-genes.org, where we provide every sequence, functional annotation, published primer and relevant article for every annotated gene of major pathogenic bacterial species listed as key agents to be used for a bioterrorism attack. Each published primer was analysed to determine its melting temperature, its specificity and its coverage (i.e. its sensitivity against every allele of its target gene). Data generated have been organized in the form of data sheet for each gene, which are available through multiple browser panels and query systems.

Published
2012

35. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Author

Mélanie Lelievre, Patrick Wincker, Christophe Mougel, Claudy Jolivet, Sébastien Terrat, Richard Christen, Dipankar Bachar, Pierre-Alain Maron, Pierre Plassart, Antonio Bispo, Philippe Lemanceau, Samuel Dequiedt, Tiffanie Regnier, Lionel Ranjard, and Virginie Nowak

Subjects
2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Firmicutes, Soil chemistry, Bioengineering, 15. Life on land, biology.organism_classification, complex mixtures, Applied Microbiology and Biotechnology, Biochemistry, Actinobacteria, 03 medical and health sciences, Crenarchaeota, Metagenomics, Soil water, Botany, Pyrosequencing, Soil microbiology, 030304 developmental biology, Biotechnology
Abstract

Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.

Published
2011

36. 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

37. 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

38. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Christophe Boutte, Raphael Morard, Gaëtan Burgaud, Micah Dunthorn, Pascal Zimmermann, David Bass, Noan Le Bescot, Laure Guillou, Fabrice Not, Bente Edvardsen, Enrique Lara, Dipankar Bachar, Colomban de Vargas, Thorsten Stoeck, Anne Laure Sauvadet, Marina Montresor, Jan Pawlowski, Cédric Berney, Daniel Vaulot, Maria Holzmann, Lucie Bittner, Ramon Massana, Johan Decelle, Javier del Campo, Wiebe H. C. F. Kooistra, Ramiro Logares, Richard Christen, Stéphane Audic, Frédéric Mahé, John R. Dolan, Raffaele Siano, Ian Probert, 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), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Department of life sciences, The Natural History Museum [London] (NHM), Groupe Plancton Océanique, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Evolutionary Genetics, Stazione Zoologica Anton Dohrn (SZN), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of genetics and evolution, University of Geneva [Switzerland], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of ecology, Universität Kaiserslautern, Point Compétence Informatique, European Union [2008-6530, 287589], ANR (France), ANR Paralex (French), BIOMARKS, 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), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Computational biology, medicine.disease_cause, Ribosome, DNA, Ribosomal, DNA sequencing, 03 medical and health sciences, Genetics, medicine, DNA Barcoding, Taxonomic, Gene, 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, 0303 health sciences, Internet, biology, 030306 microbiology, fungi, Intron, Protist, Eukaryota, High-Throughput Nucleotide Sequencing, Genes, rRNA, Articles, Ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, [SDE]Environmental Sciences, Eukaryote, Databases, Nucleic Acid, Cercozoa
Abstract

Laure Guillou ... et al. -- 8 pages, 1 figure, 1 table, The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists, The European Union’s Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7)

Published
2013

39. 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

40. 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

41. 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

42. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Author

Sébastien, Terrat, Richard, Christen, Samuel, Dequiedt, Mélanie, Lelièvre, Virginie, Nowak, Tiffanie, Regnier, Dipankar, Bachar, Pierre, Plassart, Patrick, Wincker, Claudy, Jolivet, Antonio, Bispo, Philippe, Lemanceau, Pierre-Alain, Maron, Christophe, Mougel, and Lionel, Ranjard

Subjects
DNA, Bacterial, Soil, Bacteria, Molecular Sequence Data, Brief Reports, Biodiversity, Biomass, Metagenomics, complex mixtures, Phylogeny, Soil Microbiology
Abstract

Summary Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.

Published
2011

43. 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

44. 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

Catalog

Books, media, physical & digital resources
See catalog results