1
|
Million M, Alou MT, Khelaifia S, Bachar D, Lagier JC, Dione N, Brah S, Hugon P, Lombard V, Armougom F, Fromonot J, Robert C, Michelle C, Diallo A, Fabre A, Guieu R, Sokhna C, Henrissat B, Parola P, Raoult D. Retraction Note: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition. Sci Rep 2023; 13:18589. [PMID: 37903811 PMCID: PMC10616166 DOI: 10.1038/s41598-023-44597-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023] Open
Affiliation(s)
- Matthieu Million
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Dipankar Bachar
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Niokhor Dione
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, UMR 7257, 13288, Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288, Marseille cedex 9, France
| | - Fabrice Armougom
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Julien Fromonot
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Catherine Robert
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Aldiouma Diallo
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Alexandre Fabre
- Service de Pédiatrie Multidisciplinaire, hôpital de la Timone Enfant, APHM, Marseille, France
- UMR_S 910, Aix-Marseille Université, Marseille, France
| | - Régis Guieu
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Cheikh Sokhna
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, UMR 7257, 13288, Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288, Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Philippe Parola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
2
|
Fenouil R, Pradel N, Belahbib H, Roumagnac M, Bartoli M, Ben Hania W, Denis Y, Garel M, Tamburini C, Ollivier B, Summers Z, Armougom F, Dolla A. Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses. Microorganisms 2023; 11:microorganisms11030773. [PMID: 36985346 PMCID: PMC10057702 DOI: 10.3390/microorganisms11030773] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Pseudothermotoga elfii strain DSM9442 and P. elfii subsp. lettingae strain DSM14385 are hyperthermophilic bacteria. P. elfii DSM9442 is a piezophile and was isolated from a depth of over 1600 m in an oil-producing well in Africa. P. elfii subsp. lettingae is piezotolerant and was isolated from a thermophilic bioreactor fed with methanol as the sole carbon and energy source. In this study, we analyzed both strains at the genomic and transcriptomic levels, paying particular attention to changes in response to pressure increases. Transcriptomic analyses revealed common traits of adaptation to increasing hydrostatic pressure in both strains, namely, variations in transport membrane or carbohydrate metabolism, as well as species-specific adaptations such as variations in amino acid metabolism and transport for the deep P. elfii DSM9442 strain. Notably, this work highlights the central role played by the amino acid aspartate as a key intermediate of the pressure adaptation mechanisms in the deep strain P. elfii DSM9442. Our comparative genomic and transcriptomic analysis revealed a gene cluster involved in lipid metabolism that is specific to the deep strain and that was differentially expressed at high hydrostatic pressures and might, thus, be a good candidate for a piezophilic gene marker in Pseudothermotogales.
Collapse
Affiliation(s)
- Romain Fenouil
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Nathalie Pradel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
| | - Hassiba Belahbib
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Yann Denis
- Institut de Microbiologie de la Méditerranée, CNRS—Aix Marseille Université, Marseille, France
| | - Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath Summers
- LanzaTech, Illinois Science and Technology Park, Skokie, IL 60077, USA
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
| |
Collapse
|
3
|
Andrianjakarivony HF, Bettarel Y, Armougom F, Desnues C. Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing. Viruses 2022; 15:76. [PMID: 36680116 PMCID: PMC9862649 DOI: 10.3390/v15010076] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.
Collapse
Affiliation(s)
- Harilanto Felana Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEΦI), IHU—Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Université de Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon, 34090 Montpellier, France
| | - Fabrice Armougom
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEΦI), IHU—Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
| |
Collapse
|
4
|
Baumas CMJ, Le Moigne FAC, Garel M, Bhairy N, Guasco S, Riou V, Armougom F, Grossart HP, Tamburini C. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions. ISME J 2021; 15:1695-1708. [PMID: 33452475 PMCID: PMC8163737 DOI: 10.1038/s41396-020-00880-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.
Collapse
Affiliation(s)
- Chloé M. J. Baumas
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Frédéric A. C. Le Moigne
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Marc Garel
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Nagib Bhairy
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Sophie Guasco
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Virginie Riou
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Fabrice Armougom
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Hans-Peter Grossart
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany ,grid.11348.3f0000 0001 0942 1117Institute of Biochemistry and Biology, Postdam University, 14469 Potsdam, Germany
| | - Christian Tamburini
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| |
Collapse
|
5
|
Roumagnac M, Pradel N, Bartoli M, Garel M, Jones AA, Armougom F, Fenouil R, Tamburini C, Ollivier B, Summers ZM, Dolla A. Responses to the Hydrostatic Pressure of Surface and Subsurface Strains of Pseudothermotoga elfii Revealing the Piezophilic Nature of the Strain Originating From an Oil-Producing Well. Front Microbiol 2020; 11:588771. [PMID: 33343528 PMCID: PMC7746679 DOI: 10.3389/fmicb.2020.588771] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/29/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ranging from 0.1 to 50 MPa of two strains from the same species originating from subsurface, Pseudothermotoga elfii DSM9442 isolated from a deep African oil-producing well, and surface, P. elfii subsp. lettingae isolated from a thermophilic sulfate-reducing bioreactor, environments are reported for the first time. The data support evidence for the piezophilic nature of P. elfii DSM9442, with an optimal hydrostatic pressure for growth of 20 MPa and an upper limit of 40 MPa, and the piezotolerance of P. elfii subsp. lettingae with growth occurring up to 20 MPa only. Under the experimental conditions, both strains produce mostly acetate and propionate as volatile fatty acids with slight variations with respect to the hydrostatic pressure for P. elfii DSM9442. The data show that the metabolism of P. elfii DSM9442 is optimized when grown at 20 MPa, in agreement with its piezophilic nature. Both Pseudothermotoga strains form chained cells when the hydrostatic pressure increases, especially P. elfii DSM9442 for which 44% of cells is chained when grown at 40 MPa. The viability of the chained cells increases with the increase in the hydrostatic pressure, indicating that chain formation is a protective mechanism for P. elfii DSM9442.
Collapse
Affiliation(s)
- Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Nathalie Pradel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Aaron A Jones
- ExxonMobil Research and Engineering Company, Annandale, NJ, United States
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Romain Fenouil
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath M Summers
- ExxonMobil Research and Engineering Company, Annandale, NJ, United States
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| |
Collapse
|
6
|
Michotey V, Blanfuné A, Chevalier C, Garel M, Diaz F, Berline L, Le Grand L, Armougom F, Guasco S, Ruitton S, Changeux T, Belloni B, Blanchot J, Ménard F, Thibaut T. In situ observations and modelling revealed environmental factors favouring occurrence of Vibrio in microbiome of the pelagic Sargassum responsible for strandings. Sci Total Environ 2020; 748:141216. [PMID: 32798861 DOI: 10.1016/j.scitotenv.2020.141216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/25/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Historically, pelagic Sargassum were only found in the Sargasso Sea. Since 2011, blooms were regularly observed in warmer water, further south. Their developments in Central Atlantic are associated with mass strandings on the coasts, causing important damages and potentially dispersion of new bacteria. Microbiomes associated with pelagic Sargassum were analysed at large scale in Central Atlantic and near Caribbean Islands with a focus on pathogenic bacteria. Vibrio appeared widely distributed among pelagic Sargassum microbiome of our samples with higher occurrence than previously found in Mexico Gulf. Six out the 16 Vibrio-OTUs (Operational Taxonomic Unit), representing 81.2 ± 13.1% of the sequences, felt in cluster containing pathogens. Among the four different microbial profiles of pelagic Sargassum microbiome, Vibrio attained about 2% in two profiles whereas it peaked, in the two others, at 6.5 and 26.8% respectively, largely above the concentrations found in seawater surrounding raft (0.5%). In addition to sampling and measurements, we performed backward Lagrangian modelling of trajectories of rafts, and rebuilt the sampled rafts environmental history allowing us to estimate Sargassum growth rates along raft displacements. We found that Vibrio was favoured by high Sargassum growth rate and in situ ammonium and nitrite, modelled phosphate and nitrate concentrations, whereas zooplankters, benthic copepods, and calm wind (proxy of raft buoyancy near the sea surface) were less favourable for them. Relations between Vibrio and other main bacterial groups identified a competition with Alteromonas. According to forward Lagrangian tracking, part of rafts containing Vibrio could strand on the Caribbean coasts, however the strong decreases of modelled Sargassum growth rates along this displacement suggest unfavourable environment for Vibrio. For the conditions and areas observed, the sanitary risk seemed in consequence minor, but in other areas or conditions where high Sargassum growth rate occurred near coasts, it could be more important.
Collapse
Affiliation(s)
- Valérie Michotey
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Aurélie Blanfuné
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Cristèle Chevalier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Frédéric Diaz
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Léo Berline
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Louis Le Grand
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Sophie Guasco
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Sandrine Ruitton
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Thomas Changeux
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Bruno Belloni
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Jean Blanchot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Frédéric Ménard
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| | - Thierry Thibaut
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
| |
Collapse
|
7
|
Quéméneur M, Bel Hassen M, Armougom F, Khammeri Y, Lajnef R, Bellaaj-Zouari A. Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea). Front Microbiol 2020; 11:593540. [PMID: 33335519 PMCID: PMC7735998 DOI: 10.3389/fmicb.2020.593540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Received: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 01/18/2023] Open
Abstract
Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabès). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH4 + and/or PO4 3-) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabès. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.
Collapse
Affiliation(s)
- Marianne Quéméneur
- Aix-Marseille Univ, University of Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Malika Bel Hassen
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Fabrice Armougom
- Aix-Marseille Univ, University of Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Yosra Khammeri
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Rim Lajnef
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Amel Bellaaj-Zouari
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| |
Collapse
|
8
|
Summers ZM, Belahbib H, Pradel N, Bartoli M, Mishra P, Tamburini C, Dolla A, Ollivier B, Armougom F. A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations. Syst Appl Microbiol 2020; 43:126132. [DOI: 10.1016/j.syapm.2020.126132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
|
9
|
Aigle A, Bonin P, Fernandez-Nunez N, Loriod B, Guasco S, Bergon A, Armougom F, Iobbi-Nivol C, Imbert J, Michotey V. The nature of the electron acceptor (MnIV/NO3) triggers the differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3. FEMS Microbiol Lett 2019; 365:4939474. [PMID: 29566166 DOI: 10.1093/femsle/fny068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/15/2018] [Indexed: 01/05/2023] Open
Abstract
Shewanella algae C6G3 can dissimilatively reduce nitrate into ammonium and manganese oxide (MnIV) into MnII. It has the unusual ability to anaerobically produce nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources, and with either MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. The comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of a non-limiting concentration of ammonium under both culture conditions. In addition, in the presence of MnIV, ntrB/nrtC regulators, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine-dependent genes were over-represented. Under the nitrate condition, the expression of genes involved in the synthesis of several amino acids was increased. Finally, the expression level of genes associated with the general stress response was also amplified in both conditions and among them, katE, a putative catalase/peroxidase present on several Shewanella genomes, was highly expressed with a median value relatively higher in the MnIV condition.
Collapse
Affiliation(s)
- Axel Aigle
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Patricia Bonin
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | | | - Béatrice Loriod
- UMR_S 1090, TGML/TAGC, Aix-Marseille Université, Marseille F-13009, France
| | - Sophie Guasco
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Aurélie Bergon
- UMR_S 1090, TGML/TAGC, Aix-Marseille Université, Marseille F-13009, France
| | - Fabrice Armougom
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université, CNRS, BIP Bioénergétique et Ingénierie des Protéines UMR 7281, 13402, Marseille, France
| | - Jean Imbert
- UMR_S 1090, TGML/TAGC, Aix-Marseille Université, Marseille F-13009, France
| | - Valérie Michotey
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| |
Collapse
|
10
|
Garel M, Bonin P, Martini S, Guasco S, Roumagnac M, Bhairy N, Armougom F, Tamburini C. Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions. Front Microbiol 2019; 10:453. [PMID: 31024462 PMCID: PMC6465632 DOI: 10.3389/fmicb.2019.00453] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 12/07/2018] [Accepted: 02/20/2019] [Indexed: 11/24/2022] Open
Abstract
The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with <2% pressure variability). As proof of concept, we describe a field application (prokaryotic activity measurements and incubation experiment) with samples collected at 3,000m-depth in the Mediterranean Sea. Sampling, sub-sampling, transfer, and incubations were performed under in situ high pressure conditions and compared to those performed following decompression and incubation at atmospheric pressure. Three successive incubations were made for each condition using direct dissolved-oxygen concentration measurements to determine the incubation times. Subsamples were collected at the end of each incubation to monitor the prokaryotic diversity, using 16S-rDNA/rRNA high-throughput sequencing. Our results demonstrated that oxygen consumption by prokaryotes is always higher under in situ conditions than after decompression and incubation at atmospheric pressure. In addition, over time, the variations in the prokaryotic community composition and structure are seen to be driven by the different experimental conditions. Finally, within samples maintained under in situ high pressure conditions, the active (16S rRNA) prokaryotic community was dominated by sequences affiliated with rare families containing piezophilic isolates, such as Oceanospirillaceae or Colwelliaceae. These results demonstrate the biological importance of maintaining in situ conditions during and after sampling in deep-sea environments.
Collapse
Affiliation(s)
- Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Patricia Bonin
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Séverine Martini
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Sophie Guasco
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Nagib Bhairy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| |
Collapse
|
11
|
Belahbib H, Summers ZM, Fardeau ML, Joseph M, Tamburini C, Dolla A, Ollivier B, Armougom F. Towards a congruent reclassification and nomenclature of the thermophilic species of the genus Pseudothermotoga within the order Thermotogales. Syst Appl Microbiol 2018; 41:555-563. [PMID: 29801938 DOI: 10.1016/j.syapm.2018.04.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 11/24/2022]
Abstract
The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, Pseudothermotoga, a sister group of the genus Thermotoga within the order Thermotogales. Comparative genomics of both Pseudothermotoga and Thermotoga spp., including 16S-rRNA-based phylogenetic, pan-genomic analysis as well as signature indel conservation, provided evidence that Thermotoga caldifontis and Thermotoga profunda species should be reclassified within the genus Pseudothermotoga and renamed as Pseudothermotoga caldifontis comb. nov. (type strain=AZM44c09T) and Pseudothermotoga profunda comb. nov. (type strain=AZM34c06T), respectively. In addition, based upon whole-genome relatedness indices and DNA-DNA Hybridization results, the reclassification of Pseudothermotoga lettingae and Pseudothermotoga subterranea as latter heterotypic synonyms of Pseudothermotoga elfii is proposed. Finally, potential genetic elements resulting from the distinct evolutionary story of the Thermotoga and Pseudothermotoga clades are discussed.
Collapse
Affiliation(s)
- Hassiba Belahbib
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath M Summers
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801, United States
| | | | - Manon Joseph
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
| |
Collapse
|
12
|
Zaghmouri I, Michotey VD, Armougom F, Guasco S, Bonin PC. Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community. Mar Pollut Bull 2018; 130:76-83. [PMID: 29866572 DOI: 10.1016/j.marpolbul.2018.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 08/17/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera.
Collapse
Affiliation(s)
- Imen Zaghmouri
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Valerie D Michotey
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France.
| | - Fabrice Armougom
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Sophie Guasco
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Patricia C Bonin
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| |
Collapse
|
13
|
Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A, Debroas D, Armougom F, Erauso G. Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. Front Microbiol 2018; 9:102. [PMID: 29467733 PMCID: PMC5808123 DOI: 10.3389/fmicb.2018.00102] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/17/2018] [Indexed: 01/21/2023] Open
Abstract
The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing. We show that the bacterial community of the intertidal site is clearly distinct from that of the submarine sites with species distribution patterns driven by only a few abundant populations, affiliated to the Chloroflexi and Proteobacteria phyla. In contrast, the distribution of archaeal taxa seems less site-dependent, as exemplified by the co-occurrence, in both submarine and intertidal sites, of two dominant phylotypes of Methanosarcinales previously thought to be restricted to serpentinizing systems, either marine (Lost City Hydrothermal Field) or terrestrial (The Cedars ultrabasic springs). Over 70% of the phylotypes were rare and included, among others, all those affiliated to candidate divisions. We finally compared the distribution of bacterial and archaeal phylotypes of Prony Hydrothermal Field with those of five previously studied serpentinizing systems of geographically distant sites. Although sensu stricto no core microbial community was identified, a few uncultivated lineages, notably within the archaeal order Methanosarcinales and the bacterial class Dehalococcoidia (the candidate division MSBL5) were exclusively found in a few serpentinizing systems while other operational taxonomic units belonging to the orders Clostridiales, Thermoanaerobacterales, or the genus Hydrogenophaga, were abundantly distributed in several sites. These lineages may represent taxonomic signatures of serpentinizing ecosystems. These findings extend our current knowledge of the microbial diversity inhabiting serpentinizing systems and their biogeography.
Collapse
Affiliation(s)
- Eléonore Frouin
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Méline Bes
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Bernard Ollivier
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Marianne Quéméneur
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Anne Postec
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Didier Debroas
- CNRS UMR 6023, Laboratoire "Microorganismes - Génome et Environnement", Université Clermont Auvergne, Clermont-Ferrand, France
| | - Fabrice Armougom
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| |
Collapse
|
14
|
Fadhlaoui K, Ben Hania W, Armougom F, Bartoli M, Fardeau ML, Erauso G, Brasseur G, Aubert C, Hamdi M, Brochier-Armanet C, Dolla A, Ollivier B. Obligate sugar oxidation inMesotogaspp., phylumThermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor. Environ Microbiol 2017; 20:281-292. [DOI: 10.1111/1462-2920.13995] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Khaled Fadhlaoui
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
- Laboratoire d'Ecologie et de Technologie Microbienne; Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Centre Urbain Nord; Tunis BP 676, 1080 Tunisia
| | - Wagdi Ben Hania
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | | | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | | | | | - Moktar Hamdi
- Laboratoire d'Ecologie et de Technologie Microbienne; Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Centre Urbain Nord; Tunis BP 676, 1080 Tunisia
| | - Céline Brochier-Armanet
- Université de Lyon; Université Lyon 1; CNRS; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918; Villeurbanne F-69622 France
| | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB; Marseille France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| |
Collapse
|
15
|
Zouch H, Karray F, Armougom F, Chifflet S, Hirschler-Réa A, Kharrat H, Kamoun L, Ben Hania W, Ollivier B, Sayadi S, Quéméneur M. Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia). Front Microbiol 2017; 8:1583. [PMID: 28871244 PMCID: PMC5566975 DOI: 10.3389/fmicb.2017.01583] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 04/08/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.
Collapse
Affiliation(s)
- Hana Zouch
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Fabrice Armougom
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Sandrine Chifflet
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Hanen Kharrat
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Lotfi Kamoun
- Department of Research, Tunisian Chemical GroupSfax, Tunisia
| | - Wajdi Ben Hania
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Marianne Quéméneur
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| |
Collapse
|
16
|
Drancourt M, Aboudharam G, Croce O, Armougom F, Robert C, Raoult D. Dental pulp as a source of low-contaminated DNA. Microb Pathog 2017; 105:63-67. [PMID: 28188902 DOI: 10.1016/j.micpath.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 04/13/2016] [Revised: 01/10/2017] [Accepted: 02/01/2017] [Indexed: 11/19/2022]
Abstract
The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing. This yielded a total of 487,828 trimmed reads with a length of 227 ± 35 bp. Sequence analysis of the final dataset using Blast algorithm search and stringent thresholds for sequence identity and coverage against a database including both Canis lupus familiaris and Homo sapiens complete genomes showed that 95% of reads were assigned to C. familiaris whereas 0.03% was assigned to H. sapiens. In a second step, two teeth collected from two 12th century mammals were manipulated following the same protocol. A total of 13,890 trimmed reads with a 157 ± 67 bp length yielded 0-0.35% reads assigned to H. sapiens. This study indicates that the dental pulp is a useful for detecting the significant nucleic sequences in both modern and ancient samples.
Collapse
Affiliation(s)
- Michel Drancourt
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Gérard Aboudharam
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Olivier Croce
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Fabrice Armougom
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Catherine Robert
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Didier Raoult
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
| |
Collapse
|
17
|
Million M, Tidjani Alou M, Khelaifia S, Bachar D, Lagier JC, Dione N, Brah S, Hugon P, Lombard V, Armougom F, Fromonot J, Robert C, Michelle C, Diallo A, Fabre A, Guieu R, Sokhna C, Henrissat B, Parola P, Raoult D. Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition. Sci Rep 2016; 6:26051. [PMID: 27183876 PMCID: PMC4869025 DOI: 10.1038/srep26051] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [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: 10/22/2015] [Accepted: 04/27/2016] [Indexed: 02/08/2023] Open
Abstract
Severe acute malnutrition (SAM) is associated with inadequate diet, low levels of plasma antioxidants and gut microbiota alterations. The link between gut redox and microbial alterations, however, remains unexplored. By sequencing the gut microbiomes of 79 children of varying nutritional status from three centers in Senegal and Niger, we found a dramatic depletion of obligate anaerobes in malnutrition. This was confirmed in an individual patient data meta-analysis including 107 cases and 77 controls from 5 different African and Asian countries. Specifically, several species of the Bacteroidaceae, Eubacteriaceae, Lachnospiraceae and Ruminococceae families were consistently depleted while Enterococcus faecalis, Escherichia coli and Staphylococcus aureus were consistently enriched. Further analyses on our samples revealed increased fecal redox potential, decreased total bacterial number and dramatic Methanobrevibacter smithii depletion. Indeed, M. smithii was detected in more than half of the controls but in none of the cases. No causality was demonstrated but, based on our results, we propose a unifying theory linking microbiota specificity, lacking anaerobes and archaea, to low antioxidant nutrients, and lower food conversion.
Collapse
Affiliation(s)
- Matthieu Million
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Dipankar Bachar
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Niokhor Dione
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288 Marseille cedex 9, France
| | - Fabrice Armougom
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Julien Fromonot
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Catherine Robert
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Aldiouma Diallo
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Alexandre Fabre
- Service de pédiatrie multidisciplinaire, hôpital de la Timone Enfant, APHM, Marseille France
- UMR_S 910, Aix-Marseille Université, Marseille, France
| | - Régis Guieu
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Cheikh Sokhna
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288 Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Philippe Parola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
18
|
Armougom F, Bitam I, Croce O, Merhej V, Barassi L, Nguyen TT, La Scola B, Raoult D. Genomic Insights into a New Citrobacter koseri Strain Revealed Gene Exchanges with the Virulence-Associated Yersinia pestis pPCP1 Plasmid. Front Microbiol 2016; 7:340. [PMID: 27014253 PMCID: PMC4793686 DOI: 10.3389/fmicb.2016.00340] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 11/13/2015] [Accepted: 03/03/2016] [Indexed: 01/10/2023] Open
Abstract
The history of infectious diseases raised the plague as one of the most devastating for human beings. Far too often considered an ancient disease, the frequent resurgence of the plague has led to consider it as a reemerging disease in Madagascar, Algeria, Libya, and Congo. The genetic factors associated with the pathogenicity of Yersinia pestis, the causative agent of the plague, involve the acquisition of the pPCP1 plasmid that promotes host invasion through the expression of the virulence factor Pla. The surveillance of plague foci after the 2003 outbreak in Algeria resulted in a positive detection of the specific pla gene of Y. pestis in rodents. However, the phenotypic characterization of the isolate identified a Citrobacter koseri. The comparative genomics of our sequenced C. koseri URMITE genome revealed a mosaic gene structure resulting from the lifestyle of our isolate and provided evidence for gene exchanges with different enteric bacteria. The most striking was the acquisition of a continuous 2 kb genomic fragment containing the virulence factor Pla of the Y. pestis pPCP1 plasmid; however, the subcutaneous injection of the CKU strain in mice did not produce any pathogenic effect. Our findings demonstrate that fast molecular detection of plague using solely the pla gene is unsuitable and should rather require Y. pestis gene marker combinations. We also suggest that the evolutionary force that might govern the expression of pathogenicity can occur through the acquisition of virulence genes but could also require the loss or the inactivation of resident genes such as antivirulence genes.
Collapse
Affiliation(s)
- Fabrice Armougom
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille UniversitéMarseille, France; Centre National de la Recherche Scientifique, IRD, Mediterranean Institute of Oceanography, Aix Marseille Université, Université de Toulon, UM110Marseille, France
| | - Idir Bitam
- Laboratoire VALCORE, Université M'Hamed Bougara Boumerdès Boumerdès, Algeria
| | - Olivier Croce
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| | - Vicky Merhej
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| | - Lina Barassi
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| | - Ti-Thien Nguyen
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| | - Bernard La Scola
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| | - Didier Raoult
- URMITE, Faculté de Médecine, Centre National de la Recherche Scientifique UM63, CNRS 7257, IRD198, Institut National de la Santé et de la Recherche Médicale 1095, Aix-Marseille Université Marseille, France
| |
Collapse
|
19
|
Angelakis E, Armougom F, Carrière F, Bachar D, Laugier R, Lagier JC, Robert C, Michelle C, Henrissat B, Raoult D. A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity. PLoS One 2015; 10:e0137784. [PMID: 26356733 PMCID: PMC4565581 DOI: 10.1371/journal.pone.0137784] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/28/2015] [Indexed: 01/16/2023] Open
Abstract
Background Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques. Methodology/Principal Findings We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05). Conclusions/Significance The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.
Collapse
Affiliation(s)
- Emmanouil Angelakis
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Fabrice Armougom
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Frédéric Carrière
- CNRS, Aix Marseille Université, UMR7282 Enzymology at Interfaces and Physiology of Lipolysis, 13009, Marseille, France
| | - Dipankar Bachar
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - René Laugier
- Hepato-gastroenterology Department, Hôpital de la Timone, Marseille, France
| | - Jean-Christophe Lagier
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Catherine Robert
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Caroline Michelle
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Didier Raoult
- URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France
- * E-mail:
| |
Collapse
|
20
|
Dubourg G, Lagier JC, Robert C, Armougom F, Hugon P, Metidji S, Dione N, Dangui NPM, Pfleiderer A, Abrahao J, Musso D, Papazian L, Brouqui P, Bibi F, Yasir M, Vialettes B, Raoult D. Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics. Int J Antimicrob Agents 2014; 44:117-24. [DOI: 10.1016/j.ijantimicag.2014.04.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 12/20/2022]
|
21
|
Brian-Jaisson F, Ortalo-Magné A, Guentas-Dombrowsky L, Armougom F, Blache Y, Molmeret M. Identification of bacterial strains isolated from the Mediterranean Sea exhibiting different abilities of biofilm formation. Microb Ecol 2014; 68:94-110. [PMID: 24402359 DOI: 10.1007/s00248-013-0342-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 12/02/2013] [Indexed: 05/10/2023]
Abstract
The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.
Collapse
|
22
|
Angelakis E, Million M, Kankoe S, Lagier JC, Armougom F, Giorgi R, Raoult D. Abnormal weight gain and gut microbiota modifications are side effects of long-term doxycycline and hydroxychloroquine treatment. Antimicrob Agents Chemother 2014; 58:3342-7. [PMID: 24687497 PMCID: PMC4068504 DOI: 10.1128/aac.02437-14] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/24/2014] [Indexed: 12/14/2022] Open
Abstract
Doxycycline has been proposed for the treatment of malnourished children in developing countries, and its use has been associated with weight gain in healthy volunteers. No previous studies have assessed abnormal weight gain as a putative side effect of long-term doxycycline treatment; thus, the objective of the present study was to characterize this phenomenon. We also analyzed the role of the gut microbiota in this effect. We assessed changes in the body mass index in Q fever endocarditis patients treated with doxycycline and hydroxychloroquine and healthy individuals with no antibiotic treatment. Abnormal weight gain was defined as a gain in weight above that of the controls. The fecal samples were examined using molecular assays for Methanobrevibacter smithii, Bacteroidetes, Firmicutes, Escherichia coli, Lactobacillus, Lactobacillus reuteri, and total bacterial concentrations. We examined 82 patients, including 48 patients with Q fever endocarditis and 34 controls. Approximately 23% of the treated patients showed abnormal weight gain (P = 0.001). Patients treated with doxycycline and hydroxychloroquine presented significantly lower concentrations of Bacteroidetes (P = 0.002), Firmicutes (P = 0.01), and Lactobacillus (P = 0.02). The linear regression analysis revealed that the duration of treatment was significantly associated with a decrease in Bacteroidetes (P = 0.0001), Firmicutes (P = 0.002), and total bacteria (P < 0.00001). Abnormal weight gain is a side effect of long-term doxycycline and hydroxychloroquine treatment. Gut microbiota modifications at the phylum level could play an instrumental role in this effect. We highlight the need for specific nutritional care in patients undergoing long-term antibiotic treatment, particularly treatment involving the use of doxycycline.
Collapse
Affiliation(s)
- Emmanouil Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, CNRS UMR 7278, IRD 198, Aix-Marseille Université, Marseille, France
| | - Matthieu Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, CNRS UMR 7278, IRD 198, Aix-Marseille Université, Marseille, France
| | - Sallah Kankoe
- UMR 912 SESSTIM, INSERM/IRD/Aix-Marseille Université, Faculté de Médecine, Marseille Cedex, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, CNRS UMR 7278, IRD 198, Aix-Marseille Université, Marseille, France
| | - Fabrice Armougom
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, CNRS UMR 7278, IRD 198, Aix-Marseille Université, Marseille, France
| | - Roch Giorgi
- UMR 912 SESSTIM, INSERM/IRD/Aix-Marseille Université, Faculté de Médecine, Marseille Cedex, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, CNRS UMR 7278, IRD 198, Aix-Marseille Université, Marseille, France
| |
Collapse
|
23
|
|
24
|
Appelt S, Armougom F, Le Bailly M, Robert C, Drancourt M. Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One 2014; 9:e88376. [PMID: 24586319 PMCID: PMC3938422 DOI: 10.1371/journal.pone.0088376] [Citation(s) in RCA: 38] [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: 09/27/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.
Collapse
Affiliation(s)
- Sandra Appelt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Fabrice Armougom
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Matthieu Le Bailly
- Centre national de la recherche scientifique UMR 6249 Chrono-Environnement, Franche-Comté Université, Besançon, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
- * E-mail:
| |
Collapse
|
25
|
El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 2013; 11:497-504. [PMID: 23748339 DOI: 10.1038/nrmicro3050] [Citation(s) in RCA: 997] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.
Collapse
Affiliation(s)
- Abdessamad El Kaoutari
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7257, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
| | | | | | | | | |
Collapse
|
26
|
Pfleiderer A, Lagier JC, Armougom F, Robert C, Vialettes B, Raoult D. Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. Eur J Clin Microbiol Infect Dis 2013; 32:1471-81. [DOI: 10.1007/s10096-013-1900-2] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/16/2013] [Indexed: 12/01/2022]
|
27
|
Colson P, Fancello L, Gimenez G, Armougom F, Desnues C, Fournous G, Yoosuf N, Million M, La Scola B, Raoult D. Evidence of the megavirome in humans. J Clin Virol 2013; 57:191-200. [PMID: 23664726 DOI: 10.1016/j.jcv.2013.03.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/14/2013] [Accepted: 03/29/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Megavirales is a proposed new virus order composed of Mimivirus, Marseillevirus and closely related viruses, as well as members of the families Poxviridae, Iridoviridae, Ascoviridae, Phycodnaviridae and Asfarviridae. The Megavirales virome, which we refer to as the megavirome, has been largely neglected until now because of the use of technical procedures that have jeopardized the discovery of giant viruses, particularly the use of filters with pore sizes in the 0.2-0.45-μm range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia. OBJECTIVES In this paper, we describe the detection of sequences related to Mimivirus and Marseillevirus in the gut microbiota from a young Senegalese man. We also searched for sequences related to Megavirales in human metagenomes publicly available in sequence databases. RESULTS We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups. CONCLUSIONS Overall, we present convergent evidence of the presence of mimiviruses and marseilleviruses in humans. Our findings suggest that we should re-evaluate the human megavirome and investigate the prevalence, diversity and potential pathogenicity of giant viruses in humans.
Collapse
Affiliation(s)
- Philippe Colson
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Cayrou C, Sambe B, Armougom F, Raoult D, Drancourt M. Molecular diversity of the Planctomycetes in the human gut microbiota in France and Senegal. APMIS 2013; 121:1082-90. [PMID: 23594317 DOI: 10.1111/apm.12087] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 08/06/2012] [Accepted: 12/27/2012] [Indexed: 12/30/2022]
Abstract
Until now, Planctomycetes bacteria were considered as environmental organisms. Nevertheless, some studies detected Planctomycetes DNA from human gut. We therefore explored the human gut Planctomycetes content. Planctomycetes-specific PCR primers were designed to amplify a 240-bp 16S rRNA gene fragment in human stool specimens from individuals in France and in Senegal and from endocarditis patients receiving antibiotics in France. PCR products were then cloned and sequenced. PCR detection revealed a significantly higher prevalence (1.8% vs 0.4%, p = 0.05) and higher diversity (62 vs 6 phylotypes, p = 0.02) of Planctomycetes 16S rRNA gene in stool specimens collected in Senegal than in France. Also, stool specimens from endocarditis patients exhibited non-significantly higher prevalence (0.6% vs 0.4%) and the ratio of phylotypes by positive patient (3 vs 1.5) than those collected from untreated French individuals. Gemmata sp. related sequences were found in 6/12 individuals. Planctomycetes organisms are a part of the human digestive tract microbiota. Their diversity varied by environment including the geographical origin of the individual and antibiotics treatment.
Collapse
Affiliation(s)
- Caroline Cayrou
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | | | | | | | | |
Collapse
|
29
|
Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P, Raoult D. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis 2013; 32:637-45. [PMID: 23291779 DOI: 10.1007/s10096-012-1787-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 11/18/2012] [Indexed: 01/19/2023]
Abstract
Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.
Collapse
Affiliation(s)
- G Dubourg
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13005 Marseille, France
| | | | | | | | | | | | | |
Collapse
|
30
|
Dubourg G, Lagier JC, Armougom F, Robert C, Audoly G, Papazian L, Raoult D. High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment. Int J Antimicrob Agents 2013; 41:149-55. [PMID: 23294932 DOI: 10.1016/j.ijantimicag.2012.10.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/22/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
Abstract
The gut microbiota is mainly composed of the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria; the Verrucomicrobia phylum is occasionally observed. Antibiotics can change the bacterial diversity of the gut, with limited changes in the proportions of phyla. In this study, the gut repertoire of two patients who received a broad-spectrum antibiotic regimen was studied. As part of a large gut microbiota study, two stool samples were analysed: one sample was collected after broad-spectrum antibiotic therapy in a patient with Coxiella burnetii vascular infection (Patient A); and the other sample was collected from a patient admitted to the Intensive Care Unit (Patient B). Samples were subjected to Gram staining, electron microscopy, 16S rRNA V6 amplicon pyrosequencing and fluorescence in situ hybridisation (FISH). In parallel, the antibiotic susceptibility of Akkermansia muciniphila Muc(T) strain was studied and this strain was observed by electron microscopy. Pyrosequencing revealed that a large proportion of the sequences were associated with Verrucomicrobia (proportions of 44.9% and 84.6% for Patients A and B, respectively). All of the phylotypes were represented by a single species (A. muciniphila), and neither patient presented significant gastrointestinal disorders. Electron microscopy and FISH with specific Verrucomicrobia probes confirmed the presence of the bacterium. The Muc(T) strain was susceptible to imipenem and doxycycline but resistant to vancomycin and metronidazole. Dramatic colonisation of the human gut microbiota by the Verrucomicrobia phylum following a broad-spectrum antibiotic regimen occurred without significant gastrointestinal manifestations, suggesting that influenced by external factors such as antibiotics, the gut repertoire remains partially unknown.
Collapse
Affiliation(s)
- Grégory Dubourg
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France
| | | | | | | | | | | | | |
Collapse
|
31
|
Lagier JC, Million M, Hugon P, Armougom F, Raoult D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol 2012; 2:136. [PMID: 23130351 PMCID: PMC3487222 DOI: 10.3389/fcimb.2012.00136] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [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: 08/30/2012] [Accepted: 10/16/2012] [Indexed: 12/28/2022] Open
Abstract
The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species, the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea, and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics, or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.
Collapse
Affiliation(s)
- Jean-Christophe Lagier
- URMITE, UM63, CNRS 7278, L'Institut de Recherche pour le Développement 198, INSERM 1095, Aix-Marseille Université Marseille, France
| | | | | | | | | |
Collapse
|
32
|
Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, Trape JF, Koonin EV, La Scola B, Raoult D. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185-93. [PMID: 23033984 DOI: 10.1111/1469-0691.12023] [Citation(s) in RCA: 733] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.
Collapse
Affiliation(s)
- J-C Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012. [DOI: 10.4056/sigs.2685917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jean-Christophe Lagier
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Fabrice Armougom
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Ajay Kumar Mishra
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Thi-Tien Nguyen
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Pierre-Edouard Fournier
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| |
Collapse
|
34
|
Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315-24. [PMID: 23408657 PMCID: PMC3558960 DOI: 10.4056/sigs.2685971] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [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] [Indexed: 12/22/2022] Open
Abstract
Alistipes timonensis strain JC136T sp. nov. is the type strain of A. timonensis sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. A. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742 protein-coding and 50 RNA genes, including three rRNA genes.
Collapse
Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | | | | | | | | | | |
Collapse
|
35
|
Million M, Angelakis E, Paul M, Armougom F, Leibovici L, Raoult D. Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals. Microb Pathog 2012; 53:100-8. [PMID: 22634320 DOI: 10.1016/j.micpath.2012.05.007] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Obesity is associated with alteration of the gut microbiota. In order to clarify the effect of Lactobacillus-containing probiotics (LCP) on weight we performed a meta-analysis of clinical studies and experimental models. We intended to assess effects by Lactobacillus species. METHODS A broad search with no date or language restriction was performed. We included randomized controlled trials (RCTs) and comparative clinical studies in humans and animals or experimental models assessing the effect of Lactobacillus-containing probiotics on weight. We primarily attempted to extract and use change from baseline values. Data were extracted independently by two authors. Results were pooled by host and by Lactobacillus species and are summarized in a meta-analysis of standardized difference in means (SMDs). RESULTS We identified and included 17 RCTs in humans, 51 studies on farm animals and 14 experimental models. Lactobacillus acidophilus administration resulted in significant weight gain in humans and in animals (SMD 0.15; 95% confidence intervals 0.05-0.25). Results were consistent in humans and animals. Lactobacillus fermentum and Lactobacillus ingluviei were associated with weight gain in animals. Lactobacillus plantarum was associated with weight loss in animals and Lactobacillus gasseri was associated with weight loss both in obese humans and in animals. CONCLUSIONS Different Lactobacillus species are associated different effects on weight change that are host-specific. Further studies are needed to clarify the role of Lactobacillus species in the human energy harvest and weight regulation. Attention should be drawn to the potential effects of commonly marketed lactobacillus-containing probiotics on weight gain.
Collapse
Affiliation(s)
- Matthieu Million
- URMITE-CNRS UMR 7278 IRD 198, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | | | | | | | | | | |
Collapse
|
36
|
Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci 2012; 6:116-25. [PMID: 22675604 PMCID: PMC3359877 DOI: 10.4056/sigs.2415480] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [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] [Indexed: 11/20/2022] Open
Abstract
Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate anaerobic coccus. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid) contains 1,721 protein-coding and 53 RNA genes including 5 rRNA genes
Collapse
Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université
| | | | | | | | | | | |
Collapse
|
37
|
Angelakis E, Armougom F, Million M, Raoult D. The relationship between gut microbiota and weight gain in humans. Future Microbiol 2012; 7:91-109. [DOI: 10.2217/fmb.11.142] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
38
|
Leroy Q, Lebrigand K, Armougom F, Barbry P, Thiéry R, Raoult D. Coxiella burnetii transcriptional analysis reveals serendipity clusters of regulation in intracellular bacteria. PLoS One 2010; 5:e15321. [PMID: 21203564 PMCID: PMC3006202 DOI: 10.1371/journal.pone.0015321] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 10/21/2010] [Accepted: 11/05/2010] [Indexed: 11/19/2022] Open
Abstract
Coxiella burnetii, the causative agent of the zoonotic disease Q
fever, is mainly transmitted to humans through an aerosol route. A spore-like
form allows C. burnetii to resist different environmental
conditions. Because of this, analysis of the survival strategies used by this
bacterium to adapt to new environmental conditions is critical for our
understanding of C. burnetii pathogenicity. Here, we report the
early transcriptional response of C. burnetii under temperature
stresses. Our data show that C. burnetii exhibited minor
changes in gene regulation under short exposure to heat or cold shock. While
small differences were observed, C. burnetii seemed to respond
similarly to cold and heat shock. The expression profiles obtained using
microarrays produced in-house were confirmed by quantitative RT-PCR. Under
temperature stresses, 190 genes were differentially expressed in at least one
condition, with a fold change of up to 4. Globally, the differentially expressed
genes in C. burnetii were associated with bacterial division,
(p)ppGpp synthesis, wall and membrane biogenesis and, especially,
lipopolysaccharide and peptidoglycan synthesis. These findings could be
associated with growth arrest and witnessed transformation of the bacteria to a
spore-like form. Unexpectedly, clusters of neighboring genes were differentially
expressed. These clusters do not belong to operons or genetic networks; they
have no evident associated functions and are not under the control of the same
promoters. We also found undescribed but comparable clusters of regulation in
previously reported transcriptomic analyses of intracellular bacteria, including
Rickettsia sp. and Listeria monocytogenes.
The transcriptomic patterns of C. burnetii observed under
temperature stresses permits the recognition of unpredicted clusters of
regulation for which the trigger mechanism remains unidentified but which may be
the result of a new mechanism of epigenetic regulation.
Collapse
Affiliation(s)
- Quentin Leroy
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), UMR
6079 CNRS/UNSA, Sophia Antipolis, France
| | - Fabrice Armougom
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), UMR
6079 CNRS/UNSA, Sophia Antipolis, France
| | - Richard Thiéry
- Unité de Pathologie des Ruminants, Agence Française de
Sécurité Sanitaire des Aliments (AFSSA) Sophia Antipolis,
France
| | - Didier Raoult
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
- * E-mail:
| |
Collapse
|
39
|
Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 2009; 4:e7125. [PMID: 19774074 PMCID: PMC2742902 DOI: 10.1371/journal.pone.0007125] [Citation(s) in RCA: 587] [Impact Index Per Article: 39.1] [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: 06/15/2009] [Accepted: 07/28/2009] [Indexed: 12/11/2022] Open
Abstract
Background Studies of the bacterial communities of the gut microbiota have revealed a shift in the ratio of Firmicutes and Bacteroidetes in obese patients. Determining the variations of microbial communities in feces may be beneficial for the identification of specific profiles in patients with abnormal weights. The roles of the archaeon Methanobrevibacter smithii and Lactobacillus species have not been described in these studies. Methods and Findings We developed an efficient and robust real-time PCR tool that includes a plasmid-based internal control and allows for quantification of the bacterial divisions Bacteroidetes, Firmicutes, and Lactobacillus as well as the methanogen M. smithii. We applied this technique to the feces of 20 obese subjects, 9 patients with anorexia nervosa, and 20 normal-weight healthy controls. Our results confirmed a reduction in the Bacteroidetes community in obese patients (p<0.01). We found a significantly higher Lactobacillus species concentration in obese patients than in lean controls (p = 0.0197) or anorexic patients (p = 0.0332). The M. smithii concentration was much higher in anorexic patients than in the lean population (p = 0.0171). Conclusions Lactobacillus species are widely used as growth promoters in the farm industry and are now linked to obesity in humans. The study of the bacterial flora in anorexic patients revealed an increase in M. smithii. This increase might represent an adaptive use of nutrients in this population.
Collapse
Affiliation(s)
- Fabrice Armougom
- URMITE - UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, Faculté de médecine, Marseille, France
| | - Mireille Henry
- URMITE - UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, Faculté de médecine, Marseille, France
| | - Bernard Vialettes
- Service de Nutrition, Maladies Métaboliques et Endocrinologie, UMR Université méditerranée-INRA U1260, CHU de la Timone, Marseille, France
| | - Denis Raccah
- Nutrition and Diabetology Department, University Hospital Sainte Marguerite, Marseille, France
| | - Didier Raoult
- URMITE - UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, Faculté de médecine, Marseille, France
- * E-mail:
| |
Collapse
|
40
|
Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC, Sarles J, Raoult D, La Scola B. Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Eur J Clin Microbiol Infect Dis 2009; 28:1151-4. [PMID: 19449045 DOI: 10.1007/s10096-009-0749-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 04/15/2009] [Indexed: 01/28/2023]
Abstract
Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.
Collapse
Affiliation(s)
- F Armougom
- URMITE-UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Al Masalma M, Armougom F, Scheld W, Dufour H, Roche P, Drancourt M, Raoult D. The Expansion of the Microbiological Spectrum of Brain Abscesses with Use of Multiple 16S Ribosomal DNA Sequencing. Clin Infect Dis 2009; 48:1169-78. [DOI: 10.1086/597578] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
42
|
|
43
|
Armougom F, Raoult D. Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. BMC Genomics 2008; 9:576. [PMID: 19046425 PMCID: PMC2625370 DOI: 10.1186/1471-2164-9-576] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [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: 06/18/2008] [Accepted: 12/01/2008] [Indexed: 12/20/2022] Open
Abstract
Background Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sanger sequencing approach which is time-consuming and requires laborious data analysis. In contrast, new high-throughput pyrosequencing technology offers an inexpensive alternative to clonal Sanger sequencing and would significantly advance our understanding of obesity via the development of a clinical diagnostic method. Here we present a cost-effective method that combines 16S rRNA pyrosequencing and DNA barcodes of the Firmicutes and Bacteroidetes 16S rRNA genes to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota of obese humans. Results The main result was the identification of DNA barcodes targeting the Firmicutes and Bacteroidetes phyla. These barcodes were validated using previously published 16S rRNA gut microbiota clone libraries. In addition, an accurate F/B ratio was found when the DNA barcodes were applied to short pyrosequencing reads of published gut metagenomes. Finally, the barcodes were utilized to define the F/B ratio of 16S rRNA pyrosequencing data generated from brain abscess pus and cystic fibrosis sputum. Conclusion Using DNA barcodes of Bacteroidetes and Firmicutes 16S rRNA genes combined with pyrosequencing is a cost-effective method for monitoring relevant changes in the relative abundance of Firmicutes and Bacteroidetes bacterial communities in microbial ecosystems.
Collapse
Affiliation(s)
- Fabrice Armougom
- URMITE - UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, Faculté de médecine, Marseille, France.
| | | |
Collapse
|
44
|
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res 2007; 35:W645-8. [PMID: 17526519 PMCID: PMC1933118 DOI: 10.1093/nar/gkm333] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [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] [Indexed: 11/12/2022] Open
Abstract
The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.
Collapse
Affiliation(s)
- Sebastien Moretti
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
| | - Fabrice Armougom
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
| | - Iain M. Wallace
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
| | - Desmond G. Higgins
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
| | - Cornelius V. Jongeneel
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
| | - Cedric Notredame
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France
- *To whom correspondence should be addressed. +33 491 106 486 +33 491 106 489
| |
Collapse
|
45
|
Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C. APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics 2006; 22:2439-40. [PMID: 17032685 DOI: 10.1093/bioinformatics/btl404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local evaluation. Any sequence alignment can be analyzed with APDB provided it includes at least two proteins with known structures. Sequences without a known structure are simply ignored and do not contribute to the scoring procedure. AVAILABILITY APDB is part of the T-Coffee suite of tools for alignment analysis, it is available on www.tcoffee.org. A stand-alone version of the package is also available as a freeware open source from the same address.
Collapse
Affiliation(s)
- Fabrice Armougom
- CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR-13288, Marseille cedex 09, France
| | | | | | | | | | | | | |
Collapse
|
46
|
Moretti S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res 2006; 34:W600-3. [PMID: 16845080 PMCID: PMC1538918 DOI: 10.1093/nar/gkl170] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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] [Indexed: 11/13/2022] Open
Abstract
We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify the gene sequence. This gene sequence is then aligned with the query protein using Exonerate in order to extract a coding nucleotide sequence matching the original protein. Protogene can handle protein fragments and will return every CDS coding for a given protein, even if they occur in different genomes. Protogene is available from .
Collapse
Affiliation(s)
| | | | | | | | | | | | - Cédric Notredame
- To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420;
| |
Collapse
|
47
|
Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res 2006; 34:W604-8. [PMID: 16845081 PMCID: PMC1538866 DOI: 10.1093/nar/gkl092] [Citation(s) in RCA: 377] [Impact Index Per Article: 20.9] [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] [Indexed: 11/14/2022] Open
Abstract
Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on http://www.tcoffee.org/.
Collapse
Affiliation(s)
| | | | | | | | - Pierre Dumas
- Laboratoire de systèmes périphériques, Ecole Polytechnique Fédérale de LausanneCH 1015 Lausanne, Switzerland
| | - Basile Schaeli
- Laboratoire de systèmes périphériques, Ecole Polytechnique Fédérale de LausanneCH 1015 Lausanne, Switzerland
| | | | - Cedric Notredame
- To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420;
| |
Collapse
|
48
|
Abstract
MOTIVATION We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures. RESULTS We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab. AVAILABILITY The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/).
Collapse
Affiliation(s)
- Fabrice Armougom
- Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09
| | | | | | | |
Collapse
|