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  1. Article: Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems

    Günther, Babett / Marre, Sophie / Defois, Clémence / Merzi, Thomas / Blanc, Philippe / Peyret, Pierre / Arnaud‐Haond, Sophie

    Molecular ecology resources. 2022 Feb., v. 22, no. 2

    2022  

    Abstract: Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future ... ...

    Abstract Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep‐sea sediment samples and compared the results with those obtained through an up‐to‐date metabarcoding PCR‐based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full‐length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data‐poor ecosystems such as those in the deep sea.
    Keywords Animalia ; DNA barcoding ; barcoding ; biodiversity ; databases ; environmental DNA ; environmental monitoring ; eukaryotic cells ; hybridization ; inventories ; marine sediments ; phylogeny ; polymerase chain reaction
    Language English
    Dates of publication 2022-02
    Size p. 623-637.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2406816-0
    ISSN 1471-8286 ; 1755-098X
    ISSN (online) 1471-8286
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13500
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Metformin treatment for 8 days impacts multiple intestinal parameters in high-fat high-sucrose fed mice.

    Bravard, Amélie / Gérard, Céline / Defois, Clémence / Benoit, Bérengère / Makki, Kassem / Meugnier, Emmanuelle / Rainteau, Dominique / Rieusset, Jennifer / Godet, Murielle / Vidal, Hubert

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 16684

    Abstract: Although the mechanism of action of the antidiabetic drug metformin is still a matter of discussions, it is well accepted that the gut plays an important role. To gain more insights into the mechanisms occurring in the different regions of the intestine, ...

    Abstract Although the mechanism of action of the antidiabetic drug metformin is still a matter of discussions, it is well accepted that the gut plays an important role. To gain more insights into the mechanisms occurring in the different regions of the intestine, adult male mice were fed a high-fat-high sucrose (HFS) diet for 8 days and treated with metformin by gavage (300 mg/day/kg body weight) during the HFS diet. Metformin counteracted HFS diet-induced overexpression of a network of genes involved in the transport of glucose and fatty acids in the different regions of the small intestine. It also induced beneficial modification of secondary bile acid profile in the caecum, with a reduction of deoxycholic acid and lithocholic acid levels and increased abundance of ursodeoxycholic acid and tauroursodeoxycholic acid, potentially leading to FRX inhibition. In parallel, metformin treatment was associated with specific changes of the microbiota composition in the lumen of the different regions of the intestine. Metformin induced a marked increase in the abundance of Akkermansia muciniphila in the lumen all along the gut and counteracted the effects of HFS diet on the abundances of some bacterial groups generally associated with metabolic disturbances (f-Lachnospiraceae, f-Petostreptococcaceae, g-Clostidium). Therefore, the present work clearly emphasises the role of all the regions of the intestinal tract in the beneficial action of the antidiabetic drug metformin in a prediabetic mouse model.
    MeSH term(s) Animals ; Diet, Carbohydrate Loading/adverse effects ; Dietary Sucrose/metabolism ; Gastrointestinal Microbiome/drug effects ; Hypoglycemic Agents/pharmacology ; Hypoglycemic Agents/therapeutic use ; Intestinal Mucosa/drug effects ; Intestinal Mucosa/metabolism ; Intestines/drug effects ; Male ; Metformin/pharmacology ; Metformin/therapeutic use ; Mice ; Mice, Inbred C57BL ; Prediabetic State/drug therapy ; Prediabetic State/etiology ; Prediabetic State/metabolism ; Prediabetic State/microbiology
    Chemical Substances Dietary Sucrose ; Hypoglycemic Agents ; Metformin (9100L32L2N)
    Language English
    Publishing date 2021-08-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-95117-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems.

    Günther, Babett / Marre, Sophie / Defois, Clémence / Merzi, Thomas / Blanc, Philippe / Peyret, Pierre / Arnaud-Haond, Sophie

    Molecular ecology resources

    2021  Volume 22, Issue 2, Page(s) 623–637

    Abstract: Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future ... ...

    Abstract Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.
    MeSH term(s) Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Ribosomal ; Ecosystem ; Eukaryota ; Phylogeny
    Chemical Substances DNA, Ribosomal
    Language English
    Publishing date 2021-09-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13500
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer.

    Ranchou-Peyruse, Magali / Guignard, Marion / Casteran, Franck / Abadie, Maïder / Defois, Clémence / Peyret, Pierre / Dequidt, David / Caumette, Guilhem / Chiquet, Pierre / Cézac, Pierre / Ranchou-Peyruse, Anthony

    Frontiers in microbiology

    2021  Volume 12, Page(s) 688929

    Abstract: Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can ... ...

    Abstract Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH
    Language English
    Publishing date 2021-10-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.688929
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  5. Article ; Online: ASaiM: a Galaxy-based framework to analyze microbiota data.

    Batut, Bérénice / Gravouil, Kévin / Defois, Clémence / Hiltemann, Saskia / Brugère, Jean-François / Peyretaillade, Eric / Peyret, Pierre

    GigaScience

    2018  Volume 7, Issue 6

    Abstract: Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination ... ...

    Abstract Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.
    Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io).
    Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.
    MeSH term(s) Base Sequence ; Metagenomics ; Microbiota ; Software ; Statistics as Topic
    Language English
    Publishing date 2018-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giy057
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems.

    Defois, Clémence / Ratel, Jérémy / Garrait, Ghislain / Denis, Sylvain / Le Goff, Olivier / Talvas, Jérémie / Mosoni, Pascale / Engel, Erwan / Peyret, Pierre

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 11006

    Abstract: Growing evidence indicates that the human gut microbiota interacts with xenobiotics, including persistent organic pollutants and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern since ... ...

    Abstract Growing evidence indicates that the human gut microbiota interacts with xenobiotics, including persistent organic pollutants and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern since chemicals may disrupt gut microbiota functions, with a potential impairment of host homeostasis. Herein we report within batch fermentation systems the impact of food contaminants (polycyclic aromatic hydrocarbons, polychlorobiphenyls, brominated flame retardants, dioxins, pesticides and heterocyclic amines) on the human gut microbiota by metatranscriptome and volatolome i.e. "volatile organic compounds" analyses. Inflammatory host cell response caused by microbial metabolites following the pollutants-gut microbiota interaction, was evaluated on intestinal epithelial TC7 cells. Changes in the volatolome pattern analyzed via solid-phase microextraction coupled to gas chromatography-mass spectrometry mainly resulted in an imbalance in sulfur, phenolic and ester compounds. An increase in microbial gene expression related to lipid metabolism processes as well as the plasma membrane, periplasmic space, protein kinase activity and receptor activity was observed following dioxin, brominated flame retardant and heterocyclic amine exposure. Conversely, all food contaminants tested induced a decreased in microbial transcript levels related to ribosome, translation and nucleic acid binding. Finally, we demonstrated that gut microbiota metabolites resulting from pollutant disturbances may promote the establishment of a pro-inflammatory state in the gut, as stated with the release of cytokine IL-8 by intestinal epithelial cells.
    MeSH term(s) Cell Line ; Environmental Pollutants/adverse effects ; Epithelial Cells/drug effects ; Food Contamination/analysis ; Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Homeostasis/drug effects ; Humans ; Intestines/microbiology ; Intestines/physiology ; Transcriptome/drug effects ; Xenobiotics/pharmacology
    Chemical Substances Environmental Pollutants ; Xenobiotics
    Language English
    Publishing date 2018-07-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-29376-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Environmental Pollutant Benzo[

    Defois, Clémence / Ratel, Jérémy / Denis, Sylvain / Batut, Bérénice / Beugnot, Réjane / Peyretaillade, Eric / Engel, Erwan / Peyret, Pierre

    Frontiers in microbiology

    2017  Volume 8, Page(s) 1562

    Abstract: Benzo[ ...

    Abstract Benzo[
    Language English
    Publishing date 2017-08-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2017.01562
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  8. Article ; Online: Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.

    Ribière, Céline / Beugnot, Réjane / Parisot, Nicolas / Gasc, Cyrielle / Defois, Clémence / Denonfoux, Jérémie / Boucher, Delphine / Peyretaillade, Eric / Peyret, Pierre

    Methods in molecular biology (Clifton, N.J.)

    2016  Volume 1399, Page(s) 167–182

    Abstract: Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary ...

    Abstract Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
    MeSH term(s) Biomarkers ; Computational Biology ; DNA, Bacterial/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/methods ; Nucleic Acid Hybridization/methods ; RNA Probes ; Sequence Analysis, DNA/methods
    Chemical Substances Biomarkers ; DNA, Bacterial ; RNA Probes
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-3369-3_10
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  9. Article ; Online: Capturing prokaryotic dark matter genomes.

    Gasc, Cyrielle / Ribière, Céline / Parisot, Nicolas / Beugnot, Réjane / Defois, Clémence / Petit-Biderre, Corinne / Boucher, Delphine / Peyretaillade, Eric / Peyret, Pierre

    Research in microbiology

    2015  Volume 166, Issue 10, Page(s) 814–830

    Abstract: Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the ... ...

    Abstract Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
    MeSH term(s) Archaea/genetics ; Archaea/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Ecosystem ; Genome, Archaeal ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Prokaryotic Cells ; Single-Cell Analysis
    Language English
    Publishing date 2015-12
    Publishing country France
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1004220-9
    ISSN 1769-7123 ; 0923-2508
    ISSN (online) 1769-7123
    ISSN 0923-2508
    DOI 10.1016/j.resmic.2015.06.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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