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Kothe CI, Monnet C, Irlinger F, Virsolvy M, Frühling A, Neumann-Schaal M, Wolf J, Renault P. Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov., isolated from French cheese rinds. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265421 DOI: 10.1099/ijsem.0.006234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Eight Gram-stain-negative bacterial strains were isolated from cheese rinds sampled in France. On the basis of 16S rRNA gene sequence analysis, all isolates were assigned to the genus Halomonas. Phylogenetic investigations, including 16S rRNA gene studies, multilocus sequence analysis, reconstruction of a pan-genome phylogenetic tree with the concatenated core-genome content and average nucleotide identity (ANI) calculations, revealed that they constituted three novel and well-supported clusters. The closest relative species, determined using the whole-genome sequences of the strains, were Halomonas zhanjiangensis for two groups of cheese strains, sharing 82.4 and 93.1 % ANI, and another cluster sharing 92.2 % ANI with the Halomonas profundi type strain. The strains isolated herein differed from the previously described species by ANI values <95 % and several biochemical, enzymatic and colony characteristics. The results of phenotypic, phylogenetic and chemotaxonomic analyses indicated that the isolates belonged to three novel Halomonas species, for which the names Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov. are proposed, with isolates FME63T (=DSM 113315T=CIRM-BIA2430T=CIP 111880T=LMG 32013T), FME64T (=DSM 113316T=CIRM-BIA2431T=CIP 111877T=LMG 32015T) and FME66T (=DSM 113318T=CIRM-BIA2433T=CIP 111876T=LMG 32014T) as type strains, respectively.
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Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christophe Monnet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Françoise Irlinger
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Mathieu Virsolvy
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Anja Frühling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Ammoun I, Kothe CI, Mohellibi N, Beal C, Yaacoub R, Renault P. Lebanese fermented goat milk products: From tradition to meta-omics. Food Res Int 2023; 168:112762. [PMID: 37120212 DOI: 10.1016/j.foodres.2023.112762] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.
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Affiliation(s)
- I Ammoun
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Lebanese Agricultural Research Institute (LARI), Milk and Milk Products Department, Fanar, Lebanon
| | - C I Kothe
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - N Mohellibi
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| | - C Beal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120, Palaiseau, France
| | - R Yaacoub
- Lebanese University, Faculty of Agricultural and Veterinary Sciences, Food Science and Technology Department, Dekwaneh, Lebanon
| | - P Renault
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France.
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Michel E, Néel MC, Capowiez Y, Sammartino S, Lafolie F, Renault P, Pelosi C. Making Waves: Modeling bioturbation in soils - are we burrowing in the right direction? Water Res 2022; 216:118342. [PMID: 35349922 DOI: 10.1016/j.watres.2022.118342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The burrowing, feeding and foraging activities of terrestrial and benthic organisms induce displacements of soil and sediment materials, leading to a profound mixing of these media. Such particle movements, called "sediment reworking" in aquatic environments and "bioturbation" in soils, have been thoroughly studied and modeled in sediments, where they affect organic matter mineralization and contaminant fluxes. In comparison, studies characterizing the translocation, by soil burrowers, of mineral particles, organic matter and adsorbed contaminants are paradoxically fewer. Nevertheless, models borrowed from aquatic ecology are used to predict the impact of bioturbation on organic matter turnover and contaminant transport in the soil. However, these models are based on hypotheses that have not been tested with adequate observations in soils, and may not necessarily reflect the actual impact of soil burrowers on particle translocation. This paper aims to (i) highlight the possible shortcomings linked to the current use of sediment reworking models for soils, (ii) identify how recent progresses in aquatic ecology could help to circumvent these limitations, and (iii) propose key steps to ensure that soil bioturbation models are built on solid foundations: more accurate models of organic matter turnover, soil evolution and contaminant transport in the soil are at stake.
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Affiliation(s)
- Eric Michel
- EMMAH, INRAE, Avignon Université, 84000 Avignon, France.
| | | | - Yvan Capowiez
- EMMAH, INRAE, Avignon Université, 84000 Avignon, France
| | | | | | | | - Céline Pelosi
- EMMAH, INRAE, Avignon Université, 84000 Avignon, France.
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Papadimitriou K, Kline K, Renault P, Kok J. Editorial: Omics and Systems Approaches to Study the Biology and Applications of Lactic Acid Bacteria. Front Microbiol 2020; 11:1786. [PMID: 32973691 PMCID: PMC7468460 DOI: 10.3389/fmicb.2020.01786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - Kimberly Kline
- Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pierre Renault
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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Aka S, Dridi B, Bolotin A, Yapo EA, Koussemon-Camara M, Bonfoh B, Renault P. Characterization of lactic acid bacteria isolated from a traditional Ivoirian beer process to develop starter cultures for safe sorghum-based beverages. Int J Food Microbiol 2020; 322:108547. [PMID: 32097827 DOI: 10.1016/j.ijfoodmicro.2020.108547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/13/2019] [Accepted: 01/31/2020] [Indexed: 12/31/2022]
Abstract
The present study aimed to characterize lactic acid bacteria involved in the different processing steps of tchapalo, a traditional Ivoirian beverage, for their potential application as starter cultures in food and beverages. Lactic acid bacteria (LAB) were therefore isolated and enumerated at different steps of the process on MRS and BEA agars. Of the 465 isolates, 27 produced bacteriocins that inhibit Lactobacillus delbrueckii F/31 strain. Of those, two also inhibited Listeria innocua ATCC 33090, while two others displayed inhibitory activity against L.innocua ATCC 33090, E. faecalis CIP 105042, E. faecalis ATCC 29212, Streptococcus sp. clinical LNSP, E. faecalis CIP 105042 and E. faecium ATCC 51558. The dominant species involved in tchapalo LAB fermentation, as determined by 16S rRNA gene sequencing, were Lactobacillus fermentum (64%), followed by Pediococcus acidilactici (14%). Two strains representing the two dominant species, L. fermentum S6 and P. acidilactici S7, and two potential bacteriocin producers, Weissella confusa AB3E41 and Enterococcus faecium AT1E22, were selected for further characterization. First, genome analysis showed that these strains do not display potential harmful genes such as pathogenic factors or transmissible antibiotic resistance genes. Furthermore, phylogenetic analyses were performed to assess evidence of eventual links to groups of strains with particular properties. They revealed that (i) L. fermentum S6 and P. acidilactici S7 are closely related to strains that ferment plants, (ii) E. faecium AT1E22 belongs to the environmental clade B of E. faecium, while W. confusa is quite similar to other strains also isolated from plant fermentations. Further genome analysis showed that E. faecium AT1E22 contains the Enterocin P gene probably carried by a megaplasmid, whereas no evidence of a bacteriocin gene was found in W. confusa AB3E41. The metabolic and the first step of the probiotic potentials of the different strains were analyzed. Lactobacillus fermentum S6 and P. acidilactici S7 are good candidates to develop starter cultures, and E. faecium AT1E22 should be further tested to confirm its potential as a probiotic strain in the production of sorghum wort.
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Affiliation(s)
- Solange Aka
- UFR des Sciences et Technologies des Aliments, Université Nangui Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), BP 1303 Abidjan 01, Côte d'Ivoire.
| | - Bedis Dridi
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alexandre Bolotin
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Elysée Armel Yapo
- UFR des Sciences et Technologies des Aliments, Université Nangui Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), BP 1303 Abidjan 01, Côte d'Ivoire
| | - Marina Koussemon-Camara
- UFR des Sciences et Technologies des Aliments, Université Nangui Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), BP 1303 Abidjan 01, Côte d'Ivoire
| | - Pierre Renault
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Gboko KDT, Traoré SG, Sanhoun AR, Kirioua J, Otaru N, Kurt F, Jaeger FN, Isenring J, Kaindi DWM, Kreikemeyer B, Renault P, Hattendorf J, Meile L, Jans C, Nguetta R, Bonfoh B. Risk factors for the carriage of Streptococcus infantarius subspecies infantarius isolated from African fermented dairy products. PLoS One 2019; 14:e0225452. [PMID: 31774832 PMCID: PMC6881063 DOI: 10.1371/journal.pone.0225452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/05/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii) has been identified as predominant lactic acid bacteria in spontaneously fermented dairy products (FDPs) in sub-Saharan Africa including Côte d'Ivoire. However, Sii belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Most SBSEC members are assumed to be involved as opportunistic pathogens in serious diseases in both humans and animals. A population-based cross-sectional survey, including 385 participants was conducted in Korhogo, northern Côte d'Ivoire, to identify risk factors for Sii fecal carriage, including consumption of local FDPs. A structured questionnaire was used to gather participant's socio-demographic and economic characteristics, their relation to livestock and dietary habits. In addition, fresh stool and milk samples were collected. The identification of Sii was done using a SBSEC-specific PCR assay targeting 16S rRNA and groEL genes. The overall prevalence of SBSEC and Sii carriage was 23.2% (confidence interval CI 95% = 18.9-27.5) and 12.0% (CI 95% = 8.4-15.5) for stool, respectively. Prevalence of Sii was significantly higher in consumers of artisanal butter compared with non-consumers (57.1% vs 10.1%, odds ratio OR: 11.9, 95% CI: 3.9-36.6), as well as in persons handling livestock (OR = 3.9; 95% CI = 1.6-9.3) and livestock primary products (OR = 5.7; 95% CI = 2.3-14.3). The closer contact with livestock was a risk factor for Sii fecal carriage. Sii strains were isolated from fresh and fermented milk products with a prevalence of 30.4% and 45.4%, respectively. Analysis of Sii population structure through the SBSEC multi locus sequence typing assay revealed a close relationship across human and dairy isolates, possibly linked to a Kenyan human isolate. All these outcomes underline the interest of in-depth investigations on the ecology, potential reservoirs and pathways of contamination by Sii at the human-animal-environment interface in comparison to yet to be collected data from Europe, Asia and the Americas to further elucidate the various roles of Sii.
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Affiliation(s)
- Kossia D T Gboko
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire
| | - Sylvain G Traoré
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Aimé R Sanhoun
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Jérôme Kirioua
- University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Nize Otaru
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne Kurt
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne N Jaeger
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Dasel W M Kaindi
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Roland Nguetta
- Institut de cardiologie d'Abidjan (ICA), Abidjan, Côte d'Ivoire.,Université Felix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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7
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Baize N, Monnet I, Greillier L, Geier M, Lena H, Janicot H, Vergnenegre A, Crequit J, Lamy R, Auliac J, Le Treut J, Le Caer H, Gervais R, Dansin E, Madroszyk A, Renault P, Legarff G, Schott R, Saulnier P, Chouaid C. OA15.02 Carboplatin-Etoposide Versus Topotecan as Second-Line Treatment for Sensitive Relapsed Small-Cell Lung Cancer: Phase 3 Trial. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Renault P, Rouchet S. Transient global amnesia and transient cortical blindness secondary to contrast induced encephalopathy after renal artery angiography. Rev Neurol (Paris) 2019; 175:335-336. [DOI: 10.1016/j.neurol.2018.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/02/2018] [Accepted: 08/26/2018] [Indexed: 10/27/2022]
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Tesson V, Belliot G, Estienney M, Wurtzer S, Renault P. Vomiting symptom of acute gastroenteritis estimated from epidemiological data can help predict river contamination by human pathogenic enteric viruses. Environ Int 2019; 123:114-123. [PMID: 30508731 DOI: 10.1016/j.envint.2018.11.058] [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] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Contamination of fresh water bodies by human enteric viruses from wastewater discharge is a well-established phenomenon. Here we propose a model of viral contamination of rivers based on acute gastroenteritis epidemiology and assess how well it can simulate in situ experimental monitoring. Noroviruses, rotaviruses, enteroviruses, adenoviruses and hepatitis A viruses were quantified by molecular methods after water concentration. Water flows were obtained from the Hydro databank and wastewater treatment plant (WWTP) data. Acute gastroenteritis cases based on medical prescriptions were recorded by the French public health agency. We estimated the total number of daily viral acute gastroenteritis cases and modeled virus shedding and fate in WWTPs and rivers. Simulated virus concentrations were compared to the weighted sum of measured concentrations. Seasonal variations in viral acute gastroenteritis were predicted from vomiting occurrence. All viruses except hepatitis A virus were widely detected in wastewaters and river, in concentrations reaching 10+6 genome copies·L-1 for adenoviruses in the Artière River. We were able to predict virus load in raw wastewater and in the Artière River. Estimated weighting coefficients showed the high impact of noroviruses GII. This model can thus serve to compare water treatment, discharge and reuse scenarios.
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Affiliation(s)
- Vincent Tesson
- INRA, UMR 1114 EMMAH, 228 route de l'Aérodrome, CS 40 509, 84914 Avignon Cedex 9, France
| | - Gaël Belliot
- CNR des Virus des Gastro-Entérites, CHU François Mitterrand, 2 rue Angélique Ducoudray, BP37013, 21070 Dijon Cedex, France; Université de Bourgogne/AgroSup Dijon, UMR PAM A 02.102, 7 boulevard Jeanne-d'Arc, 21000 Dijon, France
| | - Marie Estienney
- CNR des Virus des Gastro-Entérites, CHU François Mitterrand, 2 rue Angélique Ducoudray, BP37013, 21070 Dijon Cedex, France
| | - Sébastien Wurtzer
- Eau de Paris, DRDQE, R&D Biologie, 33 avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
| | - Pierre Renault
- INRA, UMR 1114 EMMAH, 228 route de l'Aérodrome, CS 40 509, 84914 Avignon Cedex 9, France.
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10
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Kaindi DWM, Kogi-Makau W, Lule GN, Kreikemeyer B, Renault P, Bonfoh B, Otaru N, Schmid T, Meile L, Hattendorf J, Jans C. Colorectal cancer-associated Streptococcus infantarius subsp. infantarius differ from a major dairy lineage providing evidence for pathogenic, pathobiont and food-grade lineages. Sci Rep 2018; 8:9181. [PMID: 29907746 PMCID: PMC6003927 DOI: 10.1038/s41598-018-27383-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii), a member of the Streptococcus bovis/Streptococcus equinus complex (SBSEC), predominates as dairy-adapted and non-adapted variants in fermented dairy products (FDP) in East and West Africa. Epidemiologic data suggest an association with colorectal cancer for most SBSEC members, including Sii from Kenyan patients. Phylogenetic relationships of East African human (EAH) isolates to those of dairy and pathogenic origin were analysed to better estimate potential health implications via FDP consumption. The MLST-derived population structure was also evaluated to provide host, disease, geography and dairy adaptation associations for 157 SBSEC isolates, including 83 novel Sii/SBSEC isolates of which 40 originated from Kenyan colonoscopy patients. Clonal complex (CC) 90 was delineated as potential pathogenic CC for Sii. Single EAH, West African dairy (WAD), food and animal Sii isolates clustered within CC-90, suggesting a potential link to pathogenic traits for CC-90. The majority of EAH and WAD Sii were clustered in a shared clade distinct from CC-90 and East African dairy (EAD) isolates. This indicates shared ancestry for the EAH and WAD clade and limitations to translate disease associations of EAH and CC-90 to EAD Sii, which could support the separation of pathogenic, pathobiont/commensal and food lineages.
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Affiliation(s)
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | | | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Adiopodoume, Ivory Coast
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nize Otaru
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Thomas Schmid
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland.
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Couvigny B, Kulakauskas S, Pons N, Quinquis B, Abraham AL, Meylheuc T, Delorme C, Renault P, Briandet R, Lapaque N, Guédon E. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Front Microbiol 2018. [PMID: 29515553 PMCID: PMC5826255 DOI: 10.3389/fmicb.2018.00273] [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] [Indexed: 12/12/2022] Open
Abstract
Biofilm formation is crucial for bacterial community development and host colonization by Streptococcus salivarius, a pioneer colonizer and commensal bacterium of the human gastrointestinal tract. This ability to form biofilms depends on bacterial adhesion to host surfaces, and on the intercellular aggregation contributing to biofilm cohesiveness. Many S. salivarius isolates auto-aggregate, an adhesion process mediated by cell surface proteins. To gain an insight into the genetic factors of S. salivarius that dictate host adhesion and biofilm formation, we developed a screening method, based on the differential sedimentation of bacteria in semi-liquid conditions according to their auto-aggregation capacity, which allowed us to identify twelve mutations affecting this auto-aggregation phenotype. Mutations targeted genes encoding (i) extracellular components, including the CshA surface-exposed protein, the extracellular BglB glucan-binding protein, the GtfE, GtfG and GtfH glycosyltransferases and enzymes responsible for synthesis of cell wall polysaccharides (CwpB, CwpK), (ii) proteins responsible for the extracellular localization of proteins, such as structural components of the accessory SecA2Y2 system (Asp1, Asp2, SecA2) and the SrtA sortase, and (iii) the LiaR transcriptional response regulator. These mutations also influenced biofilm architecture, revealing that similar cell-to-cell interactions govern assembly of auto-aggregates and biofilm formation. We found that BglB, CshA, GtfH and LiaR were specifically associated with bacterial auto-aggregation, whereas Asp1, Asp2, CwpB, CwpK, GtfE, GtfG, SecA2 and SrtA also contributed to adhesion to host cells and host-derived components, or to interactions with the human pathogen Fusobacterium nucleatum. Our study demonstrates that our screening method could also be used to identify genes implicated in the bacterial interactions of pathogens or probiotics, for which aggregation is either a virulence trait or an advantageous feature, respectively.
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Affiliation(s)
- Benoit Couvigny
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Saulius Kulakauskas
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nicolas Pons
- MetaGenoPoliS, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benoit Quinquis
- MetaGenoPoliS, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Thierry Meylheuc
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,INRA, Plateforme MIMA2, Jouy-en-Josas, France
| | - Christine Delorme
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pierre Renault
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nicolas Lapaque
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eric Guédon
- STLO, UMR 1253, INRA, Agrocampus Ouest, Rennes, France
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12
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Isenring J, Köhler J, Nakata M, Frank M, Jans C, Renault P, Danne C, Dramsi S, Kreikemeyer B, Oehmcke-Hecht S. Streptococcus gallolyticus subsp. gallolyticus endocarditis isolate interferes with coagulation and activates the contact system. Virulence 2017; 9:248-261. [PMID: 29072555 PMCID: PMC5955193 DOI: 10.1080/21505594.2017.1393600] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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] [Indexed: 12/30/2022] Open
Abstract
Streptococcus gallolyticus subsp. gallolyticus, formerly classified as S. bovis biotype I, is an increasing cause of bacteremia and infective endocarditis in the elderly. The physiopathology of infective endocarditis is poorly understood and involves immune and coagulation systems. In this study, we found that S. gallolyticus subsp. gallolyticus activates the human contact system, which in turn has two consequences: cleavage of high-molecular-weight kininogen (HK) resulting in release of the potent pro-inflammatory peptide bradykinin, and initiation of the intrinsic pathway of coagulation. S. gallolyticus subsp. gallolyticus was found to bind and activate factors of the human contact system at its surface, leading to a significant prolongation of the intrinsic coagulation time and to the release of bradykinin. High-affinity binding of factor XII to the bacterial Pil1 collagen binding protein was demonstrated with a KD of 13 nM. Of note, Pil1 expression was exclusively found in S. gallolyticus subsp. gallolyticus, further supporting an essential contribution of this pilus in virulence.
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Affiliation(s)
- Julia Isenring
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany.,b Nutrition and Health, Laboratory of Food Biotechnology, Institute of Food, ETH Zürich , Zürich , Switzerland
| | - Juliane Köhler
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
| | - Masanobu Nakata
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany.,c Department of Oral and Molecular Microbiology , Osaka University Graduate School of Dentistry , Suita , Osaka , Japan
| | - Marcus Frank
- d Medical Biology and Electron Microscopy Centre, Rostock University Medical Center , Rostock , Germany
| | - Christoph Jans
- b Nutrition and Health, Laboratory of Food Biotechnology, Institute of Food, ETH Zürich , Zürich , Switzerland
| | - Pierre Renault
- e Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Camille Danne
- f Unité de Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur , Paris , France , Centre National de la Recherche Scientifique (CNRS) ERL3526
| | - Shaynoor Dramsi
- f Unité de Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur , Paris , France , Centre National de la Recherche Scientifique (CNRS) ERL3526
| | - Bernd Kreikemeyer
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
| | - Sonja Oehmcke-Hecht
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
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13
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Courault D, Albert I, Perelle S, Fraisse A, Renault P, Salemkour A, Amato P. Assessment and risk modeling of airborne enteric viruses emitted from wastewater reused for irrigation. Sci Total Environ 2017; 592:512-526. [PMID: 28320526 DOI: 10.1016/j.scitotenv.2017.03.105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 12/23/2016] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 04/13/2023]
Abstract
Reclamation of wastewater (WW) for irrigation, after treatment represents a challenge that could alleviate pressure on water resources and address the increasing demand for agriculture. However, the risks to human health must be assessed, particularly those related to human enteric viruses that resist standard treatments in most wastewater treatment plants (WWTP). The risks associated with exposure to viral bioaerosols near WWTP and near agricultural plots irrigated with WW are poorly documented. The objectives of this study were to 1) better characterize human enteric viruses found in bioaerosols near a "standard WWTP" and over fields irrigated with treated WW and 2) propose a numeric model to assess the health risk to populations located close to the irrigated areas, with particular attention to norovirus, which is responsible for most viral gastroenteritis in France. Water and air samples were collected at various locations in the largest French WW-irrigated site near Clermont-Ferrand, at the WWTP entrance and after treatment, in the air above activated sludge basins, and above fields irrigated with WW. Various enteric viruses were found in the water samples collected both before and after treatment. Norovirus was the most abundant with >10e4 genome copies/l (GC/L) before treatment and ~10e3 GC/L after treatment. Low quantities (<10e3GC/m3) were detected in the air above active sludge pools and irrigated plots. Hepatitis E virus was detected in all sampled compartments. A quantitative microbial risk assessment (QMRA) approach, including a simplified atmospheric dispersion model, allowed assessment of norovirus infection risk. The Bayesian QMRA approach considered wind speed measurements over 21years, and the variability and uncertainty of all measurements throughout the chain up to the risk. The probability of infection within one year for the most exposed WWTP employees was >10e-4 for strong wind speed (≥3m/s) and a constant emission rate of 8e3 GC/m3/s. This probability decreases by 3 log when the distance to the emission source is doubled. This information can aid development of safe water reuse policies in terms of local setback distance and wind conditions for wastewater reuse.
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Affiliation(s)
- D Courault
- UMR 1114 EMMAH, INRA, Université d'Avignon et des Pays du Vaucluse, Domaine St Paul, 84914 Avignon, France.
| | - I Albert
- UMR 518, Math-Info Appliquées, INRA-AgroParisTech 16, rue Claude Bernard, 75231 Paris Cedex 5, France
| | - S Perelle
- Université Paris Est, ANSES, Maisons-Alfort Laboratory for food safety, F-94701 Maisons-Alfort, France
| | - A Fraisse
- Université Paris Est, ANSES, Maisons-Alfort Laboratory for food safety, F-94701 Maisons-Alfort, France
| | - P Renault
- UMR 1114 EMMAH, INRA, Université d'Avignon et des Pays du Vaucluse, Domaine St Paul, 84914 Avignon, France
| | - A Salemkour
- UMR 1114 EMMAH, INRA, Université d'Avignon et des Pays du Vaucluse, Domaine St Paul, 84914 Avignon, France; UMR 518, Math-Info Appliquées, INRA-AgroParisTech 16, rue Claude Bernard, 75231 Paris Cedex 5, France
| | - P Amato
- UMR 6296, ICCF Université B Pascal, 24 av des landais, 63171 Aubière, France
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14
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Couvigny B, Lapaque N, Rigottier-Gois L, Guillot A, Chat S, Meylheuc T, Kulakauskas S, Rohde M, Mistou MY, Renault P, Doré J, Briandet R, Serror P, Guédon E. Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium,Streptococcus salivarius. Environ Microbiol 2017; 19:3579-3594. [DOI: 10.1111/1462-2920.13853] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Benoit Couvigny
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Nicolas Lapaque
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Lionel Rigottier-Gois
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alain Guillot
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Sophie Chat
- INRA, Plateforme MIMA2; Jouy-en-josas France
| | - Thierry Meylheuc
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
- INRA, Plateforme MIMA2; Jouy-en-josas France
| | - Saulius Kulakauskas
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Manfred Rohde
- HZI, Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Michel-Yves Mistou
- Laboratory for Food Safety; Université Paris-Est, ANSES; Maisons-Alfort France
| | - Pierre Renault
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Joel Doré
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Romain Briandet
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Pascale Serror
- MICALIS Institute, INRA, AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Eric Guédon
- STLO, UMR1253, INRA, Agrocampus Ouest; Rennes France
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15
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Jans C, Meile L, Kaindi DWM, Kogi-Makau W, Lamuka P, Renault P, Kreikemeyer B, Lacroix C, Hattendorf J, Zinsstag J, Schelling E, Fokou G, Bonfoh B. African fermented dairy products - Overview of predominant technologically important microorganisms focusing on African Streptococcus infantarius variants and potential future applications for enhanced food safety and security. Int J Food Microbiol 2017; 250:27-36. [PMID: 28364623 DOI: 10.1016/j.ijfoodmicro.2017.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 11/17/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022]
Abstract
Milk is a major source of nutrients, but can also be a vehicle for zoonotic foodborne diseases, especially when raw milk is consumed. In Africa, poor processing and storage conditions contribute to contamination, outgrowth and transmission of pathogens, which lead to spoilage, reduced food safety and security. Fermentation helps mitigate the impact of poor handling and storage conditions by enhancing shelf life and food safety. Traditionally-fermented sour milk products are culturally accepted and widely distributed in Africa, and rely on product-specific microbiota responsible for aroma, flavor and texture. Knowledge of microbiota and predominant, technologically important microorganisms is critical in developing products with enhanced quality and safety, as well as sustainable interventions for these products, including Africa-specific starter culture development. This narrative review summarizes current knowledge of technologically-important microorganisms of African fermented dairy products (FDP) and raw milk, taking into consideration novel findings and taxonomy when re-analyzing data of 29 publications covering 25 products from 17 African countries. Technologically-important lactic acid bacteria such as Lactococcus lactis and Streptococcus infantarius subsp. infantarius (Sii), Lactobacillus spp. and yeasts predominated in raw milk and FDP across Africa. Re-analysis of data also suggests a much wider distribution of Sii and thus a potentially longer history of use than previously expected. Therefore, evaluating the role and safety of African Sii lineages is important when developing interventions and starter cultures for FDP in Africa to enhance food safety and food security. In-depth functional genomics, epidemiologic investigations and latest identification approaches coupled with stakeholder involvement will be required to evaluate the possibility of African Sii lineages as novel food-grade Streptococcus lineage.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Peter Lamuka
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Schillingallee 70, 18055 Rostock, Germany
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Esther Schelling
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Gilbert Fokou
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Km 17, Adiopodoumé, Rte Dabou, 01 BP 1303 Abidjan 01, Côte d'Ivoire
| | - Bassirou Bonfoh
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Km 17, Adiopodoumé, Rte Dabou, 01 BP 1303 Abidjan 01, Côte d'Ivoire.
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16
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Delorme C, Legravet N, Jamet E, Hoarau C, Alexandre B, El-Sharoud WM, Darwish MS, Renault P. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme. Int J Food Microbiol 2016; 242:70-81. [PMID: 27894009 DOI: 10.1016/j.ijfoodmicro.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/27/2023]
Abstract
We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.
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Affiliation(s)
- Christine Delorme
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nicolas Legravet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuel Jamet
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Caroline Hoarau
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Bolotin Alexandre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Walid M El-Sharoud
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Mohamed S Darwish
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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17
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Nguyen-The C, Bardin M, Berard A, Berge O, Brillard J, Broussolle V, Carlin F, Renault P, Tchamitchian M, Morris CE. Agrifood systems and the microbial safety of fresh produce: Trade-offs in the wake of increased sustainability. Sci Total Environ 2016; 562:751-759. [PMID: 27110986 DOI: 10.1016/j.scitotenv.2016.03.241] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Fresh produce has been a growing cause of food borne outbreaks world-wide prompting the need for safer production practices. Yet fresh produce agrifood systems are diverse and under constraints for more sustainability. We analyze how measures taken to guarantee safety interact with other objectives for sustainability, in light of the diversity of fresh produce agrifood systems. The review is based on the publications at the interface between fresh produce safety and sustainability, with sustainability defined by low environmental impacts, food and nutrition security and healthy life. The paths for more sustainable fresh produce are diverse. They include an increased use of ecosystem services to e.g. favor predators of pests, or to reduce impact of floods, to reduce soil erosion, or to purify run-off waters. In contrast, they also include production systems isolated from the environment. From a socio-economical view, sustainability may imply maintaining small tenures with a higher risk of pathogen contamination. We analyzed the consequences for produce safety by focusing on risks of contamination by water, soil, environment and live stocks. Climate change may increase the constraints and recent knowledge on interactions between produce and human pathogens may bring new solutions. Existing technologies may suffice to resolve some conflicts between ensuring safety of fresh produce and moving towards more sustainability. However, socio-economic constraints of some agri-food systems may prevent their implementation. In addition, current strategies to preserve produce safety are not adapted to systems relying on ecological principles and knowledge is lacking to develop the new risk management approaches that would be needed.
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Affiliation(s)
- Christophe Nguyen-The
- UMR408 SQPOV «Sécurité et Qualité des Produits d'Origine Végétale», INRA, Avignon Université, 84000 Avignon, France.
| | - Marc Bardin
- INRA, UR0407 Plant Pathology, F-84143 Montfavet, France.
| | | | - Odile Berge
- INRA, UR0407 Plant Pathology, F-84143 Montfavet, France.
| | - Julien Brillard
- UMR408 SQPOV «Sécurité et Qualité des Produits d'Origine Végétale», INRA, Avignon Université, 84000 Avignon, France.
| | - Véronique Broussolle
- UMR408 SQPOV «Sécurité et Qualité des Produits d'Origine Végétale», INRA, Avignon Université, 84000 Avignon, France.
| | - Frédéric Carlin
- UMR408 SQPOV «Sécurité et Qualité des Produits d'Origine Végétale», INRA, Avignon Université, 84000 Avignon, France.
| | | | | | - Cindy E Morris
- INRA, UR0407 Plant Pathology, F-84143 Montfavet, France.
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18
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Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud T, Brygoo Y. Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun 2015; 5:2876. [PMID: 24407037 PMCID: PMC3896755 DOI: 10.1038/ncomms3876] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/06/2013] [Indexed: 02/01/2023] Open
Abstract
While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti—called Wallaby—present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes. Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region.
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Affiliation(s)
- Kevin Cheeseman
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France; Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- LIMP Toulouse, INRA/CNRS, INRA, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France; INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France
| | - Antoine Branca
- Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Anne-Laure Abraham
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Maurizio Ceppi
- Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France
| | | | - Robert Debuchy
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; CNRS, Institut de Génétique et Microbiologie UMR8621, 91405 Orsay, France
| | - Fabienne Malagnac
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; Univ Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), 75205 Paris, France
| | - Anne Goarin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France
| | - Philippe Silar
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; Univ Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), 75205 Paris, France
| | - Sandrine Lacoste
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Erika Sallet
- LIMP Toulouse, INRA/CNRS, INRA, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France; INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France
| | - Aaron Bensimon
- Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France
| | - Tatiana Giraud
- Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Yves Brygoo
- 13 ruelle d'Aigrefoin 78470 St Rémy-lès-Chevreuse
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Couvigny B, Thérial C, Gautier C, Renault P, Briandet R, Guédon E. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life? PLoS One 2015; 10:e0128099. [PMID: 26035177 PMCID: PMC4452758 DOI: 10.1371/journal.pone.0128099] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 04/23/2015] [Indexed: 12/27/2022] Open
Abstract
Microorganisms have a long history of use in food production and preservation. Their adaptation to food environments has profoundly modified their features, mainly through genomic flux. Streptococcus thermophilus, one of the most frequent starter culture organisms consumed daily by humans emerged recently from a commensal ancestor. As such, it is a useful model for genomic studies of bacterial domestication processes. Many streptococcal species form biofilms, a key feature of the major lifestyle of these bacteria in nature. However, few descriptions of S. thermophilus biofilms have been reported. An analysis of the ability of a representative collection of natural isolates to form biofilms revealed that S. thermophilus was a poor biofilm producer and that this characteristic was associated with an inability to attach firmly to surfaces. The identification of three biofilm-associated genes in the strain producing the most biofilms shed light on the reasons for the rarity of this trait in this species. These genes encode proteins involved in crucial stages of biofilm formation and are heterogeneously distributed between strains. One of the biofilm genes appears to have been acquired by horizontal transfer. The other two are located in loci presenting features of reductive evolution, and are absent from most of the strains analyzed. Their orthologs in commensal bacteria are involved in adhesion to host cells, suggesting that they are remnants of ancestral functions. The biofilm phenotype appears to be a commensal trait that has been lost during the genetic domestication of S. thermophilus, consistent with its adaptation to the milk environment and the selection of starter strains for dairy fermentations.
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Affiliation(s)
- Benoit Couvigny
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Claire Thérial
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Céline Gautier
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Pierre Renault
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Romain Briandet
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Eric Guédon
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
- * E-mail:
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20
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Papadimitriou K, Anastasiou R, Maistrou E, Plakas T, Papandreou NC, Hamodrakas SJ, Ferreira S, Supply P, Renault P, Pot B, Tsakalidou E. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One 2015; 10:e0116337. [PMID: 25584532 PMCID: PMC4293149 DOI: 10.1371/journal.pone.0116337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 03/03/2013] [Accepted: 12/05/2014] [Indexed: 12/22/2022] Open
Abstract
Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- * E-mail:
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Eleni Maistrou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Thomas Plakas
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Nikos C. Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stéphanie Ferreira
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
| | - Philip Supply
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, F-78352, France
| | - Bruno Pot
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Almeida M, Hébert A, Abraham AL, Rasmussen S, Monnet C, Pons N, Delbès C, Loux V, Batto JM, Leonard P, Kennedy S, Ehrlich SD, Pop M, Montel MC, Irlinger F, Renault P. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics 2014; 15:1101. [PMID: 25496341 PMCID: PMC4320590 DOI: 10.1186/1471-2164-15-1101] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [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: 06/20/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022] Open
Abstract
Background Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. Results We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Conclusions Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, 78352 Jouy-en-Josas, France.
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22
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Delorme C, Abraham AL, Renault P, Guédon E. Genomics of Streptococcus salivarius, a major human commensal. Infect Genet Evol 2014; 33:381-92. [PMID: 25311532 DOI: 10.1016/j.meegid.2014.10.001] [Citation(s) in RCA: 37] [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] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/30/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022]
Abstract
The salivarius group of streptococci is of particular importance for humans. This group consists of three genetically similar species, Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus. S. salivarius and S. vestibularis are commensal organisms that may occasionally cause opportunistic infections in humans, whereas S. thermophilus is a food bacterium widely used in dairy production. We developed Multilocus sequence typing (MLST) and comparative genomic analysis to confirm the clear separation of these three species. These analyses also identified a subgroup of four strains, with a core genome diverging by about 10%, in terms of its nucleotide sequence, from that of S. salivarius sensu stricto. S. thermophilus species displays a low level of nucleotide variability, due to its recent emergence with the development of agriculture. By contrast, nucleotide variability is high in the other two species of the salivarius group, reflecting their long-standing association with humans. The species of the salivarius group have genome sizes ranging from the smallest (∼ 1.7 Mb for S. thermophilus) to the largest (∼ 2.3 Mb for S. salivarius) among streptococci, reflecting genome reduction linked to a narrow, nutritionally rich environment for S. thermophilus, and natural, more competitive niches for the other two species. Analyses of genomic content have indicated that the core genes of S. salivarius account for about two thirds of the genome, indicating considerable variability of gene content and differences in potential adaptive features. Furthermore, we showed that the genome of this species is exceptionally rich in genes encoding surface factors, glycosyltransferases and response regulators. Evidence of widespread genetic exchanges was obtained, probably involving a natural competence system and the presence of diverse mobile elements. However, although the S. salivarius strains studied were isolated from several human body-related sites (all levels of the digestive tract, skin, breast milk, and body fluids) and included clinical strains, no genetic or genomic niche-specific features could be identified to discriminate specific group.
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Affiliation(s)
- Christine Delorme
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Anne-Laure Abraham
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Pierre Renault
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Eric Guédon
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France.
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Ceuppens S, Li D, Uyttendaele M, Renault P, Ross P, Ranst MV, Cocolin L, Donaghy J. Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection. Compr Rev Food Sci Food Saf 2014; 13:551-577. [DOI: 10.1111/1541-4337.12072] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/09/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Siele Ceuppens
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Dan Li
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Mieke Uyttendaele
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Pierre Renault
- Inst. Scientifique de Recherche Agronomique (INRA); France
| | - Paul Ross
- Moorepark Biotechnology Centre; Teagasc; Moorepark; Fermoy Co. Cork Ireland
| | | | - Luca Cocolin
- Dept. of Agricultural; Forest and Food Sciences; Univ. of Torino; Grugliasco Torino Italy
| | - John Donaghy
- Food Safety Microbiology Group; Nestle Research Center; Lausanne Switzerland
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24
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Papadimitriou K, Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E. Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics 2014; 15:272. [PMID: 24713045 PMCID: PMC4051162 DOI: 10.1186/1471-2164-15-272] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 09/29/2013] [Accepted: 04/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background Within the genus Streptococcus, only Streptococcus
thermophilus is used as a starter culture in food fermentations.
Streptococcus macedonicus though, which belongs to the
Streptococcus bovis/Streptococcus equinus complex
(SBSEC), is also frequently isolated from fermented foods mainly of dairy
origin. Members of the SBSEC have been implicated in human endocarditis and
colon cancer. Here we compare the genome sequence of the dairy isolate
S. macedonicus ACA-DC 198 to the other SBSEC genomes in order
to assess in silico its potential adaptation to milk and its
pathogenicity status. Results Despite the fact that the SBSEC species were found tightly related based on
whole genome phylogeny of streptococci, two distinct patterns of evolution
were identified among them. Streptococcus macedonicus, Streptococcus
infantarius CJ18 and Streptococcus pasteurianus ATCC 43144
seem to have undergone reductive evolution resulting in significantly
diminished genome sizes and increased percentages of potential pseudogenes
when compared to Streptococcus gallolyticus subsp.
gallolyticus. In addition, the three species seem to have lost
genes for catabolizing complex plant carbohydrates and for detoxifying toxic
substances previously linked to the ability of S. gallolyticus to
survive in the rumen. Analysis of the S. macedonicus genome
revealed features that could support adaptation to milk, including an extra
gene cluster for lactose and galactose metabolism, a proteolytic system for
casein hydrolysis, auxotrophy for several vitamins, an increased ability to
resist bacteriophages and horizontal gene transfer events with the dairy
Lactococcus lactis and S. thermophilus as potential
donors. In addition, S. macedonicus lacks several
pathogenicity-related genes found in S. gallolyticus. For example,
S. macedonicus has retained only one (i.e. the pil3)
of the three pilus gene clusters which may mediate the binding of S.
gallolyticus to the extracellular matrix. Unexpectedly, similar
findings were obtained not only for the dairy S. infantarius CJ18,
but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions Our whole genome analyses suggest traits of adaptation of S.
macedonicus to the nutrient-rich dairy environment. During this
process the bacterium gained genes presumably important for this new
ecological niche. Finally, S. macedonicus carries a reduced number
of putative SBSEC virulence factors, which suggests a diminished pathogenic
potential.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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Ondo J, Prudent P, Massiani C, Höhener P, Renault P. Effects of agricultural practices on properties and metal content in urban garden soils in a tropical metropolitan area. J Serb Chem Soc 2014. [DOI: 10.2298/jsc130121068o] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The appearance of agriculture in urban areas improved the healthy diet of
people by the consumption of fresh vegetables and fruits. This study assessed
the level of fertility, the impact of cropping system and of exploitation
time on physicochemical properties and pseudo-total and EDTA-extractable
metals contents of urban garden of vegetable soils in Libreville (Gabon). The
results indicated a low fertility of cultivated soils. The metal contents in
soils were generally different between culture in open field and culture
under shelters. Except Al which could be toxic for cultivated vegetables, the
soil properties and metal element concentrations decreased significantly in
open field soil with time, while they did not vary in open shade structure
soils. The pseudo-total cadmium concentration was below detection limits in
all soils. The multivariate analysis showed that Al, Fe and Pb were of
lithogenic origin, and Cu, Zn and Mn were of anthropogenic origin.
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Affiliation(s)
- Jean Ondo
- Aix-Marseille Université, CNRS, LCE, FRE, Marseille, France + Laboratoire Pluridisciplinaire des Sciences, Ecole Normale Supérieure, B.P. Libreville, Gabon
| | | | | | | | - Pierre Renault
- INRA, Unité "Climat, Sol et Environnement", Domaine Saint-Paul, Site Agroparc, Avignon Cedex, France
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Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, Gougis S, Rizkalla S, Batto JM, Renault P, consortium ANRM, Doré J, Zucker JD, Clément K, Ehrlich SD. Erratum: Corrigendum: Dietary intervention impact on gut microbial gene richness. Nature 2013. [DOI: 10.1038/nature12738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500:541-6. [DOI: 10.1038/nature12506] [Citation(s) in RCA: 2791] [Impact Index Per Article: 253.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/26/2013] [Indexed: 02/07/2023]
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Solet JL, Renault P, Denys JC, Teulé G, Dennemont RM, Domonte F, Garnier C, Aubert L, Filleul L, Polycarpe D. [Discovery and follow-up of a lead-poisoning outbreak in a shantytown of Le Port, Reunion Island]. Rev Epidemiol Sante Publique 2013; 61:329-37. [PMID: 23810628 DOI: 10.1016/j.respe.2013.01.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 11/21/2012] [Accepted: 01/29/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND A national survey conducted in 2008-2009 by the French Institute for Public Health Surveillance for detection of lead impact in childhood identified a high blood lead level in a young boy living in the town of "Le Port", Reunion Island. Previously, cases of lead-poisoning on the island had been exceptional; only a dozen cases were reported in the 1980s in adults, related to the use of lead-containing instruments for food preparations. METHODS The family of the index case was invited to participate in screening tests and an environmental investigation was conducted using a standardized questionnaire. Screening was then broadened to the neighborhood of the index case and samples of soil outside the home and in the immediate vicinity were taken. The environmental survey was then extended with soil samples taken from the entire geographical area. Information was then provided to local inhabitants (87 families and 287 people) in order to encourage lead blood testing for all children under six years and all pregnant women living in the area. RESULTS The index case lived in the neighborhood of "The Oasis", a shantytown of Le Port. The results of soil analysis revealed heterogeneous pollution of superficial soils by lead throughout the area of the shantytown, the highest level recorded (5200mg/kg) reached more than 300 times the background level of the natural soils of the island. The screening identified 76 cases of childhood lead-poisoning (blood lead level greater or equal to 100μg/L) among 148 samples (51%). All cases of blood poisoning involved children under the age of 15 years. The median age of children with a positive test was 5.6 years; the median blood lead level was 196μg/L [102-392μg/L]. CONCLUSION The main hypothesis to explain the contamination of the soil in the area of the shantytown is the presence of waste deposits (car batteries) and diffuse activities of metal recovery. The authorities managed to remove all the families from the environmental exposure to lead by rapidly ensuring rehousing outside the contaminated area.
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Affiliation(s)
- J-L Solet
- Cellule de l'Institut de veille sanitaire en région Océan Indien, département de coordination des alertes et régions, institut de veille sanitaire, 2bis, avenue Georges-Brassens, 97408 Saint-Denis, cedex 9, Réunion.
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Kasanetz F, Lafourcade M, Deroche-Gamonet V, Revest JM, Berson N, Balado E, Fiancette JF, Renault P, Piazza PV, Manzoni OJ. Prefrontal synaptic markers of cocaine addiction-like behavior in rats. Mol Psychiatry 2013; 18:729-37. [PMID: 22584869 DOI: 10.1038/mp.2012.59] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Defining the drug-induced neuroadaptations specifically associated with the behavioral manifestation of addiction is a daunting task. To address this issue, we used a behavioral model that differentiates rats controlling their drug use (Non-Addict-like) from rats undergoing transition to addiction (Addict-like). Dysfunctions in prefrontal cortex (PFC) synaptic circuits are thought to be responsible for the loss of control over drug taking that characterizes addicted individuals. Here, we studied the synaptic alterations in prelimbic PFC (pPFC) circuits associated with transition to addiction. We discovered that some of the changes induced by cocaine self-administration (SA), such as the impairment of the endocannabinoid-mediated long-term synaptic depression (eCB-LTD) was similarly abolished in Non-Addict- and Addict-like rats and thus unrelated to transition to addiction. In contrast, metabotropic glutamate receptor 2/3-mediated LTD (mGluR2/3-LTD) was specifically suppressed in Addict-like rats, which also show a concomitant postsynaptic plasticity expressed as a change in the relative contribution of AMPAR and NMDAR to basal glutamate-mediated synaptic transmission. Addiction-associated synaptic alterations in the pPFC were not fully developed at early stages of cocaine SA, when addiction-like behaviors are still absent, suggesting that pathological behaviors appear once the pPFC is compromised. These data identify specific synaptic impairments in the pPFC associated with addiction and support the idea that alterations of synaptic plasticity are core markers of drug dependence.
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Affiliation(s)
- F Kasanetz
- INSERM, Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, Bordeaux, France
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Vilain P, Larrieu S, Renault P, Baville M, Filleul L. How to explain the re-emergence of chikungunya infection in Reunion Island in 2010? Acta Trop 2012; 123:85-90. [PMID: 22525433 DOI: 10.1016/j.actatropica.2012.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 03/12/2012] [Accepted: 03/24/2012] [Indexed: 10/28/2022]
Abstract
In March 2010, a new outbreak of chikungunya infection was detected in the west of Reunion Island. An investigation was launched to describe the incident cases occurrence and to raise hypotheses on factors that could explain the occurrence of this outbreak. All probable or confirmed cases detected by the surveillance system in the western area between March 1st and July 2nd, 2010 were included in the investigation. A standardized questionnaire was performed by phone, including sociodemographic, environmental and behaviour data. A total of 74 cases were described (i.e. response rate of 72%). They were mainly women (sex ratio M/F=0.7), all ages were represented. Most of them (76%) resided in a house; 31% had recently moved, including 22% from metropolitan France. They reported to have been more exposed to mosquitoes and to infected patients than during the major epidemic of 2005-2006. In addition, 41% reported to have reduced their protection against mosquitoes. The results suggest that several concomitant factors contributed to this outbreak: the reintroduction of the chikungunya virus in the island, the population characteristics and environmental factors.
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Filleul L, Renault P, Bâville M, Larrieu S. Chikungunya surveillance on Réunion Island between 2005 and 2011. Int J Infect Dis 2012. [DOI: 10.1016/j.ijid.2012.05.895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Renault P, Balleydier E, D’Ortenzio E, Bâville M, Filleul L. Epidemiology of chikungunya infection on Reunion Island, Mayotte, and neighboring countries. Med Mal Infect 2012; 42:93-101. [DOI: 10.1016/j.medmal.2011.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/10/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
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El-Sharoud WM, Delorme C, Darwish MS, Renault P. Genotyping of Streptococcus thermophilus strains isolated from traditional Egyptian dairy products by sequence analysis of the phosphoserine phosphatase (serB) gene with phenotypic characterizations of the strains. J Appl Microbiol 2012; 112:329-37. [PMID: 22141454 DOI: 10.1111/j.1365-2672.2011.05212.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a new, simplified genotyping method for examining the genetic diversity of Streptococcus thermophilus strains isolated from traditional Egyptian fermented dairy products and to characterize phenotypic traits of those strains related to their potential use in bioprocessing applications. METHODS AND RESULTS A novel, simplified approach was developed for genotyping Strep. thermophilus involving the analysis of nucleotide sequence variations within a housekeeping gene encoding the phosphoserine phosphatase (SerB). Using this method, it was possible to identify ten genotypes involving diverse serB alleles among 54 Strep. thermophilus isolates cultured from Egyptian dairy products. These isolates harboured five de novo serB alleles that have not been detected in other Strep. thermophilus strains, deposited in a multilocus sequence typing (MLST) database. To assess distinct genotypes of the organism with phenotypic traits relevant to their potential use in industry, Strep. thermophilus strains were all subjected to a series of phenotypic characterizations. The strains were found to exhibit phenotypic diversity in terms of their ability to ferment lactose and galactose, express urease activity, produce exopolysaccharides and develop acidity. CONCLUSIONS The analysis of nucleotide sequence variations within the serB gene could serve as a suitable tool for probing diverse genotypes of Strep. thermophilus. Streptococcus thermophilus isolates associated with traditional Egyptian dairy products show high degree of genetic and phenotypic diversity. SIGNIFICANCE AND IMPACT OF THE STUDY This study presents a novel, simplified procedure based on serB nucleotide sequencing for genotyping Strep. thermophilus. It also provides a pool of phenotypically diverse Strep. thermophilus cultures, from which certain strains could be selected for use in bioprocessing applications including the preparation of fermented dairy products.
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Affiliation(s)
- W M El-Sharoud
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt.
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Hébert L, Moumen B, Pons N, Duquesne F, Breuil MF, Goux D, Batto JM, Laugier C, Renault P, Petry S. Genomic characterization of the Taylorella genus. PLoS One 2012; 7:e29953. [PMID: 22235352 PMCID: PMC3250509 DOI: 10.1371/journal.pone.0029953] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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: 10/05/2011] [Accepted: 12/07/2011] [Indexed: 01/21/2023] Open
Abstract
The Taylorella genus comprises two species: Taylorella equigenitalis, which causes contagious equine metritis, and Taylorella asinigenitalis, a closely-related species mainly found in donkeys. We herein report on the first genome sequence of T. asinigenitalis, analyzing and comparing it with the recently-sequenced T. equigenitalis genome. The T. asinigenitalis genome contains a single circular chromosome of 1,638,559 bp with a 38.3% GC content and 1,534 coding sequences (CDS). While 212 CDSs were T. asinigenitalis-specific, 1,322 had orthologs in T. equigenitalis. Two hundred and thirty-four T. equigenitalis CDSs had no orthologs in T. asinigenitalis. Analysis of the basic nutrition metabolism of both Taylorella species showed that malate, glutamate and alpha-ketoglutarate may be their main carbon and energy sources. For both species, we identified four different secretion systems and several proteins potentially involved in binding and colonization of host cells, suggesting a strong potential for interaction with their host. T. equigenitalis seems better-equipped than T. asinigenitalis in terms of virulence since we identified numerous proteins potentially involved in pathogenicity, including hemagluttinin-related proteins, a type IV secretion system, TonB-dependent lactoferrin and transferrin receptors, and YadA and Hep_Hag domains containing proteins. This is the first molecular characterization of Taylorella genus members, and the first molecular identification of factors potentially involved in T. asinigenitalis and T. equigenitalis pathogenicity and host colonization. This study facilitates a genetic understanding of growth phenotypes, animal host preference and pathogenic capacity, paving the way for future functional investigations into this largely unknown genus.
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Affiliation(s)
- Laurent Hébert
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
- * E-mail: (LH); (SP)
| | - Bouziane Moumen
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Nicolas Pons
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Fabien Duquesne
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
| | | | - Didier Goux
- Centre de Microscopie Appliquée à la Biologie, Université de Caen Basse-Normandie et IFR146 ICORE, Caen, France
| | - Jean-Michel Batto
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Claire Laugier
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
| | - Sandrine Petry
- ANSES, Dozulé Laboratory for Equine Diseases, Dozulé, France
- * E-mail: (LH); (SP)
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80. [PMID: 21508958 DOI: 10.1038/nature09944] [Citation(s) in RCA: 4496] [Impact Index Per Article: 345.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 12/18/2010] [Indexed: 02/06/2023]
Abstract
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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Wescombe PA, Upton M, Renault P, Wirawan RE, Power D, Burton JP, Chilcott CN, Tagg JR. Salivaricin 9, a new lantibiotic produced by Streptococcus salivarius. Microbiology (Reading) 2011; 157:1290-1299. [PMID: 21310787 DOI: 10.1099/mic.0.044719-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salivaricin 9 (Sal9) is a 2560 Da lantibiotic having just 46 % amino acid identity with its closest known homologue, the Streptococcus pyogenes lantibiotic SA-FF22. The Sal9 locus (designated siv) in Streptococcus salivarius strain 9 was partially sequenced and localized to an approximately 170 kb megaplasmid, which also harbours the locus for the lantibiotic salivaricin A4. The entire locus was fully characterized in the draft genome sequence of S. salivarius strain JIM8780 and shown to consist of eight genes, having the following putative functions: sivK, sensor kinase; sivR, response regulator; sivA, Sal9 precursor peptide; sivM, lantibiotic modification enzyme; sivT, ABC transporter involved in the export of Sal9 and concomitant cleavage of its leader peptide; and sivFEG, encoding lantibiotic self-immunity. Intriguingly, in contrast to strain 9, the siv locus was chromosomally located in strain JIM8780--the first lantibiotic locus shown not to be exclusively plasmid-associated in S. salivarius. Sal9-containing extracts specifically induced lantibiotic production in both strain 9 and strain JIM8780, indicating that Sal9 functions as a signal peptide for upregulation of its own biosynthesis. Screening representative strains of three streptococcal species (S. salivarius, S. pyogenes and S. mitis) for sivA indicated that it was present only in S. salivarius, with 12 of 28 tested S. salivarius positive. Since Sal9 was inhibitory to all tested S. pyogenes strains it appears to have potential as an important component of the bacteriocin armoury of S. salivarius probiotics intended to control S. pyogenes infections of the human oral cavity.
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Affiliation(s)
| | - M Upton
- Medical Microbiology, School of Translational Medicine, University of Manchester, Clinical Sciences Building, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - P Renault
- Genetique Microbienne, INRA-CRJ, 78352 Jouy en Josas Cedex, France
| | - R E Wirawan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - D Power
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - J P Burton
- BLIS Technologies Ltd, Dunedin, New Zealand
| | | | - J R Tagg
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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D'Ortenzio E, Balleydier E, Baville M, Filleul L, Renault P. [Dengue fever in the Reunion Island and in South Western islands of the Indian Ocean]. Med Mal Infect 2011; 41:475-9. [PMID: 21295427 DOI: 10.1016/j.medmal.2010.11.021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 11/04/2010] [Accepted: 11/19/2010] [Indexed: 11/17/2022]
Abstract
South Western islands of the Indian Ocean are permanently threatened by dengue fever outbreaks. On the Reunion Island, two dengue outbreaks were biologically documented (1977-1978 and 2004). And since July 2004 there has been an inter-epidemic period for the island with sporadic cases and clusters. Between January 1, 2007 and October 5, 2009, the epidemiologic surveillance system detected five confirmed autochthonous cases, five confirmed imported cases (South-East Asia), and 71 probable cases. All the five autochthonous confirmed cases occurred in Saint-Louis during two consecutive clusters. In other South Western islands of the Indian Ocean, several dengue fever outbreaks have been reported. Importation of dengue virus from South-East Asia is a major risk for a new outbreak on the island. The introduction of a new serotype could lead to the emergence of new and severe clinical forms, including dengue hemorrhagic fever.
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Affiliation(s)
- E D'Ortenzio
- Cellule de l'institut de veille sanitaire en région (Cire océan Indien, InVS), 2, bis avenue G.-Brassens, Saint-Denis Messag cedex, Réunion.
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Aleksandrzak-Piekarczyk T, Polak J, Jezierska B, Renault P, Bardowski J. Genetic characterization of the CcpA-dependent, cellobiose-specific PTS system comprising CelB, PtcB and PtcA that transports lactose in Lactococcus lactis IL1403. Int J Food Microbiol 2010; 145:186-94. [PMID: 21262549 DOI: 10.1016/j.ijfoodmicro.2010.12.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 12/10/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
Lactose metabolism is one of the most important areas of research on Lactic Acid Bacteria (LAB). In rapidly acidifying industrial Lactococcus lactis strains, lactose is transported by a lactose-specific phosphotransferase system (PTS) encoded by a plasmid. However, an alternative lactose catabolic pathway was evidenced in the plasmid-cured, and thus initially lactose-negative L. lactis IL1403. We showed that in this strain the chromosomally-encoded cellobiose-specific PTS system comprising the celB, ptcB and ptcA genes is also able to transport lactose. By expression studies in the wild type IL1403 strain and IBB550, its ccpA-deficient derivative, we demonstrated that celB, ptcB and ptcA are tightly regulated by the general catabolite repression system, whereas celB additionally requires the presence of cellobiose to be fully induced. The comparison of expression levels of sugar catabolic genes indicated that the efficiency of CcpA-mediated catabolic repression depends on conservation of the cre sequence, and that in the case of perfect matching with the cre consensus, CcpA still drives a strong repression even under non-repressing conditions.
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Pérez-Núñez D, Briandet R, David B, Gautier C, Renault P, Hallet B, Hols P, Carballido-López R, Guédon E. A new morphogenesis pathway in bacteria: unbalanced activity of cell wall synthesis machineries leads to coccus-to-rod transition and filamentation in ovococci. Mol Microbiol 2010; 79:759-71. [PMID: 21255117 DOI: 10.1111/j.1365-2958.2010.07483.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteria display a variety of shapes, which have biological relevance. In most eubacteria, cell shape is maintained by the tough peptidoglycan (PG) layer of the cell wall, the sacculus. The organization of PG synthesis machineries, orchestrated by different cytoskeletal elements, determines the specific shapes of sacculi. In rod-shaped bacteria, the actin-like (MreB) and the tubuline-like (FtsZ) cytoskeletons control synthesis of the sidewall (elongation) and the crosswall (septation) respectively. Much less is known concerning cell morphogenesis in cocci, which lack MreB proteins. While spherical cocci exclusively display septal growth, ovococci additionally display peripheral growth, which is responsible of the slight longitudinal expansion that generates their ovoid shape. Here, we report that the ovococcus Lactococcus lactis has the ability to become rod-shaped. L. lactis IL1403 wild-type cells form long aseptate filaments during both biofilm and planktonic growth in a synthetic medium. Nascent PG insertion and the division protein FtsK localize in multiple peripheral rings regularly spaced along the filaments. We show that filamentation results from septation inhibition, and that penicillin-binding proteins PBP2x and PBP2b play a direct role in this process. We propose a model for filament formation in L. lactis, and discuss the possible biological role of such morphological differentiation.
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Affiliation(s)
- Daniel Pérez-Núñez
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
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Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65. [PMID: 20203603 DOI: 10.1038/nature08821] [Citation(s) in RCA: 7150] [Impact Index Per Article: 510.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 12/23/2009] [Indexed: 11/09/2022]
Abstract
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
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D'Ortenzio E, Renault P, Jaffar-Bandjee M, Gaüzère B, Lagrange-Xélot M, Fouillet A, Poubeau P, Winer A, Bourde A, Staikowsky F, Morbidelli P, Rachou E, Thouillot F, Michault A, Filleul L. A review of the dynamics and severity of the pandemic A(H1N1) influenza virus on Réunion Island, 2009. Clin Microbiol Infect 2010; 16:309-16. [DOI: 10.1111/j.1469-0691.2010.03171.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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D'Ortenzio E, Sissoko D, Dehecq JS, Renault P, Filleul L. Malaria imported into Réunion Island: is there a risk of re-emergence of the disease? Trans R Soc Trop Med Hyg 2009; 104:251-4. [PMID: 19914673 DOI: 10.1016/j.trstmh.2009.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 11/27/2022] Open
Abstract
After a long period of endemicity until the 1950s, the World Health Organization considered autochthonous malaria eliminated from Réunion in 1979. To prevent secondary transmission and re-emergence of autochthonous malaria, permanent epidemiologic and entomological surveillance and vector control measures are conducted. The objective of this study is to report sociodemographic characteristics of imported malaria patients and incidence rates from 2003-2008 using mandatory notification with the aim of identifying risk groups and destinations. During this period, 684 imported malaria cases were reported. Median age of patients was 34.4 years and 22.1% were children </= 15 years. Men represented 67.7% of cases and 59.1% of patients reported having taken chemoprophylaxis based on chloroquine alone. Incidence of malaria was considerably different by country destination. For Comoros, incidence was stable and high during the period accounting for 1481 cases per 100000 travels in 2008. The rate was lower for travels to Madagascar, South Africa and Mayotte and decreased over the period to 37, 19 and 3 per 100000 respectively, by 2008. To avoid re-emergence of malaria on the island and to protect themselves, travelers should reduce their risks of acquisition and importation of parasites by using adequate preventive measures. A special preventive program and social mobilisation should be a priority, essentially for the Comorian community in Réunion.
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Affiliation(s)
- E D'Ortenzio
- Regional office (Cire Réunion-Mayotte) of the French Institute for Public Health Surveillance (Institut de veille sanitaire, InVS), Réunion, France.
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D’Ortenzio E, Do C, Renault P, Weber F, Filleul L. Enhanced influenza surveillance on Réunion Island (southern hemisphere) in the context of the emergence of influenza A(H1N1)v. Euro Surveill 2009; 14:19239. [DOI: 10.2807/ese.14.23.19239-en] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the winter season on the southern hemisphere that starts in Réunion Island in June seasonal influenza activity usually increases shortly afterwards. The new influenza A(H1N1)v virus is rapidly spreading worldwide and may reach the island during the coming winter season. We have therefore enhanced influenza surveillance to detect the introduction of influenza A(H1N1)v, monitor its spread and impact on public health and characterise potential viral changes, particularly if seasonal influenza A(H1N1), resistant to oseltamivir, co-circulates with A(H1N1)v.
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Affiliation(s)
- E D’Ortenzio
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
| | - C Do
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
| | - P Renault
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
| | - F Weber
- Institut National de Veille Sanitaire (Institute for Public Health Surveillance, InVS), Saint-Maurice, France
| | - L Filleul
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
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Bensalah F, Delorme C, Renault P. Characterisation of thermotolerant cocci from indigenous flora of 'leben' in algerian arid area and DNA identification of atypical Lactococcus lactis strains. Curr Microbiol 2009; 59:139-46. [PMID: 19484304 DOI: 10.1007/s00284-009-9411-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/26/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
Lactic acid bacteria (LAB) are widely used in food industry and their growth performance is important for the quality of the fermented product. By combining results from conventional isolation methods and molecular investigation of 16S rRNA gene and lactococcal/enterococcal specific genes, we identify at species level catalase negative gram positive thermoresistant cocci isolated from traditional 'leben', a 24-h fermented milk in arid area of west Algeria. Forty strains phenotypically related to cocci LAB were identified as belonging to the species Lactococcus lactis ssp. lactis, Enterococcus faecalis, Enterococcus faecium, and other Enterococcus species. No Streptococcus thermophilus strain was isolated. Ten different phenotype groups were recognized, and the species content of these groups were in some cases different from the expected features usually given in genus and species descriptions. In particular, atypical lactococci, able to grow in 6.5% NaCl, at pH 9.5 and showing high resistance to thermal stresses were isolated. Lactococci, but also enterococci isolated from traditional 'leben' produced in the desert area, may be therefore of interest in milk fermentation. Further studies to assess this source of diversity within the wild microbial population should provide starter new strains for product innovation.
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Affiliation(s)
- Farid Bensalah
- Faculté des Sciences, Département de Biologie, Université Es-Sénia, Oran, 31000, Algeria.
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Boëlle PY, Thomas G, Vergu E, Renault P, Valleron AJ, Flahault A. Investigating transmission in a two-wave epidemic of Chikungunya fever, Réunion Island. Vector Borne Zoonotic Dis 2008; 8:207-17. [PMID: 18171107 DOI: 10.1089/vbz.2006.0620] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An epidemic of Chikungunya fever, a mosquito-borne viral disease, spectacularly swept through Réunion Island (population 780,000) in 2005-2006. There were 3,000 cases in a first wave (March-June 2005) and more than 250,000 cases in a second (December 2005-April 2006). Adapting newly developed epidemiological tools to vector-borne diseases, we show that despite this massive difference in magnitude, the transmission potential as measured by the number of secondary cases per index case (or reproduction number), remained similar during the two consecutive waves. The best estimate for the initial reproduction number R(0) was 3.7, with a possible range from 2 to 11 depending on incubation duration and lifespan of the mosquito. We conclude that an increase in virulence between the two seasons was not necessary to explain the change in magnitude of the epidemics, and that the attack rate may be well over 50% in Chikungunya fever epidemics in the absence of intervention.
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Affiliation(s)
- P-Y Boëlle
- Université Pierre et Marie Curie - Parisó, UMR S 707, Paris, France.
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D'Ortenzio E, Sissoko D, Landreau D, Benoit-Cattin T, Renault P, Pierre V. [Outbreak of measles in Mayotte, Indian Ocean, 2005-2006]. Med Mal Infect 2008; 38:601-7. [PMID: 18722725 DOI: 10.1016/j.medmal.2008.06.009] [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: 01/18/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
Abstract
OBJECTIVE An outbreak of measles occurred from 2005 to 2006 in Mayotte, a French territory in the Indian Ocean. The aim of this study was to describe the outbreak, to analyze epidemiologic and sociodemographic characteristic of cases, and to suggest recommendations for measles surveillance and preventive measures in Mayotte. DESIGN An outbreak investigation was conducted and an enhanced passive surveillance system of incident cases was implemented. RESULTS During the outbreak, 1269 clinical cases, including 156 (12.3%) biologically confirmed cases, were reported. The attack rate was 0.71% and no death due to measles was recorded. The median age of cases was 12 years and the M/F sex-ratio 1.1. Teenagers and young adults (10-19 years) were the most frequently affected (44.4%) and infants less than one year of age accounted for 21.6% of the cases. In the 1269 clinical cases, 27.3% of patients had received at least one dose of measles vaccine before the outbreak. The immunization coverage in school children reached 59.1% at the end of the vaccination campaign. CONCLUSION In the future, this vaccinal coverage should be improved to prevent other outbreaks, especially in vulnerable groups like immigrants. A surveillance system with systematical report of the biologically confirmed cases is needed in Mayotte.
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Affiliation(s)
- E D'Ortenzio
- Cellule interrégionale d'épidémiologie Réunion-Mayotte, institut de veille sanitaire, 2 bis, avenue G.- Brassens, BP 50, 97408 Saint-Denis cedex, Réunion.
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D'Ortenzio E, Weill FX, Ragonneau S, Lebon JA, Renault P, Pierre V. First report of a Salmonella enterica serovar Weltevreden outbreak on Reunion Island, France, August 2007. Euro Surveill 2008; 13:18949. [PMID: 18761897] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
An outbreak of gastroenteritis involving 26 guests of a wedding dinner occurred in August 2007 in Réunion Island, a French Overseas Department. Salmonella was isolated in 61.5% of cases and the two isolates serotyped were of serovar Weltevreden. We believe this to be the first food-borne outbreak due to S. enterica serovar Weltevreden described in Réunion Island. The epidemiological and environmental investigations of this outbreak did not provide enough evidence to identify a single vehicle of infection. It is necessary to improve surveillance of salmonellosis by multidisciplinary cooperation between clinicians, epidemiologists, microbiologists and veterinarians on Réunion Island.
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Affiliation(s)
- E D'Ortenzio
- Cellule interrégionale d'épidemiologie (CIRE) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France.
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D'Ortenzio E, Weill FX, Ragonneau S, Lebon JA, Renault P, Pierre V. First report of a Salmonella enterica serovar Weltevreden outbreak on Réunion Island, France, August 2007. Euro Surveill 2008. [DOI: 10.2807/ese.13.32.18949-en] [Citation(s) in RCA: 7] [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] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- E D'Ortenzio
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
| | - F X Weill
- Centre National de Référence des Salmonella (CNR-Salm), Institut Pasteur, Paris, France
| | - S Ragonneau
- Direction régionale des affaires sanitaires et sociales (DRASS), Réunion Island, France
| | - J A Lebon
- Direction régionale des affaires sanitaires et sociales (DRASS), Réunion Island, France
| | - P Renault
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
| | - V Pierre
- Cellule interrégionale d’épidémiologie (Cire) Réunion-Mayotte, Institut de Veille Sanitaire, Réunion Island, France
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Darcheville O, Février L, Haichar FZ, Berge O, Martin-Garin A, Renault P. Aqueous, solid and gaseous partitioning of selenium in an oxic sandy soil under different microbiological states. J Environ Radioact 2008; 99:981-992. [PMID: 18289747 DOI: 10.1016/j.jenvrad.2007.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/09/2007] [Indexed: 05/25/2023]
Abstract
The aim of this study was to investigate the role of microorganisms on the behaviour of selenium in natural soil maintained under strictly aerobic conditions. Six-day batch experiments were performed with soils constrained to different microbiological states, either by sterilisation or by adding organic substrates. Selenium was added to the soil as selenite. The distribution of selenium in the gaseous, liquid and solid phases of the batch was measured. Selenium partitioning between the various solid phases was investigated by chemical sequential extractions. Active microorganisms played major effects on the distribution of selenium within the soil. On the one hand, microorganisms could promote selenium volatilisation (in relatively small amounts), leading to the spreading of selenium compounds outside the soil. On the other hand, microbial activities increased both amount of selenium retained by the soil and the strength of its retention (less exchangeable selenium), making selenium less susceptible to remobilisation.
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Affiliation(s)
- O Darcheville
- Laboratory of Radioecology and Ecotoxicology, IRSN/DEI/SECRE, Building 186, Cadarache, B.P. 3, 13115 Saint Paul-lez-Durance Cedex, France.
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Pons N, Batto JM, Ehrlich SD, Renault P. Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae. J Mol Microbiol Biotechnol 2008; 14:67-73. [PMID: 17957112 DOI: 10.1159/000106084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gene expression regulation often involves the recognition of particular DNA or RNA sequences, called motifs. Detection and characterization of such motifs together with biological expertise allow to build gene expression regulatory maps that facilitate the comprehension of complex cellular processes. In this frame, we developed a software integrating relevant information for the detection and characterization of conserved motifs in genomic sequences. A relational database was built up to host data related to genomic information and transcriptional experiments. A user-friendly interface was designed to allow a convenient representation of these data and to run the detection motif program. A set of complementary utilities was also developed to improve the determination of motif consensus sequences and the detection of additional potential regulator targets in the genome.
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Affiliation(s)
- Nicolas Pons
- Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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