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Ma J, Guo T, Ren M, Chen L, Song X, Zhang W. Cross-feeding between cyanobacterium Synechococcus and Escherichia coli in an artificial autotrophic–heterotrophic coculture system revealed by integrated omics analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:69. [PMID: 35733176 PMCID: PMC9219151 DOI: 10.1186/s13068-022-02163-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/04/2022] [Indexed: 01/21/2023]
Abstract
Background Light-driven consortia, which consist of sucrose-secreting cyanobacteria and heterotrophic species, have attracted considerable attention due to their capability for the sustainable production of valuable chemicals directly from CO2. In a previous study, we achieved a one-step conversion of sucrose secreted from cyanobacteria to fine chemicals by constructing an artificial coculture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analyses of the coculture system showed that the cyanobacterial cells grew better than their corresponding axenic cultures. To explore the underlying mechanism and to identify the metabolic nodes with the potential to further improve the coculture system, we conducted integrated transcriptomic, proteomic and metabolomic analyses. Results We first explored how the relieved oxidative stress affected cyanobacterial cell growth in a coculture system by supplementing additional ascorbic acid to CoBG-11 medium. We found that the cell growth of cyanobacteria was clearly improved with an additional 1 mM ascorbic acid under axenic culture; however, its growth was still slower than that in the coculture system, suggesting that the improved growth of Synechococcus cscB+ may be caused by multiple factors, including reduced oxidative stress. To further explore the cellular responses of cyanobacteria in the system, quantitative transcriptomics, proteomics and metabolomics were applied to Synechococcus cscB+. Analyses of differentially regulated genes/proteins and the abundance change of metabolites in the photosystems revealed that the photosynthesis of the cocultured Synechococcus cscB+ was enhanced. The decreased expression of the CO2 transporter suggested that the heterotrophic partner in the system might supplement additional CO2 to support the cell growth of Synechococcus cscB+. In addition, the differentially regulated genes and proteins involved in the nitrogen and phosphate assimilation pathways suggested that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient. Conclusion An artificial coculture system capable of converting CO2 to fine chemicals was established and then analysed by integrated omics analysis, which demonstrated that in the coculture system, the relieved oxidative stress and increased CO2 availability improved the cell growth of cyanobacteria. In addition, the results also showed that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient, which paves a new path towards the optimization of the coculture system in the future. Taken together, these results from the multiple omics analyses provide strong evidence that beneficial interactions can be achieved from cross-feeding and competition between phototrophs and prokaryotic heterotrophs and new guidelines for engineering more intelligent artificial consortia in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02163-5.
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Qian Y, Li Y, Tang Z, Wang R, Zeng M, Liu Z. The role of AI-2/LuxS system in biopreservation of fresh refrigerated shrimp: Enhancement in competitiveness of Lactiplantibacillus plantarum for nutrients. Food Res Int 2022; 161:111838. [DOI: 10.1016/j.foodres.2022.111838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/13/2022] [Accepted: 08/21/2022] [Indexed: 11/04/2022]
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Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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Affiliation(s)
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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5
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Bartle L, Sumby K, Sundstrom J, Jiranek V. The microbial challenge of winemaking: yeast-bacteria compatibility. FEMS Yeast Res 2020; 19:5513997. [PMID: 31187141 DOI: 10.1093/femsyr/foz040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/10/2019] [Indexed: 12/25/2022] Open
Abstract
The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.
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Affiliation(s)
- Louise Bartle
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Krista Sumby
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Joanna Sundstrom
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
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Abhisingha M, Dumnil J, Pitaksutheepong C. Selection of Potential Probiotic Lactobacillus with Inhibitory Activity Against Salmonella and Fecal Coliform Bacteria. Probiotics Antimicrob Proteins 2019; 10:218-227. [PMID: 28712023 DOI: 10.1007/s12602-017-9304-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Three hundred and sixty presumptive lactic acid bacteria (LAB) isolated from pregnant sows, newborn, suckling, and weaned piglets were preliminarily screened for anti-Salmonella activity. Fifty-eight isolates consisting of Lactobacillus reuteri (n = 32), Lactobacillus salivarius (n = 10), Lactobacillus mucosae (n = 8), Lactobacillus johnsonii (n = 5), and Lactobacillus crispatus (n = 3) were selected and further characterized for probiotic properties including production of antimicrobial substances, acid and bile tolerance, and cell adherence to Caco-2 cells. Eight isolates including Lact. johnsonii LJ202 and Lact. reuteri LR108 were identified as potential probiotics. LJ202 was selected for further use in co-culture studies of two-bacterial and multiple-bacterial species to examine its inhibitory activity against Salmonella enterica serovar Enteritidis DMST7106 (SE7106). Co-culture of LJ202 and SE7106 showed that LJ202 could completely inhibit the growth of SE7106 in 10 h of co-culture. In co-culture of multiple-bacterial species, culturable fecal bacteria from pig feces were used as representative of multiple-bacterial species. The study was performed to examine whether interactions among multiple-bacterial species would influence antagonistic activity of LJ202 against SE7106 and fecal coliform bacteria. Co-culture of SE7106 with different combinations of fecal bacteria and probiotic (LJ202 and LR108) or non-probiotic (Lact. mucosae LM303) strains revealed that the growth of SE7106 was completely inhibited either in the presence or in the absence of probiotic strains. Intriguingly, LJ202 exhibited notable inhibitory activity against fecal coliform bacteria while LR108 did not. Taken together, the results of co-culture studies suggested that LJ202 is a good probiotic candidate for further study its inhibitory effects against pathogen infections in pigs.
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Affiliation(s)
- Mattika Abhisingha
- Food Biotechnology Laboratory, Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Jureeporn Dumnil
- Food Biotechnology Laboratory, Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chetsadaporn Pitaksutheepong
- Food Biotechnology Laboratory, Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
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8
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Delpech P, Rifa E, Ball G, Nidelet S, Dubois E, Gagne G, Montel MC, Delbès C, Bornes S. New Insights into the Anti-pathogenic Potential of Lactococcus garvieae against Staphylococcus aureus Based on RNA Sequencing Profiling. Front Microbiol 2017; 8:359. [PMID: 28337182 PMCID: PMC5340753 DOI: 10.3389/fmicb.2017.00359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H2O2) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro. This effector was neither a protein, nor a lipid, nor a polysaccharide, nor related to an L-threonine deficiency. To better understand the H2O2-related inhibition mechanism at the transcriptome level and to identify other mechanisms potentially involved, we used RNA sequencing to determine the transcriptome response of L. garvieae to different aeration levels and to the presence or absence of S. aureus. The L. garvieae transcriptome differed radically between different aeration levels mainly in biological processes related to fundamental functions and nutritional adaptation. The transcriptomic response of L. garvieae to aeration level differed according to the presence or absence of S. aureus. The higher concentration of H2O2 with high aeration was not associated with a higher expression of L. garvieae H2O2-synthesis genes (pox, sodA, and spxA1) but rather with a repression of L. garvieae H2O2-degradation genes (trxB1, ahpC, ahpF, and gpx). We showed that L. garvieae displayed an original, previously undiscovered, H2O2 production regulation mechanism among bacteria. In addition to the key factor H2O2, the involvement of another extracellular effector in the antagonism against S. aureus was shown. Future studies should explore the relation between H2O2-metabolism, H2O2-producing LAB and the pathogen they inhibit. The nature of the other extracellular effector should also be determined.
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Affiliation(s)
- Pierre Delpech
- Université Clermont Auvergne, INRA, UMRF Aurillac, France
| | - Etienne Rifa
- Université Clermont Auvergne, INRA, UMRF Aurillac, France
| | - Graham Ball
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University Nottingham, UK
| | - Sabine Nidelet
- Montpellier GenomiX, Institut de Génomique Fonctionnelle Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, Institut de Génomique Fonctionnelle Montpellier, France
| | | | | | - Céline Delbès
- Université Clermont Auvergne, INRA, UMRF Aurillac, France
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Tauzin AS, Laville E, Xiao Y, Nouaille S, Le Bourgeois P, Heux S, Portais J, Monsan P, Martens EC, Potocki‐Veronese G, Bordes F. Functional characterization of a gene locus from an uncultured gut
Bacteroides
conferring xylo‐oligosaccharides utilization to
Escherichia coli. Mol Microbiol 2016; 102:579-592. [DOI: 10.1111/mmi.13480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/01/2016] [Accepted: 08/08/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Alexandra S. Tauzin
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
- TWB, INRARamonville Saint‐Agne France
| | | | - Yao Xiao
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn Arbor MI USA
| | | | | | - Stéphanie Heux
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
| | | | | | - Eric C. Martens
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn Arbor MI USA
| | | | - Florence Bordes
- LISBP, CNRS, INRA, INSAT, Université de ToulouseToulouse France
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Zdenkova K, Alibayov B, Karamonova L, Purkrtova S, Karpiskova R, Demnerova K. Transcriptomic and metabolic responses of Staphylococcus aureus in mixed culture with Lactobacillus plantarum, Streptococcus thermophilus and Enterococcus durans in milk. J Ind Microbiol Biotechnol 2016; 43:1237-47. [PMID: 27342241 DOI: 10.1007/s10295-016-1794-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a major food-borne pathogen due to the production of enterotoxin and is particularly prevalent in contaminated milk and dairy products. The lactic acid bacteria (LAB) are widely used as biocontrol agents in fermented foods which can inhibit pathogenic flora. In our work, we investigated the influence of three strains of LAB (Lactobacillus plantarum, Streptococcus thermophilus and Enterococcus durans) on the relative expression of three enterotoxin genes (sea, sec, sell) and eight virulence and/or regulatory genes (sarA, saeS, codY, srrA, rot, hld/RNAIII, agrA/RNAII, sigB) in two S. aureus strains (MW2 and Sa1612) in TSB and reduced-fat milk (1.5 %) at 30 °C over a 24-h period. The tested LAB and S. aureus strains proved to be mutually non-competitive or only slightly competitive during co-cultivation. In addition, under the above-mentioned conditions, differential gene expression between the S. aureus MW2 and Sa1612 strains was well documented. S. aureus growth was changed in mixed culture with LAB; however, its effect on the repression of sea and sec expression correlated with production of these virulence factors. In comparison, the presence of LAB strains generally inhibited the expression of sec, sell, sarA, seaS, agrA/RNAII and hld/RNAIII genes. The effect of LAB strains presence on the expression of sea, codY, srrA, rot and sigB genes was medium, time, LAB and S. aureus strain specific. SEA and SEC production was significantly reduced in milk compared to TSB in pure culture. After the 24-h cultivation, S. aureus MW2 and Sa1612 SEC production was 187 and 331 times lower in milk compared to TSB, respectively (0.07 and 0.39 ng/mL in milk, versus 13.1 and 129.2 ng/mL in TSB, respectively). At the same time S. aureus MW2 and Sa1612 SEA production was 77 and 68 times lower in milk compared to TSB, respectively (0.99 and 0.17 ng/mL in milk, versus 76.4 and 11.5 ng/mL in TSB, respectively). This study has revealed new insights into the interaction between S. aureus and LAB (L. plantarum, S. thermophilus, E. durans) on the level of the expression and/or production of S. aureus enterotoxins, regulatory and virulence genes in different media, including milk. This study provides data which may improve the quality of food production.
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Affiliation(s)
- Kamila Zdenkova
- Department of Biochemistry and Microbiology, University of Chemical and Technology, Prague, Czech Republic.
| | - Babek Alibayov
- Department of Biochemistry and Microbiology, University of Chemical and Technology, Prague, Czech Republic.
| | - Ludmila Karamonova
- Department of Biochemistry and Microbiology, University of Chemical and Technology, Prague, Czech Republic
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, University of Chemical and Technology, Prague, Czech Republic
| | - Renata Karpiskova
- Department of Bacteriology, Veterinary Research Institute, Brno, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, University of Chemical and Technology, Prague, Czech Republic
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Vermassen A, Dordet-Frisoni E, de La Foye A, Micheau P, Laroute V, Leroy S, Talon R. Adaptation of Staphylococcus xylosus to Nutrients and Osmotic Stress in a Salted Meat Model. Front Microbiol 2016; 7:87. [PMID: 26903967 PMCID: PMC4742526 DOI: 10.3389/fmicb.2016.00087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/18/2016] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus xylosus is commonly used as starter culture for meat fermentation. Its technological properties are mainly characterized in vitro, but the molecular mechanisms for its adaptation to meat remain unknown. A global transcriptomic approach was used to determine these mechanisms. S. xylosus modulated the expression of about 40-50% of the total genes during its growth and survival in the meat model. The expression of many genes involved in DNA machinery and cell division, but also in cell lysis, was up-regulated. Considering that the S. xylosus population remained almost stable between 24 and 72 h of incubation, our results suggest a balance between cell division and cell lysis in the meat model. The expression of many genes encoding enzymes involved in glucose and lactate catabolism was up-regulated and revealed that glucose and lactate were used simultaneously. S. xylosus seemed to adapt to anaerobic conditions as revealed by the overexpression of two regulatory systems and several genes encoding cofactors required for respiration. In parallel, genes encoding transport of peptides and peptidases that could furnish amino acids were up-regulated and thus concomitantly a lot of genes involved in amino acid synthesis were down-regulated. Several genes involved in glutamate homeostasis were up-regulated. Finally, S. xylosus responded to the osmotic stress generated by salt added to the meat model by overexpressing genes involved in transport and synthesis of osmoprotectants, and Na(+) and H(+) extrusion.
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Affiliation(s)
| | | | - Anne de La Foye
- INRA, Plateforme d'Exploration du MétabolismeSaint-Genès Champanelle, France
| | - Pierre Micheau
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
| | - Valérie Laroute
- Université de Toulouse, INSA, UPS, INP, LISBPToulouse, France
| | - Sabine Leroy
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
| | - Régine Talon
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
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12
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Izac M, Garnier D, Speck D, Lindley ND. A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates. PLoS One 2015; 10:e0145251. [PMID: 26684737 PMCID: PMC4684311 DOI: 10.1371/journal.pone.0145251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/30/2015] [Indexed: 12/31/2022] Open
Abstract
It has been claimed that citrate synthase, aconitase and isocitrate dehydrogenase activities are non-functional in Bordetella pertussis and that this might explain why this bacterium’s growth is sometimes associated with accumulation of polyhydroxybutyrate (PHB) and/or free fatty acids. However, the sequenced genome includes the entire citric acid pathway genes. Furthermore, these genes were expressed and the corresponding enzyme activities detected at high levels for the pathway when grown on a defined medium imitating the amino acid content of complex media often used for growth of this pathogenic microorganism. In addition, no significant PHB or fatty acids could be detected. Analysis of the carbon balance and stoichiometric flux analysis based on specific rates of amino acid consumption, and estimated biomass requirements coherent with the observed growth rate, clearly indicate that a fully functional tricarboxylic acid cycle operates in contrast to previous reports.
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Affiliation(s)
- Marie Izac
- Université de Toulouse; INSA, UPSr, INP, LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | | | | | - Nic D Lindley
- Université de Toulouse; INSA, UPSr, INP, LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
- * E-mail:
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Flavor Profile of Chinese Liquor Is Altered by Interactions of Intrinsic and Extrinsic Microbes. Appl Environ Microbiol 2015; 82:422-30. [PMID: 26475111 DOI: 10.1128/aem.02518-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/14/2015] [Indexed: 12/23/2022] Open
Abstract
The flavor profile of Chinese liquor is the result of the metabolic activity of its microbial community. Given the importance of the microbial interaction, a novel way to control the liquor's flavor is by regulating the composition of the community. In this study, we efficiently improved the liquor's flavor by perturbing the intrinsic microbial metabolism with extrinsic microbes. We first constructed a basic microbial group (intrinsic) containing Saccharomyces cerevisiae, Wickerhamomyces anomalus, and Issatchenkia orientalis and added special flavor producers (extrinsic), Saccharomyces uvarum and Saccharomyces servazzii, to this intrinsic group. Upon the addition of the extrinsic microbes, the maximum specific growth rates of S. cerevisiae and I. orientalis increased from 6.19 to 43.28/day and from 1.15 to 14.32/day, respectively, but that of W. anomalus changed from 1.00 to 0.96/day. In addition, most volatile compounds known to be produced by the extrinsic strains were not produced. However, more esters, alcohols, and acids were produced by S. cerevisiae and I. orientalis. Six compounds were significantly different by random forest analysis after perturbation. Among them, increases in ethyl hexanoate, isobutanol, and 3-methylbutyric acid were correlated with S. cerevisiae and I. orientalis, and a decrease in geranyl acetone was correlated with W. anomalus. Variations in ethyl acetate and 2-phenylethanol might be due to the varied activity of W. anomalus and S. cerevisiae. This work showed the effect of the interaction between the intrinsic and extrinsic microbes on liquor flavor, which would be beneficial for improving the quality of Chinese liquor.
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Abdelmohsen UR, Grkovic T, Balasubramanian S, Kamel MS, Quinn RJ, Hentschel U. Elicitation of secondary metabolism in actinomycetes. Biotechnol Adv 2015; 33:798-811. [PMID: 26087412 DOI: 10.1016/j.biotechadv.2015.06.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt.
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Srikkanth Balasubramanian
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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Iversen H, Lindbäck T, L’Abée-Lund TM, Roos N, Aspholm M, Stenfors Arnesen L. The gut bacterium Bacteroides thetaiotaomicron influences the virulence potential of the enterohemorrhagic Escherichia coli O103:H25. PLoS One 2015; 10:e0118140. [PMID: 25719195 PMCID: PMC4342160 DOI: 10.1371/journal.pone.0118140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/17/2014] [Indexed: 11/18/2022] Open
Abstract
Enterohemorrhagic E. coli (EHEC) is associated with severe gastrointestinal disease. Upon entering the gastrointestinal tract, EHEC is exposed to a fluctuating environment and a myriad of other bacterial species. To establish an infection, EHEC strains have to modulate their gene expression according to the GI tract environment. In order to explore the interspecies interactions between EHEC and an human intestinal commensal, the global gene expression profile was determined of EHEC O103:H25 (EHEC NIPH-11060424) co-cultured with B. thetaiotaomicron (CCUG 10774) or grown in the presence of spent medium from B. thetaiotaomicron. Microarray analysis revealed that approximately 1% of the EHEC NIPH-11060424 genes were significantly up-regulated both in co-culture (30 genes) and in the presence of spent medium (44 genes), and that the affected genes differed between the two conditions. In co-culture, genes encoding structural components of the type three secretion system were among the most affected genes with an almost 4-fold up-regulation, while the most affected genes in spent medium were involved in chemotaxis and were more than 3-fold up-regulated. The operons for type three secretion system (TTSS) are located on the Locus of enterocyte effacement (LEE) pathogenicity island, and qPCR showed that genes of all five operons (LEE1-LEE5) were up-regulated. Moreover, an increased adherence to HeLa cells was observed in EHEC NIPH-11060424 exposed to B. thetaiotaomicron. Expression of stx2 genes, encoding the main virulence factor of EHEC, was down-regulated in both conditions (co-culture/spent medium). These results show that expression of EHEC genes involved in colonization and virulence is modulated in response to direct interspecies contact between cells, or to diffusible factors released from B. thetaiotaomicron. Such interspecies interactions could allow the pathogen to recognize its predilection site and modulate its behaviour accordingly, thus increasing the efficiency of colonization of the colon mucosa, facilitating its persistence and increasing its virulence potential.
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Affiliation(s)
- Hildegunn Iversen
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Toril Lindbäck
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Trine M. L’Abée-Lund
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Norbert Roos
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marina Aspholm
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Lotte Stenfors Arnesen
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
- * E-mail:
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Saraoui T, Fall PA, Leroi F, Antignac JP, Chéreau S, Pilet MF. Inhibition mechanism of Listeria monocytogenes by a bioprotective bacteria Lactococcus piscium CNCM I-4031. Food Microbiol 2015; 53:70-8. [PMID: 26611171 DOI: 10.1016/j.fm.2015.01.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/31/2014] [Accepted: 01/09/2015] [Indexed: 11/27/2022]
Abstract
Listeria monocytogenes is a pathogenic Gram positive bacterium and the etiologic agent of listeriosis, a severe food-borne disease. Lactococcus piscium CNCM I-4031 has the capacity to prevent the growth of L. monocytogenes in contaminated peeled and cooked shrimp. To investigate the inhibititory mechanism, a chemically defined medium (MSMA) based on shrimp composition and reproducing the inhibition observed in shrimp was developed. In co-culture at 26 °C, L. monocytogenes was reduced by 3-4 log CFU g(-1) after 24 h. We have demonstrated that the inhibition was not due to secretion of extracellular antimicrobial compounds as bacteriocins, organic acids and hydrogen peroxide. Global metabolomic fingerprints of these strains in pure culture were assessed by liquid chromatography coupled with high resolution mass spectrometry. Consumption of glucose, amino-acids, vitamins, nitrogen bases, iron and magnesium was measured and competition for some molecules could be hypothesized. However, after 24 h of co-culture, when inhibition of L. monocytogenes occurred, supplementation of the medium with these compounds did not restore its growth. The inhibition was observed in co-culture but not in diffusion chamber when species were separated by a filter membrane. Taken together, these data indicate that the inhibition mechanism of L. monocytogenes by L. piscium is cell-to-cell contact-dependent.
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Affiliation(s)
- Taous Saraoui
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM(3)B), Ifremer, Rue de l'Ile d'Yeu, 44311 Nantes Cedex 03, France; LUNAM Université, Oniris, UMR 1014 Secalim, Site de la Chantrerie, Nantes, F-44307, France; INRA, Nantes, F-44307, France
| | - Papa Abdoulaye Fall
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM(3)B), Ifremer, Rue de l'Ile d'Yeu, 44311 Nantes Cedex 03, France; LUNAM Université, Oniris, UMR 1014 Secalim, Site de la Chantrerie, Nantes, F-44307, France; INRA, Nantes, F-44307, France
| | - Françoise Leroi
- Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM(3)B), Ifremer, Rue de l'Ile d'Yeu, 44311 Nantes Cedex 03, France
| | - Jean-Philippe Antignac
- LUNAM Université, Oniris, USC INRA 1329, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, F-44307, France
| | - Sylvain Chéreau
- LUNAM Université, Oniris, USC INRA 1329, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, F-44307, France
| | - Marie France Pilet
- LUNAM Université, Oniris, UMR 1014 Secalim, Site de la Chantrerie, Nantes, F-44307, France; INRA, Nantes, F-44307, France.
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Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum. Heredity (Edinb) 2015; 114:476-84. [PMID: 25585922 DOI: 10.1038/hdy.2014.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 11/19/2014] [Accepted: 12/03/2014] [Indexed: 01/07/2023] Open
Abstract
Social bacteria use chemical communication to coordinate and synchronize gene expression via the quorum-sensing (QS) regulatory pathway. In Pectobacterium, a causative agent of the blackleg and soft-rot diseases on potato plants and tubers, expression of the virulence factors is collectively controlled by the QS-signals N-acylhomoserine lactones (NAHLs). Several soil bacteria, such as the actinobacterium Rhodococcus erythropolis, are able to degrade NAHLs, hence quench the chemical communication and virulence of Pectobacterium. Here, next-generation sequencing was used to investigate structural and functional genomics of the NAHL-degrading R. erythropolis strain R138. The R. erythropolis R138 genome (6.7 Mbp) contained a single circular chromosome, one linear (250 kbp) and one circular (84 kbp) plasmid. Growth of R. erythropolis and P. atrosepticum was not altered in mixed-cultures as compared with monocultures on potato tuber slices. HiSeq-transcriptomics revealed that no R. erythropolis genes were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the avirulent P. atrosepticum mutant expI, which is defective for QS-signal synthesis. By contrast 50 genes (<1% of the R. erythropolis genome) were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the NAHL-producing virulent P. atrosepticum. Among them, quantitative real-time reverse-transcriptase-PCR confirmed that the expression of some alkyl-sulfatase genes decreased in the presence of a virulent P. atrosepticum, as well as deprivation of organic sulfur such as methionine, which is a key precursor in the synthesis of NAHL by P. atrosepticum.
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Engineering propionibacteria as versatile cell factories for the production of industrially important chemicals: advances, challenges, and prospects. Appl Microbiol Biotechnol 2014; 99:585-600. [PMID: 25431012 DOI: 10.1007/s00253-014-6228-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/11/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Propionibacteria are actinobacteria consisting of two principal groups: cutaneous and dairy. Cutaneous propionibacteria are considered primary pathogens to humans, whereas dairy propionibacteria are widely used in the food and pharmaceutical industries. Increasing attention has been focused on improving the performance of dairy propionibacteria for the production of industrially important chemicals, and significant advances have been made through strain engineering and process optimization in the production of flavor compounds, nutraceuticals, and antimicrobial compounds. In addition, genome sequencing of several propionibacteria species has been completed, deepening understanding of the metabolic and physiological features of these organisms. However, the metabolic engineering of propionibacteria still faces several challenges owing to the lack of efficient genome manipulation tools and the existence of various types of strong restriction-modification systems. The emergence of systems and synthetic biology provides new opportunities to overcome these bottlenecks. In this review, we first introduce the major species of propionibacteria and their properties and provide an overview of their functions and applications. We then discuss advances in the genome sequencing and metabolic engineering of these bacteria. Finally, we discuss systems and synthetic biology approaches for engineering propionibacteria as efficient and robust cell factories for the production of industrially important chemicals.
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Contribution of Lactococcus lactis reducing properties to the downregulation of a major virulence regulator in Staphylococcus aureus, the agr system. Appl Environ Microbiol 2014; 80:7028-35. [PMID: 25192992 DOI: 10.1128/aem.02287-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major cause of food poisoning outbreaks associated with dairy products, because of the ingestion of preformed enterotoxins. The biocontrol of S. aureus using lactic acid bacteria (LAB) offers a promising opportunity to fight this pathogen while respecting the product ecosystem. We had previously established the ability of Lactococcus lactis, a lactic acid bacterium widely used in the dairy industry, to downregulate a major staphylococcal virulence regulator, the accessory gene regulator (agr) system, and, as a consequence, agr-controlled enterotoxins. In the present paper, we have shown that the oxygen-independent reducing properties of L. lactis contribute to agr downregulation. Neutralizing lactococcal reduction by adding potassium ferricyanide or maintaining the oxygen pressure constant at 50% released agr downregulation in the presence of L. lactis. This downregulation still occurred in an S. aureus srrA mutant, indicating that the staphylococcal respiratory response regulator SrrAB was not the only component in the signaling pathway. Therefore, this study clearly demonstrates the ability of L. lactis reducing properties to interfere with the expression of S. aureus virulence, thus highlighting this general property of LAB as a lever to control the virulence expression of this major pathogen in a food context and beyond.
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Bajaj I, Veiga T, van Dissel D, Pronk JT, Daran JM. Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis. BMC Microbiol 2014; 14:114. [PMID: 24884713 PMCID: PMC4077275 DOI: 10.1186/1471-2180-14-114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/17/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other microorganisms, a common occurrence in nature, is rarely studied under laboratory conditions. To explore cellular responses of the antibiotic-producing fungus Penicillium chrysogenum to prokaryotes, the present study investigates its transcriptional responses during co-cultivation with Bacillus subtilis. RESULTS Steady-state glucose-limited chemostats of P. chrysogenum grown under penillicin-non-producing conditions were inoculated with B. subtilis. Physiological and transcriptional responses of P. chrysogenum in the resulting mixed culture were monitored over 72 h. Under these conditions, B. subtilis outcompeted P. chrysogenum, as reflected by a three-fold increase of the B. subtilis population size and a two-fold reduction of the P. chrysogenum biomass concentration. Genes involved in the penicillin pathway and in synthesis of the penicillin precursors and side-chain were unresponsive to the presence of B. subtilis. Moreover, Penicillium polyketide synthase and nonribosomal peptide synthase genes were either not expressed or down-regulated. Among the highly responsive genes, two putative α-1,3 endoglucanase (mutanase) genes viz Pc12g07500 and Pc12g13330 were upregulated by more than 15-fold and 8-fold, respectively. Measurement of enzyme activity in the supernatant of mixed culture confirmed that the co-cultivation with B. subtilis induced mutanase production. Mutanase activity was neither observed in pure cultures of P. chrysogenum or B. subtilis, nor during exposure of P. chrysogenum to B. subtilis culture supernatants or heat-inactivated B. subtilis cells. However, mutanase production was observed in cultures of P. chrysogenum exposed to filter-sterilized supernatants of mixed cultures of P. chrysogenum and B. subtilis. Heterologous expression of Pc12g07500 and Pc12g13330 genes in Saccharomyces cerevisiae confirmed that Pc12g07500 encoded an active α-1,3 endoglucanase. CONCLUSION Time-course transcriptional profiling of P. chrysogenum revealed differentially expressed genes during co-cultivation with B. subtilis. Penicillin production was not induced under these conditions. However, induction of a newly characterized P. chrysogenum gene encoding α-1,3 endoglucanase may enhance the efficacy of fungal antibiotics by degrading bacterial exopolysaccharides.
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Affiliation(s)
- Ishwar Bajaj
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Tânia Veiga
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Dino van Dissel
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, the Netherlands
- Platform for Green Synthetic Biology, P.O. Box 5057, 2600 GA Delft, the Netherlands
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Genotypic and phenotypic analysis of dairy Lactococcus lactis biodiversity in milk: volatile organic compounds as discriminating markers. Appl Environ Microbiol 2013; 79:4643-52. [PMID: 23709512 DOI: 10.1128/aem.01018-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The diversity of nine dairy strains of Lactococcus lactis subsp. lactis in fermented milk was investigated by both genotypic and phenotypic analyses. Pulsed-field gel electrophoresis and multilocus sequence typing were used to establish an integrated genotypic classification. This classification was coherent with discrimination of the L. lactis subsp. lactis bv. diacetylactis lineage and reflected clonal complex phylogeny and the uniqueness of the genomes of these strains. To assess phenotypic diversity, 82 variables were selected as important dairy features; they included physiological descriptors and the production of metabolites and volatile organic compounds (VOCs). Principal-component analysis (PCA) demonstrated the phenotypic uniqueness of each of these genetically closely related strains, allowing strain discrimination. A method of variable selection was developed to reduce the time-consuming experimentation. We therefore identified 20 variables, all associated with VOCs, as phenotypic markers allowing discrimination between strain groups. These markers are representative of the three metabolic pathways involved in flavor: lipolysis, proteolysis, and glycolysis. Despite great phenotypic diversity, the strains could be divided into four robust phenotypic clusters based on their metabolic orientations. Inclusion of genotypic diversity in addition to phenotypic characters in the classification led to five clusters rather than four being defined. However, genotypic characters make a smaller contribution than phenotypic variables (no genetic distances selected among the most contributory variables). This work proposes an original method for the phenotypic differentiation of closely related strains in milk and may be the first step toward a predictive classification for the manufacture of starters.
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Souza EL, Oliveira CEV, Stamford TLM, Conceição ML, Neto NJG. Influence of carvacrol and thymol on the physiological attributes, enterotoxin production and surface characteristics of Staphylococcus aureus strains isolated from foods. Braz J Microbiol 2013; 44:29-35. [PMID: 24159280 PMCID: PMC3804174 DOI: 10.1590/s1517-83822013005000001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/02/2012] [Indexed: 11/25/2022] Open
Abstract
This study evaluated the influence of the phenolic compounds carvacrol (CAR) and thymol (THY) on some physiological characteristics and on the modulation of the secretion of some staphylococcal virulence factors, that is, coagulase and enterotoxin. This study also investigated possible mechanisms for the establishment of the anti-staphylococcal activity of these compounds. Sublethal concentrations (0.3 and 0.15 μL/mL) of CAR and THY inhibited the activity of the enzymes coagulase and lipase and led to a decrease in salt tolerance. At the tested sublethal concentrations, both CAR and THY led to a total suppression of enterotoxin production. The loss of a 260-nm-absorbing material and an efflux of potassium ions occurred immediately after the addition of CAR and THY at 0.6 and 1.2 μL/mL and increased up to 120 min of exposure. Electron microscopy of cells exposed to CAR and THY (0.6 μL/mL) revealed that individual cells appeared to be deformed, with projections of cellular material. The observations of leakage of cellular material and an altered cell surface suggest that gross damage to a cell’s cytoplasmic membrane, which results in a disruption in protein secretion, could be responsible for the anti-staphylococcal properties of CAR and THY.
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Affiliation(s)
- E L Souza
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
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Porosity of Lactococcus lactis subsp. lactis LD61 colonies immobilised in model cheese. Int J Food Microbiol 2013; 163:64-70. [PMID: 23558188 DOI: 10.1016/j.ijfoodmicro.2013.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 02/19/2013] [Accepted: 02/23/2013] [Indexed: 11/23/2022]
Abstract
During cheese ripening, micro-organisms grow as immobilised colonies, metabolising substrates present in the matrix which generate products triggered by enzymatic reactions. Local limitation rates of diffusion, either in the matrix or within the bacterial colonies, can be responsible for modulation in the metabolic and enzymatic activities of micro-organisms during ripening. How bacterial colonies immobilised in cheese are porous to these diffusing solutes has never been explored. The objective of this study was to determine if fluorescent dextrans of different sizes (4.4, 70 and 155 kDa) are able to penetrate through colonies of Lactococcus lactis LD61 immobilised in solid media, either agar or model cheese. Confocal microscopic observations showed that lactococcus colonies immobilised in these two media were porous to dextrans from 4 kDa to 155 kDa. However, the rate of diffusion of the solutes was faster inside the colonies immobilised in ultrafiltered-cheese than in agar when large dextrans were considered (≥70 kDa). The colonial shape of the lactococcus strain was also shown to be lenticular in agar and spherical in the model cheese, indicating that the physical pressure exerted on the colony by the surrounding casein network was probably isotropous in the UF-cheese but not in agar. In both cases, the fact that lactococcus colonies immobilised in solid media are porous to large dextran solutes suggests that substrates or enzymes are likely also to be able to migrate inside the colonies during cheese ripening.
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Comparative analysis of temperature-dependent transcriptome of Pseudomonas aeruginosa strains from rhizosphere and human habitats. Appl Microbiol Biotechnol 2012; 96:1007-19. [PMID: 23053111 DOI: 10.1007/s00253-012-4466-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 01/13/2023]
Abstract
In this study, we investigated the effects of a change in growth temperature on the transcriptome of two strains of Pseudomonas aeruginosa. The chosen P. aeruginosa strains were M18 and PAO1, which are adapted to two different niches, rhizosphere and human, respectively. To assess the changes induced by a change in temperature, we used a newly designed microarray covering the complete genome of four P. aeruginosa strains: PAO1, M18, PA14 and LESB58, which proved informative and reliable for the transcriptome study. Using the microarray, we analysed the transcriptome profile changes of two P. aeruginosa strains of M18 and PAO1 at their originating and non-originating temperatures: 28 °C for the rhizosphere and 37 °C for the human. The transcriptome profiles showed significant temperature-dependent differences (64.8 % in M18 and 66.8 % in PAO1) compared with the genome structure (6 % in M18 and 4.1 % in PAO1). Furthermore, we found that the specific induced genes at the non-originating growth temperature of the each strain (207 genes in M18 and 229 genes in PAO1) were evidently more than those induced at the originating growth temperature (158 genes in M18 and 169 genes in PAO1). The functional analysis of several newly found specific regulated operons (such as phh, liu, hmg) in the two strains indicated possible strategies implemented to respond to the non-originating temperature. This study provides new insight into how P. aeruginosa species responds to temperature change and a microarray platform covering the complete genomes of four widely studied P. aeruginosa strains.
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Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A. Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev 2011; 75:583-609. [PMID: 22126995 PMCID: PMC3232736 DOI: 10.1128/mmbr.00020-11] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology.
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Affiliation(s)
- P Frey-Klett
- INRA, UMR1136 Interactions Arbres-Microorganismes, 54280 Champenoux, France.
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26
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Changes in transcription profiles reflect strain contributions to defined cultures of Lactococcus lactis subsp. cremoris during milk fermentation. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Cretenet M, Nouaille S, Thouin J, Rault L, Stenz L, François P, Hennekinne JA, Piot M, Maillard MB, Fauquant J, Loubière P, Le Loir Y, Even S. Staphylococcus aureus virulence and metabolism are dramatically affected by Lactococcus lactis in cheese matrix. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:340-351. [PMID: 23761280 DOI: 10.1111/j.1758-2229.2010.00230.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In complex environments such as cheeses, the lack of relevant information on the physiology and virulence expression of pathogenic bacteria and the impact of endogenous microbiota has hindered progress in risk assessment and control. Here, we investigated the behaviour of Staphylococcus aureus, a major foodborne pathogen, in a cheese matrix, either alone or in the presence of Lactococcus lactis, as a dominant species of cheese ecosystems. The dynamics of S. aureus was explored in situ by coupling a microbiological and, for the first time, a transcriptomic approach. Lactococcus lactis affected the carbohydrate and nitrogen metabolisms and the stress response of S. aureus by acidifying, proteolysing and decreasing the redox potential of the cheese matrix. Enterotoxin expression was positively or negatively modulated by both L. lactis and the cheese matrix itself, depending on the enterotoxin type. Among the main enterotoxins involved in staphylococcal food poisoning, sea expression was slightly favoured in the presence of L. lactis, whereas a strong repression of sec4 was observed in cheese matrix, even in the absence of L. lactis, and correlated with a reduced saeRS expression. Remarkably, the agr system was downregulated by the presence of L. lactis, in part because of the decrease in pH. This study highlights the intimate link between environment, metabolism and virulence, as illustrated by the influence of the cheese matrix context, including the presence of L. lactis, on two major virulence regulators, the agr system and saeRS.
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Affiliation(s)
- Marina Cretenet
- INRA, UMR1253 STLO, 85 rue de Saint Brieuc, F-35000 Rennes, France. Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, F-35000 Rennes, France. Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France. INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France. CNRS, UMR5504, F-31400 Toulouse, France. Genomic Research Laboratory, University of Geneva Hospitals, Rue Gabrielle-Perret-Gentil, 4 CH-1211 Geneva 14, Switzerland. University Medical Center, Department of Microbiology and Molecular Medicine, CH-1211 Geneva 4, Switzerland. Laboratory for Study and Research on Quality of Food and on Food Processes, French Agency for Food Safety (AFSSA-lerqap), National and Community Reference Laboratory, 94704 Maisons-Alfort cedex, France
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Cretenet M, Even S, Le Loir Y. Unveiling Staphylococcus aureus enterotoxin production in dairy products: a review of recent advances to face new challenges. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0014-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Dynamic analysis of the Lactococcus lactis transcriptome in cheeses made from milk concentrated by ultrafiltration reveals multiple strategies of adaptation to stresses. Appl Environ Microbiol 2010; 77:247-57. [PMID: 21075879 DOI: 10.1128/aem.01174-10] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis is used extensively for the production of various cheeses. At every stage of cheese fabrication, L. lactis has to face several stress-generating conditions that result from its own modification of the environment as well as externally imposed conditions. We present here the first in situ global gene expression profile of L. lactis in cheeses made from milk concentrated by ultrafiltration (UF-cheeses), a key economical cheese model. The transcriptomic response of L. lactis was analyzed directly in a cheese matrix, starting from as early as 2 h and continuing for 7 days. The growth of L. lactis stopped after 24 h, but metabolic activity was maintained for 7 days. Conservation of its viability relied on an efficient proteolytic activity measured by an increasing, quantified number of free amino acids in the absence of cell lysis. Extensive downregulation of genes under CodY repression was found at day 7. L. lactis developed multiple strategies of adaptation to stressful modifications of the cheese matrix. In particular, expression of genes involved in acidic- and oxidative-stress responses was induced. L. lactis underwent unexpected carbon limitation characterized by an upregulation of genes involved in carbon starvation, principally due to the release of the CcpA control. We report for the first time that in spite of only moderately stressful conditions, lactococci phage is repressed under UF-cheese conditions.
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Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures. Appl Environ Microbiol 2009; 75:4459-72. [PMID: 19429556 DOI: 10.1128/aem.02388-08] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Staphylococcus aureus is responsible for numerous food poisonings due to the production of enterotoxins by strains contaminating foodstuffs, especially dairy products. Several parameters, including interaction with antagonistic flora such as Lactococcus lactis, a lactic acid bacterium widely used in the dairy industry, can modulate S. aureus proliferation and virulence expression. We developed a dedicated S. aureus microarray to investigate the effect of L. lactis on staphylococcal gene expression in mixed cultures. This microarray was used to establish the transcriptomic profile of S. aureus in mixed cultures with L. lactis in a chemically defined medium held at a constant pH (6.6). Under these conditions, L. lactis hardly affected S. aureus growth. The expression of most genes involved in the cellular machinery, carbohydrate and nitrogen metabolism, and stress responses was only slightly modulated: a short time lag in mixed compared to pure cultures was observed. Interestingly, the induction of several virulence factors and regulators, including the agr locus, sarA, and some enterotoxins, was strongly affected. This work clearly underlines the complexity of L. lactis antagonistic potential for S. aureus and yields promising leads for investigations into nonantibiotic biocontrol of this major pathogen.
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