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Chakoory O, Barra V, Rochette E, Blanchon L, Sapin V, Merlin E, Pons M, Gallot D, Comtet-Marre S, Peyret P. DeepMPTB: a vaginal microbiome-based deep neural network as artificial intelligence strategy for efficient preterm birth prediction. Biomark Res 2024; 12:25. [PMID: 38355595 PMCID: PMC10865581 DOI: 10.1186/s40364-024-00557-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
In recent decades, preterm birth (PTB) has become a significant research focus in the healthcare field, as it is a leading cause of neonatal mortality worldwide. Using five independent study cohorts including 1290 vaginal samples from 561 pregnant women who delivered at term (n = 1029) or prematurely (n = 261), we analysed vaginal metagenomics data for precise microbiome structure characterization. Then, a deep neural network (DNN) was trained to predict term birth (TB) and PTB with an accuracy of 84.10% and an area under the receiver operating characteristic curve (AUROC) of 0.875 ± 0.11. During a benchmarking process, we demonstrated that our DL model outperformed seven currently used machine learning algorithms. Finally, our results indicate that overall diversity of the vaginal microbiota should be taken in account to predict PTB and not specific species. This artificial-intelligence based strategy should be highly helpful for clinicians in predicting preterm birth risk, allowing personalized assistance to address various health issues. DeepMPTB is open source and free for academic use. It is licensed under a GNU Affero General Public License 3.0 and is available at https://deepmptb.streamlit.app/ . Source code is available at https://github.com/oschakoory/DeepMPTB and can be easily installed using Docker ( https://www.docker.com/ ).
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Affiliation(s)
- Oshma Chakoory
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Vincent Barra
- Université Clermont Auvergne, CNRS, Mines de Saint-Étienne, Clermont-Auvergne-INP, LIMOS, Clermont-Ferrand, France
| | - Emmanuelle Rochette
- Department of Pediatrics, CRECHE Unit, CHU Clermont-Ferrand, Inserm CIC 1405, F-63000, Clermont-Ferrand, France
| | - Loïc Blanchon
- Team "Translational approach to epithelial injury and repair", Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000, Clermont-Ferrand, France
| | - Vincent Sapin
- Team "Translational approach to epithelial injury and repair", Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000, Clermont-Ferrand, France
- Biochemistry and Molecular Genetics Department, CHU Clermont-Ferrand, 63000, Clermont- Ferrand, France
| | - Etienne Merlin
- Department of Pediatrics, CRECHE Unit, CHU Clermont-Ferrand, Inserm CIC 1405, F-63000, Clermont-Ferrand, France
| | - Maguelonne Pons
- Department of Pediatrics, CRECHE Unit, CHU Clermont-Ferrand, Inserm CIC 1405, F-63000, Clermont-Ferrand, France
| | - Denis Gallot
- Team "Translational approach to epithelial injury and repair", Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000, Clermont-Ferrand, France
- Department of Obstetrics, CHU Clermont-Ferrand, F-63000, Clermont- Ferrand, France
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France.
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France.
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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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Comtet-Marre S, Chakoory O, Peyret P. Targeted 16S rRNA Gene Capture by Hybridization and Bioinformatic Analysis. Methods Mol Biol 2022; 2605:187-208. [PMID: 36520395 DOI: 10.1007/978-1-0716-2871-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used approach, suffers from several biases impacting the picture of microbial communities. Here, we describe an innovative method based on gene capture by hybridization for the targeted enrichment of 16S rDNA biomarker from metagenomic samples. Coupled to near full-length 16S rDNA reconstruction, this approach enables an exhaustive and accurate description of microbial communities by enhancing taxonomic and phylogenetic resolutions. Furthermore, access of captured 16S flanking regions opens link between structure and function in microbial communities.
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Affiliation(s)
| | - Oshma Chakoory
- Université Clermont-Auvergne, INRAE, MEDiS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont-Auvergne, INRAE, MEDiS, Clermont-Ferrand, France.
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Chakoory O, Comtet-Marre S, Peyret P. RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties. NAR Genom Bioinform 2022; 4:lqac070. [PMID: 36159175 PMCID: PMC9492272 DOI: 10.1093/nargab/lqac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic classifiers are widely used for the taxonomic profiling of metagenomics data and estimation of taxa relative abundance. Small subunit rRNA genes are a gold standard for phylogenetic resolution of microbiota, although the power of this marker comes down to its use as full-length. We aimed at identifying the tools that can efficiently lead to taxonomic resolution down to the species level. To reach this goal, we benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then compiled the best tools (BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2’s Sklearn classifier) to build a pipeline called RiboTaxa. Using metagenomics datasets, RiboTaxa gave the best results compared to other tools (i.e. Kraken2, Centrifuge, METAXA2, phyloFlash, SPINGO, BLCA, MEGAN) with precise taxonomic identification and relative abundance description without false positive detection (F-measure of 100% and 83.7% at genus level and species level, respectively). Using real datasets from various environments (i.e. ocean, soil, human gut) and from different approaches (e.g. metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not discerned by current bioinformatics analysis opening new biological perspectives in human and environmental health.
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Affiliation(s)
- Oshma Chakoory
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDIS , F-63000 Clermont-Ferrand, France
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Abstract
Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales, 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.
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Affiliation(s)
- Sophie Marre
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Cyrielle Gasc
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France.,Present address: MaaT Pharma, F-69007 LYON, France
| | - Camille Forest
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Yacine Lebbaoui
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Pascale Mosoni
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
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Ranchou-Peyruse M, Guignard M, Casteran F, Abadie M, Defois C, Peyret P, Dequidt D, Caumette G, Chiquet P, Cézac P, Ranchou-Peyruse A. Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. Front Microbiol 2021; 12:688929. [PMID: 34721313 PMCID: PMC8549729 DOI: 10.3389/fmicb.2021.688929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
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 (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L-1 and a phosphate content of 0.02mg.L-1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria ("Candidatus Acetothermia") with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
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Affiliation(s)
- Magali Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Marion Guignard
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Franck Casteran
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Maïder Abadie
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - David Dequidt
- STORENGY – Geosciences Department, Bois-Colombes, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
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7
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Günther B, Marre S, Defois C, Merzi T, Blanc P, Peyret P, Arnaud-Haond S. Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems. Mol Ecol Resour 2021; 22:623-637. [PMID: 34486815 DOI: 10.1111/1755-0998.13500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/04/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
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.
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Affiliation(s)
- Babett Günther
- MARBEC, Universite of Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Sophie Marre
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Thomas Merzi
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Philippe Blanc
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
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8
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Ben Ayed A, Saint-Genis G, Vallon L, Linde D, Turbé-Doan A, Haon M, Daou M, Bertrand E, Faulds CB, Sciara G, Adamo M, Marmeisse R, Comtet-Marre S, Peyret P, Abrouk D, Ruiz-Dueñas FJ, Marchand C, Hugoni M, Luis P, Mechichi T, Record E. Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts. J Fungi (Basel) 2021; 7:jof7050321. [PMID: 33919051 PMCID: PMC8143184 DOI: 10.3390/jof7050321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/21/2023] Open
Abstract
The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either Avicennia marina or Rhizophora stylosa trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the R. stylosa area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform. This OFU was found in all sediment samples, representing 51–100% of the total DyP-encoding sequences in 70% of the samples. The complete cDNA sequence corresponding to this abundant DyP (OFU 1) was retrieved by gene capture, cloned, and heterologously expressed in Pichia pastoris. The recombinant enzyme, called DyP1, was purified and characterized, leading to the description of its physical–chemical properties, its ability to oxidize diverse phenolic substrates, and its potential to decolorize textile dyes; DyP1 was more active at low pH, though moderately stable over a wide pH range. The enzyme was very stable at temperatures up to 50 °C, retaining 60% activity after 180 min incubation. Its ability to decolorize industrial dyes was also tested on Reactive Blue 19, Acid Black, Disperse Blue 79, and Reactive Black 5. The effect of hydrogen peroxide and sea salt on DyP1 activity was studied and compared to what is reported for previously characterized enzymes from terrestrial and marine-derived fungi.
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Affiliation(s)
- Amal Ben Ayed
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Geoffroy Saint-Genis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Laurent Vallon
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Annick Turbé-Doan
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Mireille Haon
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Marianne Daou
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Emmanuel Bertrand
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Craig B. Faulds
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Giuliano Sciara
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Martino Adamo
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Roland Marmeisse
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Cyril Marchand
- IMPMC, Institut de Recherche Pour le Développement (IRD), UPMC, CNRS, MNHN, 98851 Noumea, France;
- ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851 Noumea, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Patricia Luis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Tahar Mechichi
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Eric Record
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Correspondence:
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Jaeger N, Besaury L, Röhling AN, Koch F, Delort AM, Gasc C, Greule M, Kolb S, Nadalig T, Peyret P, Vuilleumier S, Amato P, Bringel F, Keppler F. Chloromethane formation and degradation in the fern phyllosphere. Sci Total Environ 2018; 634:1278-1287. [PMID: 29660879 DOI: 10.1016/j.scitotenv.2018.03.316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/25/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
Chloromethane (CH3Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH3Cl budget are approximate. The strength of the CH3Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly ferns, have been identified as substantial emitters of CH3Cl. Their ability to degrade CH3Cl remains uncertain. In this study, we investigated the potential of leaves from 3 abundant ferns (Osmunda regalis, Cyathea cooperi, Dryopteris filix-mas) to produce and degrade CH3Cl by measuring their production and consumption rates and their stable carbon and hydrogen isotope signatures. Investigated ferns are able to degrade CH3Cl at rates from 2.1 to 17 and 0.3 to 0.9μggdw-1day-1 for C. cooperi and D. filix-mas respectively, depending on CH3Cl supplementation and temperature. The stable carbon isotope enrichment factor of remaining CH3Cl was -39±13‰, whereas negligible isotope fractionation was observed for hydrogen (-8±19‰). In contrast, O. regalis did not consume CH3Cl, but produced it at rates ranging from 0.6 to 128μggdw-1day-1, with stable isotope values of -97±8‰ for carbon and -202±10‰ for hydrogen, respectively. Even though the 3 ferns showed clearly different formation and consumption patterns, their leaf-associated bacterial diversity was not notably different. Moreover, we did not detect genes associated with the only known chloromethane utilization pathway "cmu" in the microbial phyllosphere of the investigated ferns. Our study suggests that still unknown CH3Cl biodegradation processes on plants play an important role in global cycling of atmospheric CH3Cl.
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Affiliation(s)
- Nicole Jaeger
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany.
| | - Ludovic Besaury
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France; Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France; UMR FARE, Université de Reims Champagne Ardenne, INRA, Reims, France
| | - Amelie Ninja Röhling
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Fabien Koch
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Anne-Marie Delort
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France
| | - Cyrielle Gasc
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
| | - Markus Greule
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Thierry Nadalig
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand (ICCF), UMR6096 CNRS-UCA-Sigma, Clermont-Ferrand, France
| | - Françoise Bringel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 236, Heidelberg, Germany; Heidelberg Center for the Environment HCE, Heidelberg University, Heidelberg, Germany.
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10
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Allario T, Tixier A, Awad H, Lemaire C, Brunel N, Badel E, Barigah TS, Julien JL, Peyret P, Mellerowicz EJ, Cochard H, Herbette S. PtxtPME1 and homogalacturonans influence xylem hydraulic properties in poplar. Physiol Plant 2018; 163:502-515. [PMID: 29412468 DOI: 10.1111/ppl.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/15/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
While the xylem hydraulic properties, such as vulnerability to cavitation (VC), are of paramount importance in drought resistance, their genetic determinants remain unexplored. There is evidence that pectins and their methylation pattern are involved, but the detail of their involvement and the corresponding genes need to be clarified. We analyzed the hydraulic properties of the 35S::PME1 transgenic aspen that ectopically under- or over-express a xylem-abundant pectin methyl esterase, PtxtPME1. We also produced and analyzed 4CL1::PGII transgenic poplars expressing a fungal polygalacturonase, AnPGII, under the control of the Ptxa4CL1 promoter that is active in the developing xylem after xylem cell expansion. Both the 35S::PME1 under- and over-expressing aspen lines developed xylem with lower-specific hydraulic conductivity and lower VC, while the 4CL1::PGII plants developed xylem with a higher VC. These xylem hydraulic changes were associated with modifications in xylem structure or in intervessel pit structure that can result in changes in mechanical behavior of the pit membrane. This study shows that homogalacturonans and their methylation pattern influence xylem hydraulic properties, through its effect on xylem cell expansion and on intervessel pit properties and it show a role for PtxtPME1 in the xylem hydraulic properties.
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Affiliation(s)
- Thierry Allario
- UCA, INRA, PIAF, 63000, Clermont-Ferrand, France
- UCA, EA 4678 CIDAM, 63000, Clermont-Ferrand, France
| | - Aude Tixier
- UCA, INRA, PIAF, 63000, Clermont-Ferrand, France
| | - Hosam Awad
- Agriculture and Botany Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom, Egypt
| | | | | | - Eric Badel
- UCA, INRA, PIAF, 63000, Clermont-Ferrand, France
| | | | | | | | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
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11
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Defois C, Ratel J, Garrait G, Denis S, Le Goff O, Talvas J, Mosoni P, Engel E, Peyret P. Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems. Sci Rep 2018; 8:11006. [PMID: 30030472 PMCID: PMC6054606 DOI: 10.1038/s41598-018-29376-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
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.
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12
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Cariou M, Ribière C, Morlière S, Gauthier JP, Simon JC, Peyret P, Charlat S. Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis. BMC Res Notes 2018; 11:461. [PMID: 29996907 PMCID: PMC6042230 DOI: 10.1186/s13104-018-3559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. RESULTS All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.
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Affiliation(s)
- Marie Cariou
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université de Lyon, Université Lyon 1, 43 Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
- Present Address: Department of Biology, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Céline Ribière
- INRA, MEDIS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Stéphanie Morlière
- INRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1, 35653 Le Rheu, France
| | - Jean-Pierre Gauthier
- INRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1, 35653 Le Rheu, France
| | - Jean-Christophe Simon
- INRA, UMR 1349 (IGEPP “Institut de Génétique, Environnement et Protection des Plantes”) INRA/Agrocampus Ouest/Université Rennes 1, 35653 Le Rheu, France
| | - Pierre Peyret
- INRA, MEDIS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Sylvain Charlat
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université de Lyon, Université Lyon 1, 43 Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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13
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Batut B, Gravouil K, Defois C, Hiltemann S, Brugère JF, Peyretaillade E, Peyret P. ASaiM: a Galaxy-based framework to analyze microbiota data. Gigascience 2018; 7:5001424. [PMID: 29790941 PMCID: PMC6007547 DOI: 10.1093/gigascience/giy057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 05/10/2018] [Indexed: 12/24/2022] Open
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.
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Affiliation(s)
- Bérénice Batut
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Kévin Gravouil
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, LMGE, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, LIMOS, 63000 Clermont-Ferrand, France
| | - Clémence Defois
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
| | - Saskia Hiltemann
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3015 CE, Netherlands
| | - Jean-François Brugère
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
| | - Eric Peyretaillade
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
- Université Clermont Auvergne, CNRS, LMGE, 63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, EA 4678 CIDAM, 63000 Clermont-Ferrand, France (previous address)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
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14
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Gasc C, Peyret P. Hybridization capture reveals microbial diversity missed using current profiling methods. Microbiome 2018; 6:61. [PMID: 29587880 PMCID: PMC5870382 DOI: 10.1186/s40168-018-0442-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 03/13/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution. RESULTS Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa. CONCLUSIONS Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.
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Affiliation(s)
- Cyrielle Gasc
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
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15
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Comtet-Marre S, Chaucheyras-Durand F, Bouzid O, Mosoni P, Bayat AR, Peyret P, Forano E. FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota. Front Microbiol 2018; 9:215. [PMID: 29487591 PMCID: PMC5816793 DOI: 10.3389/fmicb.2018.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/30/2018] [Indexed: 01/22/2023] Open
Abstract
Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
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Affiliation(s)
- Sophie Comtet-Marre
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Frédérique Chaucheyras-Durand
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Ourdia Bouzid
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pascale Mosoni
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ali R Bayat
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Pierre Peyret
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
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16
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Defois C, Ratel J, Denis S, Batut B, Beugnot R, Peyretaillade E, Engel E, Peyret P. Environmental Pollutant Benzo[ a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota. Front Microbiol 2017; 8:1562. [PMID: 28861070 PMCID: PMC5559432 DOI: 10.3389/fmicb.2017.01562] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/02/2017] [Indexed: 01/23/2023] Open
Abstract
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.
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Affiliation(s)
- Clémence Defois
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Jérémy Ratel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Sylvain Denis
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Bérénice Batut
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Réjane Beugnot
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Eric Peyretaillade
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Erwan Engel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Pierre Peyret
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
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17
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Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res 2017; 24:251-260. [PMID: 28338834 PMCID: PMC5499648 DOI: 10.1093/dnares/dsx002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/21/2017] [Indexed: 11/14/2022] Open
Abstract
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.
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Affiliation(s)
- Abdel Belkorchia
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | | | - Valérie Polonais
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Nicolas Parisot
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Frédéric Delbac
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Jean-François Brugère
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | | | - Eric Peyretaillade
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
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18
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Gasc C, Peyret P. Revealing large metagenomic regions through long DNA fragment hybridization capture. Microbiome 2017; 5:33. [PMID: 28292322 PMCID: PMC5351058 DOI: 10.1186/s40168-017-0251-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/05/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies. METHODS To overcome these limitations, we developed an innovative target enrichment method for the reconstruction of large unknown genomic regions. Based on a hybridization capture strategy, this approach enables the enrichment of large genomic regions allowing the reconstruction of tens of kilobase pairs flanking a short, targeted DNA sequence. RESULTS Applied to a metagenomic soil sample targeting the linA gene, the biomarker of hexachlorocyclohexane (HCH) degradation, our method permitted the enrichment of the gene and its flanking regions leading to the reconstruction of several contigs and complete plasmids exceeding tens of kilobase pairs surrounding linA. Thus, through gene association and genome reconstruction, we identified microbial species involved in HCH degradation which constitute targets to improve biostimulation treatments. CONCLUSIONS This new hybridization capture strategy makes surveying and deconvoluting complex genomic regions possible through large genomic regions enrichment and allows the efficient exploration of metagenomic diversity. Indeed, this approach enables to assign identity and function to microorganisms in natural environments, one of the ultimate goals of microbial ecology.
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Affiliation(s)
- Cyrielle Gasc
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
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Comtet-Marre S, Parisot N, Lepercq P, Chaucheyras-Durand F, Mosoni P, Peyretaillade E, Bayat AR, Shingfield KJ, Peyret P, Forano E. Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet. Front Microbiol 2017; 8:67. [PMID: 28197133 PMCID: PMC5281551 DOI: 10.3389/fmicb.2017.00067] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community. Functional analysis identified 12,237 CAZymes, accounting for 1% of the transcripts. The CAZyme profile was dominated by families GH94 (cellobiose-phosphorylase), GH13 (amylase), GH43 and GH10 (hemicellulases), GH9 and GH48 (cellulases), PL11 (pectinase) as well as GH2 and GH3 (oligosaccharidases). Our data support the pivotal role of the most characterized fibrolytic bacteria (Prevotella, Ruminocccus and Fibrobacter), and highlight a substantial, although most probably underestimated, contribution of fungi and ciliate protozoa to polysaccharide degradation. Particularly these results may motivate further exploration of the role and the functions of protozoa in the rumen. Moreover, an important part of the fibrolytic bacterial community remains to be characterized since one third of the CAZyme transcripts originated from distantly related strains. These findings are used to highlight limitations of current metatranscriptomics approaches to understand the functional rumen microbial community and opportunities to circumvent them.
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Affiliation(s)
| | - Nicolas Parisot
- EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France
| | - Pascale Lepercq
- UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France
| | | | - Pascale Mosoni
- UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France
| | - Eric Peyretaillade
- EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France
| | - Ali R Bayat
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke) Jokioinen, Finland
| | - Kevin J Shingfield
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke)Jokioinen, Finland; Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Pierre Peyret
- EA4678 CIDAM, Clermont Université, Université d'Auvergne Clermont-Ferrand, France
| | - Evelyne Forano
- UR454 Unité de Microbiologie, INRA Saint-Genès-Champanelle, France
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Gasc C, Constantin A, Jaziri F, Peyret P. OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture. Database (Oxford) 2017; 2017:3053441. [PMID: 28365722 PMCID: PMC5467545 DOI: 10.1093/database/baw172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/29/2016] [Indexed: 11/19/2022]
Abstract
The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples. Here, we present Oligonucleotide Capture Probes for Pathogen Identification Database (OCaPPI-Db), an online capture probe database containing a set of 1,685 oligonucleotide probes allowing for the detection and identification of 30 biothreat agents up to the species level. This probe set can be used in its entirety as a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to the user’s needs. Database URL: http://ocappidb.uca.works
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Affiliation(s)
- Cyrielle Gasc
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
| | | | - Faouzi Jaziri
- Université d'Auvergne, ISIT, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
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Ranchou-Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou-Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2016; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono‐aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate‐reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m‐ and p‐xylenes was demonstrated using a culture‐based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next‐generation sequencing, was applied to the same original water sample. The bssA and bssA‐like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA‐like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low‐level representation in the biosphere.
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Affiliation(s)
- Magali Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie, IPREM-CNRS 5254, F-64013, Pau, France
| | - Cyrielle Gasc
- Université d'Auvergne, EA 4678 CIDAM, 63001, Clermont-Ferrand, France
| | - Marion Guignard
- Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie, IPREM-CNRS 5254, F-64013, Pau, France
| | - Thomas Aüllo
- TIGF - Transport et Infrastructures Gaz France, 40 Avenue de l'Europe, CS20522, 64000, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Peyret
- Université d'Auvergne, EA 4678 CIDAM, 63001, Clermont-Ferrand, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie, IPREM-CNRS 5254, F-64013, Pau, France
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Ribière C, Beugnot R, Parisot N, Gasc C, Defois C, Denonfoux J, Boucher D, Peyretaillade E, Peyret P. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning. Methods Mol Biol 2016; 1399:167-82. [PMID: 26791503 DOI: 10.1007/978-1-4939-3369-3_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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.
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Affiliation(s)
- Céline Ribière
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Réjane Beugnot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Nicolas Parisot
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Cyrielle Gasc
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Clémence Defois
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Jérémie Denonfoux
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
- Genoscreen, Campus de l'Institut Pasteur de Lille, 59000, Lille, France.
| | - Delphine Boucher
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
| | - Eric Peyretaillade
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
| | - Pierre Peyret
- EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France.
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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24
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Biderre-Petit C, Dugat-Bony E, Mege M, Parisot N, Adrian L, Moné A, Denonfoux J, Peyretaillade E, Debroas D, Boucher D, Peyret P. Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes. PLoS One 2016; 11:e0145558. [PMID: 26734727 PMCID: PMC4703385 DOI: 10.1371/journal.pone.0145558] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/04/2015] [Indexed: 12/29/2022] Open
Abstract
Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.
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Affiliation(s)
- Corinne Biderre-Petit
- Laboratoire “Microorganismes: Génome et Environnement,” Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France
- * E-mail:
| | - Eric Dugat-Bony
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Mickaël Mege
- Laboratoire “Microorganismes: Génome et Environnement,” Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France
| | - Nicolas Parisot
- Laboratoire “Microorganismes: Génome et Environnement,” Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France
- Clermont Université, Université d’Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research–UFZ, Permoserstraße 15, D-04318, Leipzig, Germany
| | - Anne Moné
- Laboratoire “Microorganismes: Génome et Environnement,” Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France
| | - Jérémie Denonfoux
- Clermont Université, Université d’Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France
| | - Eric Peyretaillade
- Clermont Université, Université d’Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France
| | - Didier Debroas
- Laboratoire “Microorganismes: Génome et Environnement,” Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171, Aubière, France
| | - Delphine Boucher
- Clermont Université, Université d’Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France
| | - Pierre Peyret
- Clermont Université, Université d’Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France
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Abstract
Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.
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Affiliation(s)
- Nicolas Parisot
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Peyretaillade
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Dugat-Bony
- Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, INRA, AgroParisTech, UMR 782, Thiverval-Grignon, France
| | - Jérémie Denonfoux
- Genomic Platform and R&D, Genoscreen, Campus de l'Institut Pasteur, Lille, France
| | | | - Pierre Peyret
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.
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Cébron A, Beguiristain T, Bongoua-Devisme J, Denonfoux J, Faure P, Lorgeoux C, Ouvrard S, Parisot N, Peyret P, Leyval C. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils. Environ Sci Pollut Res Int 2015; 22:13724-13738. [PMID: 25616383 DOI: 10.1007/s11356-015-4117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.
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Affiliation(s)
- Aurélie Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP 70239, 54506, Vandoeuvre-lès-Nancy Cedex, France,
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Izquierdo AR, Vila J, Petit C, Peyret P, Koch A, Grifoll M. Microbial populations and functions associated with the degradation of aliphatic and aromatic hydrocarbon oil fractions. J Biotechnol 2015. [DOI: 10.1016/j.jbiotec.2015.06.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gasc C, Ribière C, Parisot N, Beugnot R, Defois C, Petit-Biderre C, Boucher D, Peyretaillade E, Peyret P. Capturing prokaryotic dark matter genomes. Res Microbiol 2015; 166:814-30. [PMID: 26100932 DOI: 10.1016/j.resmic.2015.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022]
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.
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Affiliation(s)
- Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Céline Ribière
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Nicolas Parisot
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France.
| | - Réjane Beugnot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Clémence Defois
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Corinne Petit-Biderre
- Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171 Aubière, France.
| | - Delphine Boucher
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Eric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
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Bragalini C, Ribière C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis P. Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples. DNA Res 2014; 21:685-94. [PMID: 25281543 PMCID: PMC4263301 DOI: 10.1093/dnares/dsu030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.
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Affiliation(s)
- Claudia Bragalini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Céline Ribière
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Nicolas Parisot
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Laurent Vallon
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Elsa Prudent
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Eric Peyretaillade
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Mariangela Girlanda
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125, Italy
| | - Pierre Peyret
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Roland Marmeisse
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Patricia Luis
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
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Peyretaillade E, Boucher D, Parisot N, Gasc C, Butler R, Pombert JF, Lerat E, Peyret P. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems. Heredity (Edinb) 2014; 114:441-9. [PMID: 25182222 DOI: 10.1038/hdy.2014.78] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/16/2014] [Accepted: 07/21/2014] [Indexed: 12/16/2022] Open
Abstract
Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem structure and function. Unfortunately, their ecological role is not well understood. Present also as highly resistant spores in the environment, their characterisation requires special attention. Different techniques based on direct isolation and/or molecular approaches can be considered to elucidate their role in the ecosystems, but integrating environmental and genomic data (for example, genome architecture, core genome, transcriptional and translational signals) is crucial to better understand the diversity and adaptive capacities of Microsporidia. Here, we review the current status of Microsporidia in trophic networks; the various genomics tools that could be used to ensure identification and evaluate diversity and abundance of these organisms; and how these tools could be used to explore the microsporidian life cycle in different environments. Our understanding of the evolution of these widespread parasites is currently impaired by limited sampling, and we have no doubt witnessed but a small subset of their diversity.
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Affiliation(s)
- E Peyretaillade
- Genomics, Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - D Boucher
- Genomics, Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - N Parisot
- 1] Genomics, Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France [2] CNRS, UMR 6023, LMGE, Aubière, France
| | - C Gasc
- Genomics, Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - R Butler
- Illinois Institute of Technology, BCHS Biology Division, Chicago, IL, USA
| | - J-F Pombert
- Illinois Institute of Technology, BCHS Biology Division, Chicago, IL, USA
| | - E Lerat
- Université de Lyon, Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France
| | - P Peyret
- Genomics, Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
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Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E. Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans. Genome Biol Evol 2014; 6:2289-300. [PMID: 25172905 PMCID: PMC4202319 DOI: 10.1093/gbe/evu178] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.
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Affiliation(s)
- Nicolas Parisot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France CNRS, UMR 6023, LMGE, Aubière, France
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Valérie Polonais
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Abdel Belkorchia
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Johan Panek
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Hicham El Alaoui
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - David G Biron
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Éric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Emmanuelle Lerat
- Université de Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France
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Borrel G, Parisot N, Harris HMB, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW, Brugère JF. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 2014; 15:679. [PMID: 25124552 PMCID: PMC4153887 DOI: 10.1186/1471-2164-15-679] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 07/18/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, "Candidatus Methanomethylophilus alvus", "Candidatus Methanomassiliicoccus intestinalis" and Methanomassiliicoccus luminyensis. RESULTS Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, "Ca. M. alvus" and "Ca. M. intestinalis" do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata.
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Affiliation(s)
- Guillaume Borrel
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Nicolas Parisot
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />CNRS, UMR 6023, Université Blaise Pascal, 63000 Clermont-Ferrand, France
| | - Hugh MB Harris
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Eric Peyretaillade
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Nadia Gaci
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - William Tottey
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Olivier Bardot
- />GReD, CNRS, UMR 6293, Inserm, UMR 1103, Clermont Université, Université d’Auvergne 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Kasie Raymann
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Simonetta Gribaldo
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Pierre Peyret
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Paul W O’Toole
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Jean-François Brugère
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
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Panek J, El Alaoui H, Mone A, Urbach S, Demettre E, Texier C, Brun C, Zanzoni A, Peyretaillade E, Parisot N, Lerat E, Peyret P, Delbac F, Biron DG. Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae. PLoS One 2014; 9:e100791. [PMID: 24967735 PMCID: PMC4072689 DOI: 10.1371/journal.pone.0100791] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Intracellular pathogens including bacteria, viruses and protozoa hijack host cell functions to access nutrients and to bypass cellular defenses and immune responses. These strategies have been acquired through selective pressure and allowed pathogens to reach an appropriate cellular niche for their survival and growth. To get new insights on how parasites hijack host cellular functions, we developed a SILAC (Stable Isotope Labeling by Amino Acids in Cell culture) quantitative proteomics workflow. Our study focused on deciphering the cross-talk in a host-parasite association, involving human foreskin fibroblasts (HFF) and the microsporidia Anncaliia algerae, a fungus related parasite with an obligate intracellular lifestyle and a strong host dependency. The host-parasite cross-talk was analyzed at five post-infection times 1, 6, 12 and 24 hours post-infection (hpi) and 8 days post-infection (dpi). A significant up-regulation of four interferon-induced proteins with tetratricopeptide repeats IFIT1, IFIT2, IFIT3 and MX1 was observed at 8 dpi suggesting a type 1 interferon (IFN) host response. Quantitative alteration of host proteins involved in biological functions such as signaling (STAT1, Ras) and reduction of the translation activity (EIF3) confirmed a host type 1 IFN response. Interestingly, the SILAC approach also allowed the detection of 148 A. algerae proteins during the kinetics of infection. Among these proteins many are involved in parasite proliferation, and an over-representation of putative secreted effectors proteins was observed. Finally our survey also suggests that A. algerae could use a transposable element as a lure strategy to escape the host innate immune system.
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Affiliation(s)
- Johan Panek
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Hicham El Alaoui
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail: (HEA); (DGB)
| | - Anne Mone
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Serge Urbach
- Functional Proteomics Platform. UMR CNRS 5203, Montpellier, France
| | - Edith Demettre
- Functional Proteomics Platform. UMS CNRS 3426, Montpellier, France
| | - Catherine Texier
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Christine Brun
- INSERM, UMR1090 TAGC, Marseille, Marseille, France
- Aix-Marseille Université, UMR1090 TAGC, Marseille, France
- CNRS, Marseille, France
| | - Andreas Zanzoni
- INSERM, UMR1090 TAGC, Marseille, Marseille, France
- Aix-Marseille Université, UMR1090 TAGC, Marseille, France
| | - Eric Peyretaillade
- Clermont Université, Université d'Auvergne, I.U.T., UFR Pharmacie, Clermont-Ferrand, France
- Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, Clermont-Ferrand, France
| | - Nicolas Parisot
- Clermont Université, Université d'Auvergne, I.U.T., UFR Pharmacie, Clermont-Ferrand, France
- Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, Clermont-Ferrand, France
| | - Emmanuelle Lerat
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, I.U.T., UFR Pharmacie, Clermont-Ferrand, France
- Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, Clermont-Ferrand, France
| | - Frederic Delbac
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - David G. Biron
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail: (HEA); (DGB)
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Borrel G, O'Toole PW, Harris HMB, Peyret P, Brugère JF, Gribaldo S. Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis. Genome Biol Evol 2014; 5:1769-80. [PMID: 23985970 PMCID: PMC3814188 DOI: 10.1093/gbe/evt128] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and “Candidatus Methanomethylophilus alvus,” provide insights into its evolutionary history and metabolic features. Phylogenetic analysis of ribosomal proteins robustly indicates a monophyletic group independent of any previously known methanogenic order, which shares ancestry with the Marine Benthic Group D, the Marine Group II, the DHVE2 group, and the Thermoplasmatales. This phylogenetic position, along with the analysis of enzymes involved in core methanogenesis, strengthens a single ancient origin of methanogenesis in the Euryarchaeota and indicates further multiple independent losses of this metabolism in nonmethanogenic lineages than previously suggested. Genomic analysis revealed an unprecedented loss of the genes coding for the first six steps of methanogenesis from H2/CO2 and the oxidative part of methylotrophic methanogenesis, consistent with the fact that M. luminyensis and “Ca. M. alvus” are obligate H2-dependent methylotrophic methanogens. Genomic data also suggest that these methanogens may use a large panel of methylated compounds. Phylogenetic analysis including homologs retrieved from environmental samples indicates that methylotrophic methanogenesis (regardless of dependency on H2) is not restricted to gut representatives but may be an ancestral characteristic of the whole order, and possibly also of ancient origin in the Euryarchaeota. 16S rRNA and McrA trees show that this new order of methanogens is very diverse and occupies environments highly relevant for methane production, therefore representing a key lineage to fully understand the diversity and evolution of methanogenesis.
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Affiliation(s)
- Guillaume Borrel
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
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Jaziri F, Parisot N, Abid A, Denonfoux J, Ribière C, Gasc C, Boucher D, Brugère JF, Mahul A, Hill DRC, Peyretaillade E, Peyret P. PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification. Database (Oxford) 2014; 2014:bau036. [PMID: 24771669 PMCID: PMC4000467 DOI: 10.1093/database/bau036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, high-throughput molecular tools have led to an exponential growth of available 16S rRNA gene sequences. Incorporating such data, molecular tools based on target-probe hybridization were developed to monitor microbial communities within complex environments. Unfortunately, only a few 16S rRNA gene-targeted probe collections were described. Here, we present PhylOPDb, an online resource for a comprehensive phylogenetic oligonucleotide probe database. PhylOPDb provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes. Such probes set or subset could be used to globally monitor known and unknown prokaryotic communities through various techniques including DNA microarrays, polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), targeted gene capture or in silico rapid sequence identification. PhylOPDb contains 74 003 25-mer probes targeting 2178 genera including Bacteria and Archaea. Database URL: http://g2im.u-clermont1.fr/phylopdb/
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Affiliation(s)
- Faouzi Jaziri
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France, UMR CNRS 6158, ISIMA/LIMOS, Clermont Université, Université Blaise Pascal, F-63173 Aubière, France, CNRS, UMR 6023, LMGE, F-63171 Aubière, France and Clermont Université, CRRI, F-63177 Aubière, France
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Brugère JF, Mihajlovski A, Missaoui M, Peyret P. Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics. Expert Rev Mol Diagn 2014; 9:353-65. [DOI: 10.1586/erm.09.16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Feria-Gervasio D, Tottey W, Gaci N, Alric M, Cardot JM, Peyret P, Martin JF, Pujos E, Sébédio JL, Brugère JF. Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota. J Microbiol Methods 2013; 96:111-8. [PMID: 24333608 DOI: 10.1016/j.mimet.2013.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/25/2013] [Accepted: 11/30/2013] [Indexed: 02/07/2023]
Abstract
The technical and ethical difficulties in studying the gut microbiota in vivo warrant the development and improvement of in vitro systems able to simulate and control the physicochemical factors of the gut biology. Moreover, the functional regionalization of this organ implies a model simulating these differences. Here we propose an improved and alternative three-stage continuous bioreactor called 3S-ECSIM (three-stage Environmental Control System for Intestinal Microbiota) to study the human large intestine. Its main feature compared with other in vitro systems is the anaerobic atmosphere originating directly from the microbiota metabolism, leading to different gas ratios of CO2 and H2 in each compartment. Analyses of the metabolic and microbiological profiles (LC-MS and a phylogenetic microarray) show different profiles together with a maintenance of this differentiation between the three compartments, simulating respectively a proximal, a transversal and a distal colon. Moreover, the last reactor presents a high similarity with the initial fecal sample, at the microbiological diversity level. Based on our results, this in-vitro process improvement is a valuable alternative tool to dynamically study the structure and metabolism of gut microbiota, and its response to nutrients, prebiotics, probiotics, drugs or xenobiotics.
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Affiliation(s)
- David Feria-Gervasio
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - William Tottey
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Nadia Gaci
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Monique Alric
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jean-Michel Cardot
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jean-François Martin
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Estelle Pujos
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Jean-Louis Sébédio
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Jean-François Brugère
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.
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Plewniak F, Koechler S, Navet B, Dugat-Bony É, Bouchez O, Peyret P, Séby F, Battaglia-Brunet F, Bertin PN. Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments. Mol Ecol 2013; 22:4870-83. [DOI: 10.1111/mec.12432] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/13/2013] [Accepted: 06/25/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Frédéric Plewniak
- Département Microorganismes, Génomes, Environnement; Génétique Moléculaire, Génomique et Microbiologie; UMR7156 Université de Strasbourg/CNRS; 28 rue Goethe 67083 Strasbourg Cedex France
| | - Sandrine Koechler
- Département Microorganismes, Génomes, Environnement; Génétique Moléculaire, Génomique et Microbiologie; UMR7156 Université de Strasbourg/CNRS; 28 rue Goethe 67083 Strasbourg Cedex France
| | - Benjamin Navet
- Département Microorganismes, Génomes, Environnement; Génétique Moléculaire, Génomique et Microbiologie; UMR7156 Université de Strasbourg/CNRS; 28 rue Goethe 67083 Strasbourg Cedex France
| | - Éric Dugat-Bony
- Laboratoire Microorganismes: Génome et Environnement; UMR 6023 Université Blaise Pascal Clermont-Ferrand/CNRS; Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais BP 80026 63171 Aubière Cedex France
| | - Olivier Bouchez
- Plateforme génomique (PlaGe); Génopole Toulouse-Midi-Pyrénées; INRA; 31326 Castanet-Tolosan France
- INRA; UMR444 Laboratoire de Génétique Cellulaire; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Pierre Peyret
- Laboratoire Microorganismes: Génome et Environnement; UMR 6023 Université Blaise Pascal Clermont-Ferrand/CNRS; Bât de Biologie A, Les Cézeaux, 24, Avenue des Landais BP 80026 63171 Aubière Cedex France
| | - Fabienne Séby
- Ultra Traces Analyses Aquitaine (UT2A); Hélioparc Pau-Pyrénées; 2, avenue du Président Angot 64053 Pau Cedex 9 France
| | - Fabienne Battaglia-Brunet
- BRGM; Environnement et Procédés; Unité Biogéochimie Environnementale; Avenue Claude Guillemin 45060 Orléans France
| | - Philippe N. Bertin
- Département Microorganismes, Génomes, Environnement; Génétique Moléculaire, Génomique et Microbiologie; UMR7156 Université de Strasbourg/CNRS; 28 rue Goethe 67083 Strasbourg Cedex France
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Podmirseg SM, Seewald MSA, Knapp BA, Bouzid O, Biderre-Petit C, Peyret P, Insam H. Wood ash amendment to biogas reactors as an alternative to landfilling? A preliminary study on changes in process chemistry and biology. Waste Manag Res 2013; 31:829-842. [PMID: 23831776 DOI: 10.1177/0734242x13497077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Wood ash addition to biogas plants represents an alternative to commonly used landfilling by improving the reactor performance, raising the pH and alleviating potential limits of trace elements. This study is the first on the effects of wood ash on reactor conditions and microbial communities in cattle slurry-based biogas reactors. General process parameters [temperature, pH, electrical conductivity, ammonia, volatile fatty acids, carbon/nitrogen (C/N), total solids (TS), volatile solids, and gas quantity and quality] were monitored along with molecular analyses of methanogens by polymerase chain reaction- denaturing gradient gel electrophoresis and modern microarrays (archaea and bacteria). A prompt pH rise was observed, as was an increase in C/N ratio and volatile fatty acids. Biogas production was inhibited, but recovered to even higher production rates and methane concentration after single amendment. High sulphur levels in the wood ash generated hydrogen sulphide and potentially hampered methanogenesis. Methanosarcina was the most dominant methanogen in all reactors; however, diversity was higher in ash-amended reactors. Bacterial groups like Firmicutes, Proteobacteria and Acidobacteria were favoured, which could improve the hydrolytic efficiency of the reactors. We recommend constant monitoring of the chemical composition of the used wood ash and suggest that ash amendment is adequate if added to the substrate at a rate low enough to allow adaptation of the microbiota (e.g. 0.25 g g(-1) TS). It could further help to enrich digestate with important nutrients, for example phosphorus, calcium and magnesium, but further experiments are required for the evaluation of wood ash concentrations that are tolerable for anaerobic digestion.
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Polonais V, Belkorchia A, Roussel M, Peyretaillade E, Peyret P, Diogon M, Delbac F. Identification of two new polar tube proteins related to polar tube protein 2 in the microsporidian Antonospora locustae. FEMS Microbiol Lett 2013; 346:36-44. [PMID: 23763358 DOI: 10.1111/1574-6968.12198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/28/2013] [Accepted: 06/07/2013] [Indexed: 01/25/2023] Open
Abstract
Microsporidia are obligate intracellular eukaryotic parasites with a broad host spectrum characterized by a unique and highly sophisticated invasion apparatus, the polar tube (PT). In a previous study, two PT proteins, named AlPTP1 (50 kDa) and AlPTP2 (35 kDa), were identified in Antonospora locustae, an orthoptera parasite that is used as a biological control agent against locusts. Antibodies raised against AlPTP2 cross-reacted with a band migrating at ~70 kDa, suggesting that this 70-kDa antigen is closely related to AlPTP2. A blastp search against the A. locustae genome database allowed the identification of two further PTP2-like proteins named AlPTP2b (568 aa) and AlPTP2c (599 aa). Both proteins are characterized by a specific serine- and glycine-rich N-terminal extension with elastomeric structural features and share a common C-terminal end conserved with AlPTP2 (~88% identity for the last 250 aa). MS analysis of the 70-kDa band revealed the presence of AlPTP2b. Specific anti-AlPTP2b antibodies labelled the extruded PTs of the A. locustae spores, confirming that this antigen is a PT component. Finally, we showed that several PTP2-like proteins are also present in other phylogenetically related insect microsporidia, including Anncaliia algerae and Paranosema grylli.
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Affiliation(s)
- Valérie Polonais
- Clermont Université, Université d'Auvergne, Laboratoire Microorganismes: Génome et Environnement, Clermont-ferrand, France
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Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HMB, Jeffery IB, Claesson MJ, O'Toole PW, Peyret P, Brugère JF. The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level. PLoS One 2013; 8:e62544. [PMID: 23690942 PMCID: PMC3656878 DOI: 10.1371/journal.pone.0062544] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/22/2013] [Indexed: 02/07/2023] Open
Abstract
Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.
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Affiliation(s)
- William Tottey
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Jeremie Denonfoux
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Faouzi Jaziri
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - Nicolas Parisot
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Mohiedine Missaoui
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - David Hill
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - Guillaume Borrel
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Eric Peyretaillade
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Monique Alric
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Hugh M. B. Harris
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Ian B. Jeffery
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul W. O'Toole
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Pierre Peyret
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Jean-François Brugère
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- * E-mail:
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42
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Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, Boucher D, Morgavi DP, Le Paslier D, Peyretaillade E, Peyret P. Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Res 2013; 20:185-96. [PMID: 23364577 PMCID: PMC3628448 DOI: 10.1093/dnares/dst001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.
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Affiliation(s)
- Jérémie Denonfoux
- Centre de Recherche en Nutrition Humaine Auvergne, Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, Clermont-Ferrand 63000, France
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Abstract
UNLABELLED BACKGROUND High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use. RESULTS Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify "core sequences" comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility. CONCLUSIONS Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.
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Affiliation(s)
- Jeremy Dufourt
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
| | - Pierre Pouchin
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
- CHRU, F-63001, Clermont-Ferrand, France
| | - Pierre Peyret
- EA4678, Université d’Auvergne, F-63001, Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
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Peyretaillade E, Parisot N, Polonais V, Terrat S, Denonfoux J, Dugat-Bony E, Wawrzyniak I, Biderre-Petit C, Mahul A, Rimour S, Gonçalves O, Bornes S, Delbac F, Chebance B, Duprat S, Samson G, Katinka M, Weissenbach J, Wincker P, Peyret P. Annotation of microsporidian genomes using transcriptional signals. Nat Commun 2012; 3:1137. [DOI: 10.1038/ncomms2156] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 09/20/2012] [Indexed: 12/24/2022] Open
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Parisot N, Denonfoux J, Dugat-Bony E, Peyret P, Peyretaillade E. KASpOD--a web service for highly specific and explorative oligonucleotide design. Bioinformatics 2012; 28:3161-2. [PMID: 23047560 DOI: 10.1093/bioinformatics/bts597] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
SUMMARY KASpOD is a web service dedicated to the design of signature sequences using a k-mer-based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays. AVAILABILITY http://g2im.u-clermont1.fr/kaspod. CONTACT eric.peyretaillade@udamail.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicolas Parisot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, France
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Dugat-Bony E, Biderre-Petit C, Jaziri F, David MM, Denonfoux J, Lyon DY, Richard JY, Curvers C, Boucher D, Vogel TM, Peyretaillade E, Peyret P. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microb Biotechnol 2012; 5:642-53. [PMID: 22432919 PMCID: PMC3815876 DOI: 10.1111/j.1751-7915.2012.00339.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of hydrogen‐releasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis‐dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.
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Affiliation(s)
- Eric Dugat-Bony
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F63000, Clermont-Ferrand, France
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Pessiot J, Nouaille R, Jobard M, Singhania RR, Bournilhas A, Christophe G, Fontanille P, Peyret P, Fonty G, Larroche C. Fed-batch anaerobic valorization of slaughterhouse by-products with mesophilic microbial consortia without methane production. Appl Biochem Biotechnol 2012; 167:1728-43. [PMID: 22222430 DOI: 10.1007/s12010-011-9516-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 12/20/2011] [Indexed: 11/28/2022]
Abstract
This work aimed at setting up a fully instrumented, laboratory-scale bioreactor enabling anaerobic valorization of solid substrates through hydrogen and/or volatile fatty acid (VFA) production using mixed microbial populations (consortia). The substrate used was made of meat-based wastes, especially from slaughterhouses, which are becoming available in large amounts as a consequence of the growing constraints for waste disposal from meat industry. A reconstituted microbial mesophilic consortium without Archaebacteria (methanogens), named PBr, was cultivated in a 5-L anaerobic bioreactor on slaughterhouse wastes. The experiments were carried out with sequential fed-batch operations, including liquid medium removal from the bioreactor and addition of fresh substrate. VFAs and nitrogen were the main metabolites observed, while hydrogen accumulation was very low and no methane production was evidenced. After 1,300 h of culture, yields obtained for VFAs reached 0.38 g/g dry matter. Strain composition of the microbial consortium was also characterized using molecular tools (temporal temperature gradient gel electrophoresis and gene sequencing).
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Affiliation(s)
- J Pessiot
- Université Blaise Pascal Laboratoire de Génie Chimique et Biochimique, Polytech Clermont-Ferrand, Clermont Université, 24 av. des Landais, BP 206, 63174 Aubière cedex, France
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Borrel G, Jézéquel D, Biderre-Petit C, Morel-Desrosiers N, Morel JP, Peyret P, Fonty G, Lehours AC. Production and consumption of methane in freshwater lake ecosystems. Res Microbiol 2011; 162:832-47. [DOI: 10.1016/j.resmic.2011.06.004] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Boucher D, Laffaire JB, Jaziri F, David C, Biderre-Petit C, Duquenne P, Peyretaillade E, Peyret P. Bacterial community composition of biological degreasing systems and health risk assessment for workers. Microb Ecol 2011; 62:868-881. [PMID: 21698403 DOI: 10.1007/s00248-011-9887-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/31/2011] [Indexed: 05/31/2023]
Abstract
Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they were colonized by a defined and restricted group of bacteria. This group replaced the indigenous bacterial populations known for degrading complex substrates. Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, and Pantoea agglomerans were important members of the microflora found in most of the biological degreasing systems. These bacteria might represent a potential health hazard for workers.
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Affiliation(s)
- Delphine Boucher
- Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement (LMGE), BP 10448, F-63000 Clermont-Ferrand, France
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Dugat-Bony E, Peyretaillade E, Parisot N, Biderre-Petit C, Jaziri F, Hill D, Rimour S, Peyret P. Detecting unknown sequences with DNA microarrays: explorative probe design strategies. Environ Microbiol 2011; 14:356-71. [PMID: 21895914 DOI: 10.1111/j.1462-2920.2011.02559.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.
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Affiliation(s)
- Eric Dugat-Bony
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
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