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Sharma A, Gupta G, Ahmad T, Kaur B, Hakeem KR. Tailoring cellular metabolism in lactic acid bacteria through metabolic engineering. J Microbiol Methods 2020; 170:105862. [DOI: 10.1016/j.mimet.2020.105862] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 01/04/2023]
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2
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Effects of new technology on the current manufacturing process of yogurt-to increase the overall marketability of yogurt. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.03.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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3
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Kok J, van Gijtenbeek LA, de Jong A, van der Meulen SB, Solopova A, Kuipers OP. The Evolution of gene regulation research in Lactococcus lactis. FEMS Microbiol Rev 2018; 41:S220-S243. [PMID: 28830093 DOI: 10.1093/femsre/fux028] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/15/2017] [Indexed: 11/12/2022] Open
Abstract
Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism. Among many other things, this has provided an unprecedented view of the major gene regulatory pathways involved in nitrogen and carbon metabolism and their overlap, and has led to the blossoming of the field of L. lactis systems biology. All of these advances have made L. lactis the paradigm of the LAB. This review will deal with the exciting path along which the research on the genetics of and gene regulation in L. lactis has trodden.
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Affiliation(s)
- Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Lieke A van Gijtenbeek
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ana Solopova
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
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Loira N, Mendoza S, Paz Cortés M, Rojas N, Travisany D, Genova AD, Gajardo N, Ehrenfeld N, Maass A. Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. BMC SYSTEMS BIOLOGY 2017; 11:66. [PMID: 28676050 PMCID: PMC5496344 DOI: 10.1186/s12918-017-0441-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/09/2017] [Indexed: 11/10/2022]
Abstract
Background Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and triacylglycerols. It has been used as a source of biofuel, pigments and food supplements, like Omega 3. Only some Nannochloropsis species have been sequenced, but none of them benefit from a genome-scale metabolic model (GSMM), able to predict its metabolic capabilities. Results We present iNS934, the first GSMM for N. salina, including 2345 reactions, 934 genes and an exhaustive description of lipid and nitrogen metabolism. iNS934 has a 90% of accuracy when making simple growth/no-growth predictions and has a 15% error rate in predicting growth rates in different experimental conditions. Moreover, iNS934 allowed us to propose 82 different knockout strategies for strain optimization of triacylglycerols. Conclusions iNS934 provides a powerful tool for metabolic improvement, allowing predictions and simulations of N. salina metabolism under different media and genetic conditions. It also provides a systemic view of N. salina metabolism, potentially guiding research and providing context to -omics data. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0441-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolás Loira
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile. .,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.
| | - Sebastian Mendoza
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.,Universidad Adolfo Ibáñez, Diagonal Las Torres 2640, Santiago, Chile
| | - Natalia Rojas
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Alex Di Genova
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Natalia Gajardo
- Centro de Investigación Austral Biotech, Universidad Santo Tomás, Avenida Ejercito 146, Santiago, Chile
| | - Nicole Ehrenfeld
- Centro de Investigación Austral Biotech, Universidad Santo Tomás, Avenida Ejercito 146, Santiago, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
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Karami S, Roayaei M, Hamzavi H, Bahmani M, Hassanzad-Azar H, Leila M, Rafieian-Kopaei M. Isolation and identification of probiotic Lactobacillus from local dairy and evaluating their antagonistic effect on pathogens. Int J Pharm Investig 2017; 7:137-141. [PMID: 29184826 PMCID: PMC5680649 DOI: 10.4103/jphi.jphi_8_17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objective: Probiotics such as lactobacilli prevent the development of a wide range of human and animal's pathogens. The aim of this study was evaluation of antagonistic effect of isolated lactobacilli from local dairy products against three standard strains of Staphylococcus aureus, Bacillus subtilis, and Pseudomonas aeruginosa. Materials and Methods: Twenty samples of local dairy products including cow milk, buffalo milk, cheese, and yogurt were collected from different areas of Ahwaz city. Antimicrobial disc diffusion method was applied on S. aureus (ATCC-6538), B. subtilis (ATCC-12711), and P. aeruginosa (ATCC-27853). Antimicrobial effects of isolates were evaluated by disc diffusion test on Mueller-Hinton agar medium plated with three pathogens. Results: Obtained results showed that only three strains of isolated lactobacilli of local dairy samples had inhibitory effects on understudy pathogens including Lactobacillus alimentarius, Lactobacillus sake, and Lactobacillus collinoides. All three isolates showed moderate activity (inhibition zone <15 mm) except of L. collinoides and L. alimentarius that had relatively strong activity (inhibition zone ≥15 mm) against P. aeruginosa and B. subtilis, respectively. Conclusion: These bacteria can be raised for the production of various kinds of food, pharmaceutical products, and functional foods.
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Affiliation(s)
- Sahar Karami
- Department of Biology, Faculty of Science, University of Chamran, Ahwaz, Iran
| | - Mohammad Roayaei
- Department of Biology, Faculty of Science, University of Chamran, Ahwaz, Iran
| | - Hosna Hamzavi
- Department of Biology, Faculty of Science, University of Chamran, Ahwaz, Iran
| | - Mahmoud Bahmani
- Biotechnology and Medicinal Plants Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Hassan Hassanzad-Azar
- Department of Food Safety and Hygiene, School of Paramedical and Health, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mahmoodnia Leila
- Department of Internal Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
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Kavitha S, Jeevaratnam K. Molecular Characterization of Lactobacilli Isolated fromPiper betleL. var. Pachaikodi and Comparative Analysis of the Antimicrobial Effects of IsolateLactobacillus plantarumKJB23 and Betel Leaves Extract. FOOD BIOTECHNOL 2016. [DOI: 10.1080/08905436.2016.1166440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Ferrer Valenzuela J, Pinuer LA, García Cancino A, Bórquez Yáñez R. Metabolic Fluxes in Lactic Acid Bacteria—A Review. FOOD BIOTECHNOL 2015. [DOI: 10.1080/08905436.2015.1027913] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Alfano A, Donnarumma G, Cimini D, Fusco A, Marzaioli I, De Rosa M, Schiraldi C. Lactobacillus plantarum: Microfiltration experiments for the production of probiotic biomass to be used in food and nutraceutical preparations. Biotechnol Prog 2015; 31:325-33. [DOI: 10.1002/btpr.2037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/09/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Alberto Alfano
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Giovanna Donnarumma
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Donatella Cimini
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Alessandra Fusco
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Iolanda Marzaioli
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Mario De Rosa
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
| | - Chiara Schiraldi
- Dept. of Experimental Medicine; Second University of Naples; via De Crecchio n°7 80138 Naples Italy
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Smid EJ, Erkus O, Spus M, Wolkers-Rooijackers JCM, Alexeeva S, Kleerebezem M. Functional implications of the microbial community structure of undefined mesophilic starter cultures. Microb Cell Fact 2014; 13 Suppl 1:S2. [PMID: 25185941 PMCID: PMC4155819 DOI: 10.1186/1475-2859-13-s1-s2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions.
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Adeyemo S, Onilude A. Enzymatic Reduction of Anti-nutritional Factors in Fermenting Soybeans by Lactobacillus plantarum Isolates from Fermenting Cereals. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/s0189-7241(15)30080-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Papagianni M. Metabolic engineering of lactic acid bacteria for the production of industrially important compounds. Comput Struct Biotechnol J 2012; 3:e201210003. [PMID: 24688663 PMCID: PMC3962192 DOI: 10.5936/csbj.201210003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/10/2012] [Accepted: 09/15/2012] [Indexed: 01/21/2023] Open
Abstract
Lactic acid bacteria (LAB) are receiving increased attention for use as cell factories for the production of metabolites with wide use by the food and pharmaceutical industries. The availability of efficient tools for genetic modification of LAB during the past decade permitted the application of metabolic engineering strategies at the levels of both the primary and the more complex secondary metabolism. The recent developments in the area with a focus on the production of industrially important metabolites will be discussed in this review.
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Affiliation(s)
- Maria Papagianni
- Department of Hygiene and Technology of Food of Animal Origin, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
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12
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Goel A, Wortel MT, Molenaar D, Teusink B. Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett 2012; 34:2147-60. [PMID: 22936303 PMCID: PMC3487007 DOI: 10.1007/s10529-012-1038-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/16/2012] [Indexed: 04/28/2023]
Abstract
Performance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.
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Affiliation(s)
- Anisha Goel
- Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Engineering the central pathways in Lactococcus lactis: Functional expression of the phosphofructokinase (pfk) and alternative oxidase (aox1) genes from Aspergillus niger in Lactococcus lactis facilitates improved carbon conversion rates under oxidizing conditions. Enzyme Microb Technol 2012; 51:125-30. [DOI: 10.1016/j.enzmictec.2012.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/23/2012] [Accepted: 04/23/2012] [Indexed: 11/21/2022]
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Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 2012; 11:50. [PMID: 22545791 PMCID: PMC3461431 DOI: 10.1186/1475-2859-11-50] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/30/2012] [Indexed: 01/19/2023] Open
Abstract
This paper gives an overview of the recent advances in engineering the central carbon metabolism of the industrially important bacteria Escherichia coli, Bacillus subtilis, Corynobacterium glutamicum, Streptomyces spp., Lactococcus lactis and other lactic acid bacteria. All of them are established producers of important classes of products, e.g. proteins, amino acids, organic acids, antibiotics, high-value metabolites for the food industry and also, promising producers of a large number of industrially or therapeutically important chemicals. Optimization of existing or introduction of new cellular processes in these microorganisms is often achieved through manipulation of targets that reside at major points of central metabolic pathways, such as glycolysis, gluconeogenesis, the pentose phosphate pathway and the tricarboxylic acid cycle with the glyoxylate shunt. Based on the huge progress made in recent years in biochemical, genetic and regulatory studies, new fascinating engineering approaches aim at ensuring an optimal carbon and energy flow within central metabolism in order to achieve optimized metabolite production.
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Capozzi V, Russo P, Fragasso M, De Vita P, Fiocco D, Spano G. Biotechnology and pasta-making: lactic Acid bacteria as a new driver of innovation. Front Microbiol 2012; 3:94. [PMID: 22457660 PMCID: PMC3304088 DOI: 10.3389/fmicb.2012.00094] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 02/26/2012] [Indexed: 01/12/2023] Open
Abstract
Cereals-derived foods represent a key constituent in the diet of many populations. In particular, pasta is consumed in large quantities throughout the world in reason of its nutritive importance, containing significant amounts of complex carbohydrates, proteins, B-vitamins, and iron. Lactic acid bacteria (LAB) are a heterogeneous group of bacteria that play a key role in the production of fermented foods and beverages with high relevance for human and animal health. A wide literature testifies the multifaceted importance of LAB biotechnological applications in cereal-based products. Several studies focused on LAB isolation and characterization in durum wheat environment, in some cases with preliminary experimental applications of LAB in pasta-making. In this paper, using sourdough as a model, we focus on the relevant state-of-art to introduce a LAB-based biotechnological step in industrial pasta-making, a potential world driver of innovation that might represent a cutting-edge advancement in pasta production.
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Affiliation(s)
- Vittorio Capozzi
- Molecular Microbiology, Department of Food Science, Foggia University Foggia, Italy
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Sánchez A, Coton M, Coton E, Herrero M, García LA, Díaz M. Prevalent lactic acid bacteria in cider cellars and efficiency of Oenococcus oeni strains. Food Microbiol 2012; 32:32-7. [PMID: 22850371 DOI: 10.1016/j.fm.2012.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 12/19/2011] [Accepted: 02/14/2012] [Indexed: 11/29/2022]
Abstract
Malolactic fermentation (MLF) is an important step in cider production in order to allowing for improvement of microbiological stability and organoleptic characteristics of cider. Induction of this fermentation by using starter cultures enables a better control over this bioprocess, but although it is a common practice in winemaking, starters specifically focussed for cider MLF are not yet commercially available. Proper starter cultures need to present the ability to degrade l-malic acid conferring pleasing sensory characteristics while avoiding toxicological risks. In this work, lactic acid bacteria (LAB) were first isolated from MLF industrial cider samples, obtained in a cellar in the main cider-producing region of Spain, Asturias. Isolates, identified by molecular tools, belonged to the Lactobacillus brevis and Oenococcus oeni species. After a phylogenetic analysis, representative strains of both identified species were evaluated in order to determine their fermentation capacity, showing O. oeni the best behaviour in this cider fermentation, as previously demonstrated for wine in the literature. Consequently, and with the aim to test the influence at strain level, selection of O. oeni isolates as starters for cider fermentation has been undergone. In order to check the influence of geography over biodiversity, O. oeni strains from six different industrial cellars representing the distinct producing areas in the region (located in a ratio of 30 km) were analyzed by using a specific RAPD method. In this way, isolates were typed in five distinct groups, mainly corresponding to each producing area. All strains isolated from the same cellar showed the same RAPD profile revealing the significance of geographical origin in the indigenous cider LAB. Molecular tools were applied to reject those isolates exhibiting presence of genes related to organoleptic spoilage (exopolysaccharides and acrolein production) or food safety (biogenic amine production), as key selection criteria. Representative strains of each of the five O. oeni RAPD groups were tested as pure cultures to evaluate their technological utility for cider production. Experimental data of malic acid degradation and cell concentration obtained were fitted to previously selected kinetic models aimed to optimization and prediction of bioprocess performance. Four strains revealed as suitable potential starter cultures for conducting MLF in cider production.
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Affiliation(s)
- Ainoa Sánchez
- Department of Chemical Engineering and Environmental Technology, University of Oviedo, Spain
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Abstract
This review describes recent scientific and technological drivers of food fermentation research. In addition, a number of practical implications of the results of this development will be highlighted. The first part of the manuscript elaborates on the message that genome sequence information gives us an unprecedented view on the biodiversity of microbes in food fermentation. This information can be made applicable for tailoring relevant characteristics of food products through fermentation. The second part deals with the integration of genome sequence data into metabolic models and the use of these models for a number of topics that are relevant for food fermentation processes. The final part will be about metagenomics approaches to reveal the complexity and understand the functionality of undefined complex microbial consortia used in a diverse range of food fermentation processes.
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Affiliation(s)
- E J Smid
- NIZO Food Research, 6710 BA Ede, The Netherlands.
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MILLS SUSAN, O’SULLIVAN ORLA, HILL COLIN, FITZGERALD GERALD, ROSS RPAUL. The changing face of dairy starter culture research: From genomics to economics. INT J DAIRY TECHNOL 2010. [DOI: 10.1111/j.1471-0307.2010.00563.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Affiliation(s)
- Roland J Siezen
- Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, Wageningen, The Netherlands.
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Faijes M, Mars AE, Smid EJ. Comparison of quenching and extraction methodologies for metabolome analysis of Lactobacillus plantarum. Microb Cell Fact 2007; 6:27. [PMID: 17708760 PMCID: PMC2031893 DOI: 10.1186/1475-2859-6-27] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 08/20/2007] [Indexed: 11/25/2022] Open
Abstract
Background A reliable quenching and metabolite extraction method has been developed for Lactobacillus plantarum. The energy charge value was used as a critical indicator for fixation of metabolism. Results Four different aqueous quenching solutions, all containing 60% of methanol, were compared for their efficiency. Only the solutions containing either 70 mM HEPES or 0.85% (w/v) ammonium carbonate (pH 5.5) caused less than 10% cell leakage and the energy charge of the quenched cells was high, indicating rapid inactivation of the metabolism. The efficiency of extraction of intracellular metabolites from cell cultures depends on the extraction methods, and is expected to vary between micro-organisms. For L. plantarum, we have compared five different extraction methodologies based on (i) cold methanol, (ii) perchloric acid, (iii) boiling ethanol, (iv) chloroform/methanol (1:1) and (v) chloroform/water (1:1). Quantification of representative intracellular metabolites showed that the best extraction efficiencies were achieved with cold methanol, boiling ethanol and perchloric acid. Conclusion The ammonium carbonate solution was selected as the most suitable quenching buffer for metabolomics studies in L. plantarum because (i) leakage is minimal, (ii) the energy charge indicates good fixation of metabolism, and (iii) all components are easily removed during freeze-drying. A modified procedure based on cold methanol extraction combined good extractability with mild extraction conditions and high enzymatic inactivation. These features make the combination of these quenching and extraction protocols very suitable for metabolomics studies with L. plantarum.
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Affiliation(s)
- Magda Faijes
- TI Food & Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands
- Wageningen UR, Agrotechnology and Food Sciences Group, PO Box 17, 6700 AA Wageningen, The Netherlands
- Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Astrid E Mars
- TI Food & Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands
- Wageningen UR, Agrotechnology and Food Sciences Group, PO Box 17, 6700 AA Wageningen, The Netherlands
| | - Eddy J Smid
- TI Food & Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands
- NIZO food research, PO Box 20, 6710 BA, Ede, The Netherlands
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Castaldo C, Siciliano RA, Muscariello L, Marasco R, Sacco M. CcpA affects expression of the groESL and dnaK operons in Lactobacillus plantarum. Microb Cell Fact 2006; 5:35. [PMID: 17129387 PMCID: PMC1676014 DOI: 10.1186/1475-2859-5-35] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 11/27/2006] [Indexed: 11/10/2022] Open
Abstract
Background Lactic acid bacteria (LAB) are widely used in food industry and their growth performance is important for the quality of the fermented product. During industrial processes changes in temperature may represent an environmental stress to be overcome by starters and non-starters LAB. Studies on adaptation to heat shock have shown the involvement of the chaperon system-proteins in various Gram-positive bacteria. The corresponding operons, namely the dnaK and groESL operons, are controlled by a negative mechanism involving the HrcA repressor protein binding to the cis acting element CIRCE. Results We studied adaptation to heat shock in the lactic acid bacterium Lactobacillus plantarum. The LM3-2 strain, carrying a null mutation in the ccpA gene, encoding the catabolite control protein A (CcpA), showed a lower percent of survival to high temperature with respect to the LM3 wild type strain. Among proteins differentially expressed in the two strains, the GroES chaperon was more abundant in the wild type strain compared to the mutant strain under standard growth conditions. Transcriptional studies showed that class I heat shock operons were differentially expressed upon heat shock in both strains. Indeed, the dnaK and groESL operons were induced about two times more in the LM3 strain compared to the LM3-2 strain. Analysis of the regulatory region of the two operons showed the presence of cre sequences, putative binding sites for the CcpA protein. Conclusion The L. plantarum dnaK and groESL operons are characterized by the presence of the cis acting sequence CIRCE in the promoter region, suggesting a negative regulation by the HrcA/CIRCE system, which is a common type of control among the class I heat shock operons of Gram-positive bacteria. We found an additional system of regulation, based on a positive control exerted by the CcpA protein, which would interact with cre sequences present in the regulatory region of the dnaK and groESL operons. The absence of the CcpA protein results in a lower induction of the chaperon coding operons, with a consequent lower percent of survival of the LM3-2 mutant strain population with respect to the wild type when challenged with a heat insult.
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Affiliation(s)
- Cristiana Castaldo
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| | - Rosa A Siciliano
- Centro di Spettrometria di Massa Proteomica e Biomolecolare, Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy
| | - Lidia Muscariello
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| | - Rosangela Marasco
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Caserta, Italy
| | - Margherita Sacco
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
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22
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Marco ML, Bongers RS, de Vos WM, Kleerebezem M. Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl Environ Microbiol 2006; 73:124-32. [PMID: 17071785 PMCID: PMC1797133 DOI: 10.1128/aem.01475-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts, and L. plantarum strain WCFS1 is a human isolate with a known genome sequence. L. plantarum WCFS1 survives intestinal passage in an active form, and its transit time and transcriptional activities were monitored in 15 BALB/c mice at 2, 4, 6, 8, and 24 h after being fed a single intragastric dose of this organism. Enumeration of viable cells isolated from fecal material revealed that the majority of the L. plantarum inoculum transited the mouse intestine within 4 h after ingestion. Three mice were sacrificed at each time point, and total RNA was isolated from the mouse intestinal compartments (stomach through colon). Quantification of L. plantarum 16S rRNA by quantitative real-time reverse-transcription-PCR revealed that L. plantarum was present at elevated levels in the stomach and small intestine for at least 4 h following ingestion and for over 8 h in the cecum and colon. We also examined the expression of 9 L. plantarum housekeeping genes and 15 L. plantarum in vivo-inducible (ivi) genes previously identified by recombination-based in vivo expression technology to be induced in the mouse gastrointestinal tract. The relative expression levels of the ivi genes increased up to 350-fold in the mouse intestine compared to levels observed for L. plantarum WCFS1 cells grown in a rich laboratory medium. Moreover, several genes displayed intestinal compartment-specific (small intestine versus colon) activities. These results confirm that L. plantarum displays specific and differential responses at various sites along the mammalian intestine.
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Affiliation(s)
- Maria L Marco
- Wageningen Center for Food Sciences, NIZO food research, P.O. Box 20, 6710 BA Ede, The Netherlands
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23
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Liu M, van Enckevort FHJ, Siezen RJ. Genome update: lactic acid bacteria genome sequencing is booming. MICROBIOLOGY-SGM 2006; 151:3811-3814. [PMID: 16339927 DOI: 10.1099/mic.0.28557-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Mengjin Liu
- Friesland Foods Corporate Research, Deventer, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
| | - Frank H J van Enckevort
- Friesland Foods Corporate Research, Deventer, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
| | - Roland J Siezen
- Wageningen Centre for Food Sciences, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
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Trawick JD, Schilling CH. Use of constraint-based modeling for the prediction and validation of antimicrobial targets. Biochem Pharmacol 2005; 71:1026-35. [PMID: 16329998 DOI: 10.1016/j.bcp.2005.10.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 10/19/2005] [Accepted: 10/25/2005] [Indexed: 11/17/2022]
Abstract
The overall process of antimicrobial drug discovery and development seems simple, to cure infectious disease by identifying suitable antibiotic drugs. However, this goal has been difficult to fulfill in recent years. Despite the promise of the high-throughput innovations sparked by the genomics revolution, discovery, and development of new antibiotics has lagged in recent years exacerbating the already serious problem of evolution of antibiotic resistance. Therefore, both new antimicrobials are desperately needed as are improvements to speed up or improve nearly all steps in the process of discovering novel antibiotics and bringing these to clinical use. Another product of the genomic revolution is the modeling of metabolism using computational methodologies. Genomic-scale networks of metabolic reactions based on stoichiometry, thermodynamics and other physico-chemical constraints that emulate microbial metabolism have been developed into valuable research tools in metabolic engineering and other fields. This constraint-based modeling is predictive in identifying critical reactions, metabolites, and genes in metabolism. This is extremely useful in determining and rationalizing cellular metabolic requirements. In turn, these methods can be used to predict potential metabolic targets for antimicrobial research especially if used to increase the confidence in prioritization of metabolic targets. The many different capacities of constraint-based modeling also enable prediction of cellular response to specific inhibitors such as antibiotics and this may, ultimately find a role in drug discovery and development. Herein, we describe the principles of metabolic modeling and how they might initially be applied to antimicrobial research.
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Affiliation(s)
- John D Trawick
- Genomatica, Inc., 5405 Morehouse Dr., Suite 210, San Diego, CA 92121, USA.
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