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Grafakou A, Mosterd C, de Waal PP, van Rijswijck IMH, van Peij NNME, Mahony J, van Sinderen D. Functional and practical insights into three lactococcal antiphage systems. Appl Environ Microbiol 2024; 90:e0112024. [PMID: 39136492 PMCID: PMC11409693 DOI: 10.1128/aem.01120-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/21/2024] [Indexed: 09/19/2024] Open
Abstract
The persistent challenge of phages in dairy fermentations requires the development of starter cultures with enhanced phage resistance. Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members. In the present study, their effectiveness against phage infection was confirmed in milk-based medium, thus validating their potential to ensure reliable dairy fermentations. We furthermore demonstrated that Rhea and Kamadhenu do not directly hinder phage genome replication, transcription, or associated translation. Conversely, Aristaios was found to interfere with phage transcription. Two of the antiphage systems are encoded on pMRC01-like conjugative plasmids, and the Kamadhenu-encoding plasmid was successfully transferred by conjugation to three lactococcal strains, each of which acquired substantially enhanced phage resistance against Skunavirus members. Such advances in our knowledge of the lactococcal phage resistome and the possibility of mobilizing these protective functions to bolster phage protection in sensitive strains provide practical solutions to the ongoing phage problem in industrial food fermentations.IMPORTANCEIn the current study, we characterized and evaluated the mechanistic diversity of three recently described, plasmid-encoded lactococcal antiphage systems. These systems were found to confer high resistance against many members of the most prevalent and problematic lactococcal phage genus, rendering them of particular interest to the dairy industry, where persistent phage challenge requires the development of starter cultures with enhanced phage resistance characteristics. Our acquired knowledge highlights that enhanced understanding of lactococcal phage resistance systems and their encoding plasmids can provide rational and effective solutions to the enduring issue of phage infections in dairy fermentation facilities.
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Affiliation(s)
- Andriana Grafakou
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cas Mosterd
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul P. de Waal
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft, the Netherlands
| | | | - Noël N. M. E. van Peij
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft, the Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
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2
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Xie Z, McAuliffe O, Jin YS, Miller MJ. Genomic Modifications of Lactic Acid Bacteria and Their Applications in Dairy Fermentation. J Dairy Sci 2024:S0022-0302(24)00981-0. [PMID: 38969005 DOI: 10.3168/jds.2024-24989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024]
Abstract
Lactic Acid Bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. LAB are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications. Here, this review describes (1) the potential opportunities for application of genetically modified LAB strains in dairy fermentation and (2) the various genomic modification tools for LAB strains, such as random mutagenesis, adaptive laboratory evolution, conjugation, homologous recombination, recombineering, and CRISPR (clustered regularly interspaced short palindromic repeat)- Cas (CRISPR-associated protein) based genome engineering. Lastly, this review also discusses the potential future developments of these genomic modification technologies and their applications in dairy fermentations.
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Affiliation(s)
- Zifan Xie
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Yong-Su Jin
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael J Miller
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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3
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Dal Bello F, Bocquet L, Bru A, Laulund S, Machielsen R, Raneri M, Sewalt V, van Peij N, Ville P, Volonté F, White Y, Rusek J. New Genomic Techniques applied to food cultures: a powerful contribution to innovative, safe, and sustainable food products. FEMS Microbiol Lett 2024; 371:fnae010. [PMID: 38323486 PMCID: PMC10890814 DOI: 10.1093/femsle/fnae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/11/2024] [Accepted: 02/05/2024] [Indexed: 02/08/2024] Open
Abstract
Nontransgenic New Genomic Techniques (NGTs) have emerged as a promising tool for food industries, allowing food cultures to contribute to an innovative, safe, and more sustainable food system. NGTs have the potential to be applied to microorganisms, delivering on challenging performance traits like texture, flavour, and an increase of nutritional value. This paper brings insights on how nontransgenic NGTs applied to food cultures could be beneficial to the sector, enabling food industries to generate innovative, safe, and sustainable products for European consumers. Microorganisms derived from NGTs have the potentials of becoming an important contribution to achieve the ambitious targets set by the European 'Green Deal' and 'Farm to Fork' policies. To encourage the development of NGT-derived microorganisms, the current EU regulatory framework should be adapted. These technologies allow the introduction of a precise, minimal DNA modification in microbial genomes resulting in optimized products carrying features that could also be achieved by spontaneous natural genetic evolution. The possibility to use NGTs as a tool to improve food safety, sustainability, and quality is the bottleneck in food culture developments, as it currently relies on lengthy natural evolution strategies or on untargeted random mutagenesis.
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Affiliation(s)
| | | | - Audrey Bru
- Lallemand SAS, 19 rue des Briquetiers, 31700 Blagnac, France
| | - Svend Laulund
- Novonesis, Gammel Venlighedsvej 14, 2970 Hoersholm, Denmark
| | | | | | - Vincent Sewalt
- IFF, 925 Page Mill Road, Palo Alto, CA 94304, United States
| | - Noël van Peij
- DSM-Firmenich, Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands
| | - Patrice Ville
- Lesaffre, 101 rue de Menin, 59706 Marcq-en-Baroeul, France
| | | | - Yolanda White
- Lallemand SAS, 19 rue des Briquetiers, 31700 Blagnac, France
| | - Jakub Rusek
- EFFCA - European Food and Fermentation Cultures Association,c/o Kellen, 188 Avenue de Tervueren, Brussels, Postbox 4, 1150 Brussels, Belgium
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4
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Alexander LM, van Pijkeren JP. Modes of therapeutic delivery in synthetic microbiology. Trends Microbiol 2023; 31:197-211. [PMID: 36220750 PMCID: PMC9877134 DOI: 10.1016/j.tim.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 02/03/2023]
Abstract
For decades, bacteria have been exploited as vectors for vaccines and therapeutics. However, the bacterial arsenal used has historically been limited to a few strains. Advancements in immunology, combined with the development of genetic tools, have expanded our strategies and capabilities to engineer bacteria using various delivery strategies. Depending on the application, each delivery strategy requires specific considerations, optimization, and safety concerns. Here, we review various modes of therapeutic delivery used to target or vaccinate against a variety of ailments in preclinical models and in clinical trials. We highlight modes of bacteria-derived delivery best suited for different applications. Finally, we discuss current obstacles in bacteria-derived therapies and explore potential improvements of the various modes of therapeutic delivery.
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Affiliation(s)
- Laura M Alexander
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA; Food Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
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5
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Contreras Á, Díaz G, Mendoza SN, Canto M, Agosín E. Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions. Front Microbiol 2023; 14:1100501. [PMID: 36970676 PMCID: PMC10033693 DOI: 10.3389/fmicb.2023.1100501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/09/2023] [Indexed: 03/29/2023] Open
Abstract
Malolactic fermentation (MLF) positively influences the quality of the wine, and it occurs as a result of a lactic acid bacteria's metabolism, mainly of the Oenococcus oeni species. However, delays and halting of MLF are frequent problems in the wine industry. This is mainly because O. oeni's development is inhibited by different kinds of stress. Even though the sequencing of the genome of the PSU-1 strain of O. oeni, as well as other strains, has made it possible to identify genes involved in the resistance to some types of stress, all of the factors that could be involved are still unknown. With the aim of contributing to this knowledge, the random mutagenesis technique was used in this study as a strategy for genetic improvement of strains of the O. oeni species. The technique proved to be capable of generating a different and improved strain when compared to the PSU-1 strain (the parent from which it descends). Then, we evaluated the metabolic behavior of both strains in three different wines. We used synthetic MaxOeno wine (pH 3.5; 15% v/v ethanol), red wine (Cabernet Sauvignon), and white wine (Chardonnay). Furthermore, we compared the transcriptome of both strains, grown in MaxOeno synthetic wine. The specific growth rate of the E1 strain was on average 39% higher in comparison to the PSU-1 strain. Interestingly, E1 strain showed an overexpression of the OEOE_1794 gene, which encodes a UspA-like protein, which has been described as promoting growth. We observed that the E1 strain was able to convert, on average, 34% more malic acid into lactate than the PSU-1 strain, regardless of the wine being used. On the other hand, the E1 strain showed a flux rate of fructose-6-phosphate production that was 86% higher than the mannitol production rate, and the internal flux rates increase in the direction of pyruvate production. This coincides with the higher number of OEOE_1708 gene transcripts observed in the E1 strain grown in MaxOeno. This gene encodes for an enzyme fructokinase (EC 2.7.1.4) involved in the transformation of fructose to fructose-6-phosphate.
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Affiliation(s)
- Ángela Contreras
- Applied Microbiology Laboratory, Center for Biotechnology of Natural Resources, Faculty of Agricultural and Forestry Sciences, School of Biotechnology, Universidad Católica del Maule, Talca, Chile
- *Correspondence: Angela Contreras,
| | - Gabriela Díaz
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián N. Mendoza
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Mauricio Canto
- Applied Microbiology Laboratory, Center for Biotechnology of Natural Resources, Faculty of Agricultural and Forestry Sciences, School of Biotechnology, Universidad Católica del Maule, Talca, Chile
| | - Eduardo Agosín
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Eduardo Agosin,
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Swinnen S, Zurek C, Krämer M, Heger RM, Domeyer JE, Ziegler J, Svetlitchnyi VA, Läufer A. A novel SfaNI-like restriction-modification system in Caldicellulosiruptor extents the genetic engineering toolbox for this genus. PLoS One 2022; 17:e0279562. [PMID: 36580476 PMCID: PMC9799307 DOI: 10.1371/journal.pone.0279562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/11/2022] [Indexed: 12/30/2022] Open
Abstract
Caldicellulosiruptor is a genus of thermophilic to hyper-thermophilic microorganisms that express and secrete an arsenal of enzymes degrading lignocellulosic biomasses into fermentable sugars. Because of this distinguished feature, strains of Caldicellulosiruptor have been considered as promising candidates for consolidated bioprocessing. Although a few Caldicellulosiruptor strains with industrially relevant characteristics have been isolated to date, it is apparent that further improvement of the strains is essential for industrial application. The earlier identification of the HaeIII-like restriction-modification system in C. bescii strain DSM 6725 has formed the basis for genetic methods with the aim to improve the strain's lignocellulolytic activity and ethanol production. In this study, a novel SfaNI-like restriction-modification system was identified in Caldicellulosiruptor sp. strain BluCon085, consisting of an endonuclease and two methyltransferases that recognize the reverse-complement sequences 5'-GATGC-3' and 5'-GCATC-3'. Methylation of the adenine in both sequences leads to an asymmetric methylation pattern in the genomic DNA of strain BluCon085. Proteins with high percentage of identity to the endonuclease and two methyltransferases were identified in the genomes of C. saccharolyticus strain DSM 8903, C. naganoensis strain DSM 8991, C. changbaiensis strain DSM 26941 and Caldicellulosiruptor sp. strain F32, suggesting that a similar restriction-modification system may be active also in these strains and respective species. We show that methylation of plasmid and linear DNA by the identified methyltransferases, obtained by heterologous expression in Escherichia coli, is sufficient for successful transformation of Caldicellulosiruptor sp. strain DIB 104C. The genetic engineering toolbox developed in this study forms the basis for rational strain improvement of strain BluCon085, a derivative from strain DIB 104C with exceptionally high L-lactic acid production. The toolbox may also work for other species of the genus Caldicellulosiruptor that have so far not been genetically tractable.
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Meruvu H. Redefining methods for augmenting lactic acid bacteria robustness and phenyllactic acid biocatalysis: Integration valorizes simplicity. Crit Rev Food Sci Nutr 2022; 64:4397-4409. [PMID: 36322699 DOI: 10.1080/10408398.2022.2141681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production of phenyllactic acid (PLA) has been reported by several researchers, but so far, no mention has been made of augmented PLA production using an orchestrated assembly of simple techniques integrated to improve lactic acid bacteria (LAB) metabolism for the same. This review summarizes sequentially tailoring LAB growth and metabolism for augmented PLA catalysis through several strategies like monitoring LAB sustenance by choosing appropriate starter PLA-producing LAB strains isolated from natural environments, with desirably fastidious growth rates, properties like acidification, proteolysis, bacteriophage-resistance, aromatic/texturing-features, etc.; entrapping chosen LAB strains in novel cryogels and/or co-cultivating two/more LAB strains to improve their biotransformation potential and promote growth dependency/sustainability; adopting adaptive evolution methods designed to improve LAB strains under selection pressure inducing desired phenotypes tolerant to stress factors like heat, salt, acid, and solvent; monitoring physico-chemical LAB fermentation factors like temperature, pH, dissolved oxygen content, enzymes, and cofactors for PLA biosynthesis; and modulating purification/downstream processes to extract substantial PLA yields. This review paper serves as a comprehensive preliminary guide that can evoke a strategic experimental plan to produce industrial-scale PLA yields using simple techniques orchestrated together in the pursuit of conserving time, effort, and resources.
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Affiliation(s)
- Haritha Meruvu
- Department of Food Engineering, Faculty of Engineering, İzmir Institute of Technology, Urla, İzmir, Turkey
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8
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Ruiz‐Cruz S, Erazo Garzon A, Kelleher P, Bottacini F, Breum SØ, Neve H, Heller KJ, Vogensen FK, Palussière S, Courtin P, Chapot‐Chartier M, Vinogradov E, Sadovskaya I, Mahony J, van Sinderen D. Host genetic requirements for DNA release of lactococcal phage TP901-1. Microb Biotechnol 2022; 15:2875-2889. [PMID: 36259418 PMCID: PMC9733650 DOI: 10.1111/1751-7915.14156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/29/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
The first step in phage infection is the recognition of, and adsorption to, a receptor located on the host cell surface. This reversible host adsorption step is commonly followed by an irreversible event, which involves phage DNA delivery or release into the bacterial cytoplasm. The molecular components that trigger this latter event are unknown for most phages of Gram-positive bacteria. In the current study, we present a comparative genome analysis of three mutants of Lactococcus cremoris 3107, which are resistant to the P335 group phage TP901-1 due to mutations that affect TP901-1 DNA release. Through genetic complementation and phage infection assays, a predicted lactococcal three-component glycosylation system (TGS) was shown to be required for TP901-1 infection. Major cell wall saccharidic components were analysed, but no differences were found. However, heterologous gene expression experiments indicate that this TGS is involved in the glucosylation of a cell envelope-associated component that triggers TP901-1 DNA release. To date, a saccharide modification has not been implicated in the DNA delivery process of a Gram-positive infecting phage.
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Affiliation(s)
- Sofía Ruiz‐Cruz
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Andrea Erazo Garzon
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Francesca Bottacini
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland,Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Solvej Østergaard Breum
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark,Present address:
Department of Virus & Microbiological Special Diagnostics, Division of Infectious Disease Preparedness, Statens Serum InstitutCopenhagenDenmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner‐InstitutFederal Research Institute of Nutrition and FoodKielGermany
| | - Knut J. Heller
- Department of Microbiology and Biotechnology, Max Rubner‐InstitutFederal Research Institute of Nutrition and FoodKielGermany
| | - Finn K. Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Simon Palussière
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
| | - Pascal Courtin
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
| | | | - Evgeny Vinogradov
- National Research Council CanadaInstitute for Biological SciencesOttawaOntarioCanada
| | - Irina Sadovskaya
- Equipe BPA, Université du Littoral‐Côte d'Opale, Institut Charles Violette EA 7394 USC AnsesBoulogne‐sur‐merFrance
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
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Tadesse BT, Zhao G, Kempen P, Solem C. Consolidated Bioprocessing in a Dairy Setting─Concurrent Yoghurt Fermentation and Lactose Hydrolysis without Using Lactase Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11623-11630. [PMID: 36057098 DOI: 10.1021/acs.jafc.2c04191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Streptococcus thermophilus is a fast-growing lactic acid bacterium (LAB) used in yoghurt and cheese manufacturing. Recently, we reported how this bacterium could serve as a cell catalyst for hydrolyzing lactose when permeabilized by nisin A. To enhance the lactose hydrolyzing activity of S. thermophilus, we mutated a dairy strain and screened for variants with elevated β-galactosidase activity. Two isolates, ST30-8 and ST95, had 2.4-fold higher activity. Surprisingly, both strains were able to hydrolyze lactose when used as whole-cell lactase catalysts without permeabilization, and ST30-8 hydrolyzed 30 g/L lactose in 6 h at 50 °C using 0.18 g/L cells. Moreover, both strains hydrolyzed lactose while growing in milk. Genome sequencing revealed a mutation in l-lactate dehydrogenase, which we believe hampers growth and increases the capacity of S. thermophilus to hydrolyze lactose. Our findings will allow production of sweet lactose-reduced yoghurt without the use of costly purified lactase enzymes.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Technical University of Denmark, DK-2800Kongens Lyngby, Denmark
| | - Ge Zhao
- National Food Institute, Technical University of Denmark, DK-2800Kongens Lyngby, Denmark
| | - Paul Kempen
- National Centre for Nano Fabrication and Characterization, Technical University of Denmark, DK-2800Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800Kongens Lyngby, Denmark
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Erkorkmaz BA, Kırtel O, Abaramak G, Nikerel E, Öner ET. UV and Chemically Induced Halomonas smyrnensis Mutants for Enhanced Levan Productivity. J Biotechnol 2022; 356:19-29. [PMID: 35914617 DOI: 10.1016/j.jbiotec.2022.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Halomonas smyrnensis AAD6T is a moderately halophilic bacterium proven to be a powerful biotechnological tool with its ability to accumulate valuable biopolymers such as levan and poly(3-hydroxybutyrate) (PHB). Levan is a fructose homopolymer with β-2,6 fructofuranosidic linkages on the polymer backbone, and its distinctive applications in various industries such as food, pharmaceutical, medical, and chemical have been well-defined. On the other hand, PHB is a promising raw material to produce biodegradable plastics. Although it was shown in our previous studies that H. smyrnensis AAD6T exhibits one of the highest conversion yields of sucrose to levan reported to date, novel strategies are required to overcome high costs of levan production. In this study, we aimed at increasing levan productivity of H. smyrnensis AAD6T cultures using random mutagenesis techniques combined (i.e., ethyl methanesulfate treatment and/or ultraviolet irradiation). After several consecutive treatments, mutant strains BAE2, BAE5 and BAE6 were selected as efficient levan producers, as BAE2 standing out as the most efficient one not only in sucrose utilization and levan production rates, but also in final PHB concentrations. The mutants' whole genome sequences were analysed to determine the mutations occurred. Several mutations in genes related to central carbon metabolism and osmoregulation were found. Our results suggest that random mutagenesis can be a facile and efficient strategy to enhance the performance of extremophiles in adverse conditions.
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Affiliation(s)
- Burak Adnan Erkorkmaz
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Onur Kırtel
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Gülbahar Abaramak
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, 34755 Istanbul, Turkey
| | - Ebru Toksoy Öner
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey.
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11
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Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community. NPJ Biofilms Microbiomes 2022; 8:59. [PMID: 35858930 PMCID: PMC9300721 DOI: 10.1038/s41522-022-00323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
The majority of ecological, industrial and medical impacts of bacteria result from diverse communities containing multiple species. This diversity presents a significant challenge as co-cultivation of multiple bacterial species frequently leads to species being outcompeted and, with this, the possibility to manipulate, evolve and improve bacterial communities is lost. Ecological theory predicts that a solution to this problem will be to grow species in structured environments, which reduces the likelihood of competitive exclusion. Here, we explored the ability of cultivation in a structured environment to facilitate coexistence, evolution, and adaptation in an industrially important community: Lactococcus lactis and Leuconostoc mesenteroides frequently used as dairy starter cultures. As commonly occurs, passaging of these two species together in a liquid culture model led to the loss of one species in 6 of 20 lineages (30%). By contrast, when we co-cultured the two species as biofilms on beads, a stable coexistence was observed in all lineages studied for over 100 generations. Moreover, we show that the co-culture drove evolution of new high-yield variants, which compared to the ancestor grew more slowly, yielded more cells and had enhanced capability of biofilm formation. Importantly, we also show that these high-yield biofilm strains did not evolve when each species was passaged in monoculture in the biofilm model. Therefore, both co-culture and the biofilm model were conditional for these high-yield strains to evolve. Our study underlines the power of ecological thinking—namely, the importance of structured environments for coexistence—to facilitate cultivation, evolution, and adaptation of industrially important bacterial communities.
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Abstract
Fermented foods (FFs) hold global attention because of their huge advantages. Their health benefits, palatability, preserved, tasteful, and aromatic properties impart potential importance in the comprehensive evaluation of FFs. The bioactive components, such as minerals, vitamins, fatty acids, amino acids, and other phytochemicals synthesized during fermentation, provide consumers with several health benefits. Fermentation of food is an ancient process that has met with many remarkable changes owing to the development of scientific technologies over the years. Initially, fermentation relied on back-slapping. Nowadays, starter cultures strains are specifically chosen for the type of fermentation process. Modern biotechnological methods are being implemented in the fermentation process to achieve the desired product in high quality. Respiratory and gastrointestinal tract infections are the most severe health issues affecting human beings of all age groups, especially children and older adults, during this COVID-19 pandemic period. Studies suggest that the consumption of probiotic Lactobacillus strains containing fermented foods protects the subjects from common infectious diseases (CIDs, which is classified as upper respiratory tract infections, lower respiratory tract infections and gastrointestinal infections) by improving the host’s immune system. Further studies are obligatory to develop probiotic-based functional FFs that are effective against CIDs. Presently, we are urged to find alternative, safe, and cost-effective prevention measures against CIDs. The current manuscript briefs the production of FFs, functional properties of FFs, and their beneficial effects against respiratory tract infections. It summarizes the outcomes of clinical trials using human subjects on the effects of supplementation of FFs.
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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14
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Mannaa M, Han G, Seo YS, Park I. Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota. Foods 2021; 10:2861. [PMID: 34829140 PMCID: PMC8618017 DOI: 10.3390/foods10112861] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Inmyoung Park
- School of Culinary Arts, Youngsan University, Busan 48015, Korea
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15
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Kim KM, Song JW, Yang SJ, Choi JW, Sohn J, Han SK, Shin YJ, Lee DY, Lee S, Kim DH. Gut Microbiota-Mediated Immunomodulatory Effects of Lactobacillus rhamnosus HDB1258 Cultured in the Lava Seawater in the Colitis Mouse Model. J Med Food 2021; 24:1169-1171. [PMID: 34704834 DOI: 10.1089/jmf.2021.k.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The immunomodulatory effects of Lactobacillus rhamnosus HDB1258 were evaluated in mice with colitis induced by Klebsiella oxytoca (KO). L. rhamnosus HDB1258 was cultured in the lava seawater (LS) to improve its probiotic properties. It increased adhesive ability to mucin with mRNA expression levels of chaperone proteins (such as GroEL/ES, DnaKJ, and HtrA). In the in vivo experiments, administration of KO caused an inflammation on the colon with gut dysbiosis. LH group (oral gavage of HDB1258 1.0 × 109 colony forming units/day) showed that inflammatory biomarkers, including IL-1β, TNF-α, IL-6, and PGE2, were significantly decreased to less than half of the KO group, and Th1 cells were decreased in the spleen, but Treg cells were not affected. In contrast, the expression levels of secretory IgA and IL-10 were significantly increased, and the composition of gut microbiota in the LH group tended to recover similar to normal mice without any effect on the α-diversity. In conclusion, L. rhamnosus HDB1258 cultured in the LS could regulate competitively pathogenic bacteria in imbalanced flora with its improved mucin adhesive ability and was an effective immunomodulatory adjuvant for treating colitis by its regulatory function on intestinal inflammation.
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Affiliation(s)
- Kyung Min Kim
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Ji-Won Song
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Seo-Jin Yang
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Ji-Whi Choi
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Johann Sohn
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Sang-Kap Han
- Department of Life and Nanopharmaceutical Sciences, Neurobiota Research Center, College of Pharmacy, Kyung Hee University, Seoul, South Korea
| | - Yoon-Jung Shin
- Department of Life and Nanopharmaceutical Sciences, Neurobiota Research Center, College of Pharmacy, Kyung Hee University, Seoul, South Korea
| | - Dong-Yeon Lee
- Department of Life and Nanopharmaceutical Sciences, Neurobiota Research Center, College of Pharmacy, Kyung Hee University, Seoul, South Korea
| | - Seunghun Lee
- Bio R&D Center, HYUNDAI BIOLAND Co., Ltd., Ansan, South Korea
| | - Dong-Hyun Kim
- Department of Life and Nanopharmaceutical Sciences, Neurobiota Research Center, College of Pharmacy, Kyung Hee University, Seoul, South Korea
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16
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Balasubramanian S, Chen J, Wigneswaran V, Bang-Berthelsen CH, Jensen PR. Droplet-Based Microfluidic High Throughput Screening of Corynebacterium glutamicum for Efficient Heterologous Protein Production and Secretion. Front Bioeng Biotechnol 2021; 9:668513. [PMID: 34026744 PMCID: PMC8137953 DOI: 10.3389/fbioe.2021.668513] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
With emerging interests in heterologous production of proteins such as antibodies, growth factors, nanobodies, high-quality protein food ingredients, etc. the demand for efficient production hosts increases. Corynebacterium glutamicum is an attractive industrial host with great secretion capacity to produce therapeutics. It lacks extracellular protease and endotoxin activities and easily achieves high cell density. Therefore, this study focuses on improving protein production and secretion in C. glutamicum with the use of droplet-based microfluidic (DBM) high throughput screening. A library of C. glutamicum secreting β-glucosidase was generated using chemical mutagenesis coupled with DBM screening of 200,000 mutants in just 20 min. Among 100 recovered mutants, 16 mutants exhibited enhanced enzyme secretion capacity, 13 of which had unique mutation profiles. Whole-genome analysis showed that approximately 50–150 SNVs had occurred on the chromosome per mutant. Functional enrichment analysis of genes with non-synonymous mutations showed overrepresentation of genes involved in protein synthesis and secretion relevant biological processes, such as DNA and ribosome RNA synthesis, protein secretion and energy turnover. Two mutants JCMT1 and JCMT8 exhibited the highest secretion with a six and a fivefold increase in the β-glucosidase activity in the supernatant, respectively, relative to the reference strain JC0190. After plasmid curing, a new plasmid with the gene encoding α-amylase was cloned into these two mutants. The new strains SB024 and SB025 also exhibited a five and a sixfold increase in α-amylase activity in the supernatant, respectively, relative to the reference strain SB023. The results demonstrate how DBM screening can serve as a powerful development tool to improve cell factories for the production and secretion of heterologous proteins.
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Affiliation(s)
- Suvasini Balasubramanian
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Vinoth Wigneswaran
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Claus Heiner Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Ruhdal Jensen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Bhatt P, Gangola S, Bhandari G, Zhang W, Maithani D, Mishra S, Chen S. New insights into the degradation of synthetic pollutants in contaminated environments. CHEMOSPHERE 2021; 268:128827. [PMID: 33162154 DOI: 10.1016/j.chemosphere.2020.128827] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/28/2020] [Indexed: 05/11/2023]
Abstract
The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Geeta Bhandari
- Department of Biotechnology, Sardar Bhagwan Singh University, Dehradun, 248161, Uttarakhand, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology, Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
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18
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Lactic acid bacteria: little helpers for many human tasks. Essays Biochem 2021; 65:163-171. [PMID: 33739395 DOI: 10.1042/ebc20200133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022]
Abstract
Lactic acid bacteria (LAB) are a group of highly specialised bacteria specifically adapted to a diverse range of habitats. They are found in the gut of humans and other animals, in many food fermentations, and on plants. Their natural specialisation in close relation to human activities make them particularly interesting from an industrial point of view. They are relevant not only for traditional food fermentations, but also as probiotics, potential therapeutics and cell factories for the production of many different products. Many new tools and methods are being developed to analyse and modify these microorganisms. This review shall give an overview highlighting some of the most striking characteristics of lactic acid bacteria and our approaches to harness their potential in many respects - from home made food to industrial chemical production, from probiotic activities to the most modern cancer treatments and vaccines.
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19
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Samperio S, Guzmán-Herrador DL, May-Cuz R, Martín MC, Álvarez MA, Llosa M. Conjugative DNA Transfer From E. coli to Transformation-Resistant Lactobacilli. Front Microbiol 2021; 12:606629. [PMID: 33643236 PMCID: PMC7905204 DOI: 10.3389/fmicb.2021.606629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) belonging to the genus classically known as Lactobacillus, recently split into 25 different genera, include many relevant species for the food industry. The well-known properties of lactobacilli as probiotics make them an attractive model also for vaccines and therapeutic proteins delivery in humans. However, scarce tools are available to accomplish genetic modification of these organisms, and most are only suitable for laboratory strains. Here, we test bacterial conjugation as a new tool to introduce genetic modifications into many biotechnologically relevant laboratory and wild type lactobacilli. Using mobilizable shuttle plasmids from a donor Escherichia coli carrying either RP4 or R388 conjugative systems, we were able to get transconjugants to all tested Lactocaseibacillus casei strains, including many natural isolates, and to several other genera, including Lentilactobacillus parabuchneri, for which no transformation protocol has been reported. Transconjugants were confirmed by the presence of the oriT and 16S rRNA gene sequencing. Serendipitously, we also found transconjugants into researcher-contaminant Staphylococcus epidermidis. Conjugative DNA transfer from E. coli to S. aureus was previously described, but at very low frequencies. We have purified this recipient strain and used it in standard conjugation assays, confirming that both R388 and RP4 conjugative systems mediate mobilization of plasmids into S. epidermidis. This protocol could be assayed to introduce DNA into other Gram-positive microorganisms which are resistant to transformation.
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Affiliation(s)
- Sara Samperio
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Dolores L Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Rigoberto May-Cuz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | | | | | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
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20
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Sørensen KI, Kjærbølling I, Neves AR, Machielsen R, Johansen E. Use of Cell Envelope Targeting Antibiotics and Antimicrobial Agents as a Powerful Tool to Select for Lactic Acid Bacteria Strains With Improved Texturizing Ability in Milk Fermentations. Front Bioeng Biotechnol 2021; 8:623700. [PMID: 33520973 PMCID: PMC7839403 DOI: 10.3389/fbioe.2020.623700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/07/2020] [Indexed: 12/03/2022] Open
Abstract
Many antibiotics and antimicrobial agents have the bacterial cell envelope as their primary target, interfering with functions such as synthesis of peptidoglycan, membrane stability and permeability, and attachment of surface components. The cell envelope is the outermost barrier of the bacterial cell, conferring protection against environmental stresses, and maintaining structural integrity and stability of the growing cell, while still allowing for required metabolism. In this work, inhibitory concentrations of several different cell envelope targeting antibiotics and antimicrobial agents were used to select for derivatives of lactic acid bacteria (LAB) with improved properties for dairy applications. Interestingly, we observed that for several LAB species a fraction of the isolates had improved milk texturizing capabilities. To further improve our understanding of the mechanisms underlying the improved rheology and to validate the efficacy of this method for strain improvement, genetic and physiological characterization of several improved derivatives was performed. The results showed that the identified genetic changes are diverse and affect also other cellular functions than the targeted cell surface. In short, this study describes a new versatile and powerful toolbox based on targeting of the cell envelope to select for LAB derivatives with improved phenotypic traits for dairy applications.
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Affiliation(s)
- Kim I Sørensen
- Discovery, Research and Development, Chr. Hansen A/S, Hørsholm, Denmark
| | - Inge Kjærbølling
- Discovery, Research and Development, Chr. Hansen A/S, Hørsholm, Denmark
| | - Ana Rute Neves
- Discovery, Research and Development, Chr. Hansen A/S, Hørsholm, Denmark
| | - Ronnie Machielsen
- Discovery, Research and Development, Chr. Hansen A/S, Hørsholm, Denmark
| | - Eric Johansen
- Emerging Technology, Chr. Hansen A/S, Hørsholm, Denmark
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21
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Hernandez-Valdes JA, aan de Stegge M, Hermans J, Teunis J, van Tatenhove-Pel RJ, Teusink B, Bachmann H, Kuipers OP. Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metab Eng Commun 2020; 11:e00133. [PMID: 32551230 PMCID: PMC7292884 DOI: 10.1016/j.mec.2020.e00133] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
Amino acids are attractive metabolites for the pharmaceutical and food industry field. On one hand, the construction of microbial cell factories for large-scale production aims to satisfy the demand for amino acids as bulk biochemical. On the other hand, amino acids enhance flavor formation in fermented foods. Concerning the latter, flavor formation in dairy products, such as cheese is associated with the presence of lactic acid bacteria (LAB). In particular, Lactococcus lactis, one of the most important LAB, is used as a starter culture in fermented foods. The proteolytic activity of some L. lactis strains results in peptides and amino acids, which are flavor compounds or flavor precursors. However, it is still a challenge to isolate bacterial cells with enhanced amino acid production and secretion activity. In this work, we developed a growth-based sensor strain to detect the essential amino acids isoleucine, leucine, valine, histidine and methionine. Amino acids are metabolites that can be secreted by some bacteria. Therefore, our biosensor allowed us to identify wild-type L. lactis strains that naturally secrete amino acids, by using co-cultures of the biosensor strain with potential amino acid producing strains. Subsequently, we used this biosensor in combination with a droplet-based screening approach, and isolated three mutated L. lactis IPLA838 strains with 5-10 fold increased amino acid-secretion compared to the wild type. Genome re-sequencing revealed mutations in genes encoding proteins that participate in peptide uptake and peptide degradation. We argue that an unbalance in the regulation of amino acid levels as a result of these gene mutations may drive the accumulation and secretion of these amino acids. This biosensing system tackles the problem of selection for overproduction of secreted molecules, which requires the coupling of the product to the producing cell in the droplets.
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Affiliation(s)
- Jhonatan A. Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Myrthe aan de Stegge
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Johan Teunis
- Faculty of Medical Sciences, Department of Pathology and Medical Biology, Hanzeplein 1, 9713, GZ, Groningen, the Netherlands
| | - Rinke J. van Tatenhove-Pel
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
- NIZO Food Research, Kernhemseweg 2, 6718, ZB, Ede, the Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
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22
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Ji D, Ma J, Xu M, Agyei D. Cell-envelope proteinases from lactic acid bacteria: Biochemical features and biotechnological applications. Compr Rev Food Sci Food Saf 2020; 20:369-400. [PMID: 33443792 DOI: 10.1111/1541-4337.12676] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/27/2020] [Accepted: 10/30/2020] [Indexed: 01/25/2023]
Abstract
Proteins displayed on the cell surface of lactic acid bacteria (LAB) perform diverse and important biochemical roles. Among these, the cell-envelope proteinases (CEPs) are one of the most widely studied and most exploited for biotechnological applications. CEPs are important players in the proteolytic system of LAB, because they are required by LAB to degrade proteins in the growth media into peptides and/or amino acids required for the nitrogen nutrition of LAB. The most important area of application of CEPs is therefore in protein hydrolysis, especially in dairy products. Also, the physical location of CEPs (i.e., being cell-envelope anchored) allows for relatively easy downstream processing (e.g., extraction) of CEPs. This review describes the biochemical features and organization of CEPs and how this fits them for the purpose of protein hydrolysis. It begins with a focus on the genetic organization and expression of CEPs. The catalytic behavior and cleavage specificities of CEPs from various LAB are also discussed. Following this, the extraction and purification of most CEPs reported to date is described. The industrial applications of CEPs in food technology, health promotion, as well as in the growing area of water purification are discussed. Techniques for improving the production and catalytic efficiency of CEPs are also given an important place in this review.
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Affiliation(s)
- Dawei Ji
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Jingying Ma
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Min Xu
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
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23
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Marcelli B, Karsens H, Nijland M, Oudshoorn R, Kuipers OP, Kok J. Employing lytic phage-mediated horizontal gene transfer in Lactococcus lactis. PLoS One 2020; 15:e0238988. [PMID: 32925946 PMCID: PMC7489543 DOI: 10.1371/journal.pone.0238988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/27/2020] [Indexed: 12/01/2022] Open
Abstract
Lactococcus lactis is a lactic acid bacterium widely used as a starter culture in the manufacture of dairy products, especially a wide variety of cheeses. Improved industrial strains would help to manufacture better food products that can meet the industry's and consumer's demands with respect to e.g. quality, taste, texture and shelf life. Bacteriophage infection of L. lactis starter cultures represents one of the main causes of fermentation failure and consequent economic losses for the dairy industry. In this study, however, we aim at employing bacteriophages for beneficial purposes. We developed an experimental setup to assess whether phage-mediated horizontal gene transfer could be used to enhance the genetic characteristics of L. lactis strains in accordance with the European law regarding the use of genetically modified organisms (GMOs) in the food industry. Although we could not show the transfer of chromosomal DNA we did successfully transduce two dissimilar plasmids from L. lactis strain MG1363 to one of its derivatives employing three different lactococcal bacteriophages.
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Affiliation(s)
- Barbara Marcelli
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Harma Karsens
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Mark Nijland
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ruben Oudshoorn
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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24
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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25
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The Inoculation of Probiotics In Vivo Is a Challenge: Strategies to Improve Their Survival, to Avoid Unpleasant Changes, or to Enhance Their Performances in Beverages. BEVERAGES 2020. [DOI: 10.3390/beverages6020020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The inoculation of probiotics in beverages (probiotication) requires special technologies, as probiotic microorganisms can experience stress during food processing (acid, cold, drying, starvation, oxidative, and osmotic stresses) and gastrointestinal transit. Survival to harsh conditions is an essential prerequisite for probiotic bacteria before reaching the target site where they can exert their health promoting effects, but several probiotics show a poor resistance to technological processes, limiting their use to a restricted number of food products. Therefore, this paper offers a short overview of the ways to improve bacterial resistance: by inducing a phenotypic modification (adaptation) or by surrounding bacteria through a physical protection (microencapsulation). A second topic briefly addressed is genetic manipulation, while the last section addresses the control of metabolism by attenuation through physical treatments to design new kinds of food.
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Plavec TV, Berlec A. Safety Aspects of Genetically Modified Lactic Acid Bacteria. Microorganisms 2020; 8:E297. [PMID: 32098042 PMCID: PMC7074969 DOI: 10.3390/microorganisms8020297] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023] Open
Abstract
Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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Markakiou S, Gaspar P, Johansen E, Zeidan AA, Neves AR. Harnessing the metabolic potential of Streptococcus thermophilus for new biotechnological applications. Curr Opin Biotechnol 2020; 61:142-152. [DOI: 10.1016/j.copbio.2019.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023]
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Scala GD, Volontè F, Ricci G, Pedersen MB, Arioli S, Mora D. Development of a milk-based medium for the selection of urease-defective mutants of Streptococcus thermophilus. Int J Food Microbiol 2019; 308:108304. [PMID: 31425789 DOI: 10.1016/j.ijfoodmicro.2019.108304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 07/09/2019] [Accepted: 08/09/2019] [Indexed: 12/15/2022]
Abstract
Streptococcus thermophilus strains are used in fermented dairy products for their capacity to metabolize lactose into lactic acid. The rate of lactic acid production in milk is of major economic importance, as rapid acidification prevents growth of undesirable microorganisms. It is also of paramount significance for aroma, texture and flavor of the end product. Besides achieving customer satisfaction, improvement of production rate and operational costs incite industrials into selecting fast acidifying strains. Another important trait of S. thermophilus influencing acidification is the urease, which catabolizes urea into ammonia and has a detrimental effect on acidification. Unfortunately, most of the S. thermophilus strains possess the urease, and the urease-negative ones are necessary for industrial applications. Urease activity is a widely distributed activity in S. thermophilus species, and urease-negative strains are rare. The later are however interesting from an industrial point of view, as they may give faster acidification in dairy applications, because lactic acid is not buffered by urea-derived ammonia. Nowadays, the efforts to improve the characteristics of strains for industrial applications are based on natural strategies such as random mutagenesis. This implies the need of a screening method that is efficient in terms of time and success. In this context, the aim of this study was the development of a new medium that allows selection of urease-defective mutants based on S. thermophilus colony morphology. Discrimination capacity of the new medium was verified using previously characterized urease-negative recombinant strains. The new milk-based medium, applied to industrial S. thermophilus strains subjected to UV mutagenesis, allowed the selection of 3 mutants, partially or completely defective in urease activity. Genetic characterization of urease-defective mutants highlighted the presence of nonsense or missense mutations in the ureA, ureC and ureG genes, thus supporting their phenotype. Evaluation of milk acidification revealed increased performance for one out of three urease-defective mutants compared to wild-type strains.
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Affiliation(s)
- Giulia Della Scala
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy; Sacco System, via Manzoni 29/A, 22071 Cadorago, Italy
| | | | - Giovanni Ricci
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | | | - Stefania Arioli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Diego Mora
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy.
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Johansen E. Use of Natural Selection and Evolution to Develop New Starter Cultures for Fermented Foods. Annu Rev Food Sci Technol 2019; 9:411-428. [PMID: 29580139 DOI: 10.1146/annurev-food-030117-012450] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fermented foods industry is constantly seeking new starter cultures to deal with changing consumer preferences and new fermentation processes. New cultures can either be composed of strains isolated from nature or improved derivatives of existing isolates. A variety of techniques involving natural selection and evolution are available to enhance the performance of existing strains, including the isolation of mutants with desired properties, adaptive laboratory evolution, genome shuffling, and genome editing. Numerous examples of traits that can be improved are provided. These include resistance to bacteriophages; the secretion of glucose to increase sweetness; the production of vitamins, antifungal compounds, bacteriocins, texture, or aroma; enhancement of acidification rates and acid tolerance; and elimination of biofilm formation. Careful consideration is required to ensure the developed strains are suitable for the desired purpose, as some approaches may lead to regulatory concerns.
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Chen J, Vestergaard M, Shen J, Solem C, Dufva M, Jensen PR. Droplet-based microfluidics as a future tool for strain improvement in lactic acid bacteria. FEMS Microbiol Lett 2019. [DOI: 10.1093/femsle/fny258s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
ABSTRACTStrain development is frequently used to improve the performance and functionality of industrially important microbes. As traditional mutagenesis screen is especially utilized by the food industry to improve strains used in food fermentation, high-throughput and cost-effective screening tools are important in mutant selection. The emerging droplet-based microfluidics technology miniaturizes the volume for cell cultivation and phenotype interrogation down to the picoliter scales, which facilitates screening of microbes for improved phenotypical properties tremendously. In this mini review, we present recent application of the droplet-based microfluidics in microbial strain improvement with a focus on its potential use in the screening of lactic acid bacteria.
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Affiliation(s)
- Jun Chen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Mike Vestergaard
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jing Shen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Börner RA, Kandasamy V, Axelsen AM, Nielsen AT, Bosma EF. Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech. FEMS Microbiol Lett 2019; 366:5251984. [PMID: 30561594 PMCID: PMC6322438 DOI: 10.1093/femsle/fny291] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022] Open
Abstract
This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.
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Affiliation(s)
- Rosa A Börner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Amalie M Axelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Elleke F Bosma
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
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Cardoso JGR, Zeidan AA, Jensen K, Sonnenschein N, Neves AR, Herrgård MJ. MARSI: metabolite analogues for rational strain improvement. Bioinformatics 2019; 34:2319-2321. [PMID: 29949953 PMCID: PMC6022549 DOI: 10.1093/bioinformatics/bty108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/22/2018] [Indexed: 01/06/2023] Open
Abstract
Summary Metabolite analogues (MAs) mimic the structure of native metabolites, can competitively inhibit their utilization in enzymatic reactions, and are commonly used as selection tools for isolating desirable mutants of industrial microorganisms. Genome-scale metabolic models representing all biochemical reactions in an organism can be used to predict effects of MAs on cellular phenotypes. Here, we present the metabolite analogues for rational strain improvement (MARSI) framework. MARSI provides a rational approach to strain improvement by searching for metabolites as targets instead of genes or reactions. The designs found by MARSI can be implemented by supplying MAs in the culture media, enabling metabolic rewiring without the use of recombinant DNA technologies that cannot always be used due to regulations. To facilitate experimental implementation, MARSI provides tools to identify candidate MAs to a target metabolite from a database of known drugs and analogues. Availability and implementation The code is freely available at https://github.com/biosustain/marsi under the Apache License V2. MARSI is implemented in Python. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- João G R Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Kristian Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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van Tatenhove-Pel RJ, Zwering E, Solopova A, Kuipers OP, Bachmann H. Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells. Sci Rep 2019; 9:9867. [PMID: 31285492 PMCID: PMC6614399 DOI: 10.1038/s41598-019-46344-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/23/2019] [Indexed: 12/12/2022] Open
Abstract
Lactococcus lactis is used as cell-factory and strain selections are regularly performed to improve production processes. When selection regimes only allow desired phenotypes to survive, for instance by using antibiotics to select for cells that do not grow in a specific condition, the presence of more resistant subpopulations with a wildtype genotype severely slows down the procedure. While the food grade organism L. lactis is not often exposed to antibiotics we characterized its response to ampicillin in more detail, to better understand emerging population heterogeneity and how this might affect strain selection procedures. Using growth-dependent viability assays we identified persister subpopulations in stationary and exponential phase. Growth-independent viability assays revealed a 100 times larger subpopulation that did not grow on plates or in liquid medium, but had an intact membrane and could maintain a pH gradient. Over one third of these cells restored their intracellular pH when we induced a temporary collapse, indicating that this subpopulation was metabolically active and in a viable but non-culturable state. Exposure of L. lactis MG1363 to ampicillin therefore results in a heterogeneous population response with different dormancy states. These dormant cells should be considered in survival-based strain selection procedures.
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Affiliation(s)
- Rinke J van Tatenhove-Pel
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
- NIZO Food Research, Kernhemseweg 2, 6718 ZB, Ede, The Netherlands
| | - Emile Zwering
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
| | - Ana Solopova
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands.
- NIZO Food Research, Kernhemseweg 2, 6718 ZB, Ede, The Netherlands.
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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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Szymczak P, Vogensen FK, Janzen T. Novel isolates of Streptococcus thermophilus bacteriophages from group 5093 identified with an improved multiplex PCR typing method. Int Dairy J 2019. [DOI: 10.1016/j.idairyj.2018.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fiocco D, Longo A, Arena MP, Russo P, Spano G, Capozzi V. How probiotics face food stress: They get by with a little help. Crit Rev Food Sci Nutr 2019; 60:1552-1580. [DOI: 10.1080/10408398.2019.1580673] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Daniela Fiocco
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Angela Longo
- Department of Agriculture Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - Mattia Pia Arena
- Department of Agriculture Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - Pasquale Russo
- Department of Agriculture Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - Giuseppe Spano
- Department of Agriculture Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - Vittorio Capozzi
- Department of Agriculture Food and Environment Sciences, University of Foggia, Foggia, Italy
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Xiong ZQ, Kong LH, Meng HL, Cui JM, Xia YJ, Wang SJ, Ai LZ. Comparison of gal-lac operons in wild-type galactose-positive and -negative Streptococcus thermophilus by genomics and transcription analysis. J Ind Microbiol Biotechnol 2019; 46:751-758. [PMID: 30715626 DOI: 10.1007/s10295-019-02145-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022]
Abstract
Streptococcus thermophilus is one of the most important homo-fermentative thermophilic bacteria, which is widely used as a starter culture in dairy industry. Both wild-type galactose-negative (Gal-) S. thermophilus AR333 and galactose-positive (Gal+) S. thermophilus S-3 in this study were isolated from Chinese traditional dairy products. Here, to access the mechanism of the difference of galactose utilization between strains AR333 and S-3, the expression of gal-lac operons was examined using real-time qPCR in the presence of different sugars, and the gene organization of gal-lac operons was characterized using comparative genomics analysis. As compared with medium containing glucose, the expression of gal-lac operons in AR333 and S-3 was significantly activated (> 5-fold) in the presence of galactose or lactose in the medium. More importantly, the expression of gal operon in S-3 was higher than that of AR333, suggesting that the strength of gal promoter in AR333 and S-3 may be different. The genomes of AR333 and S-3 were the first time sequenced to provide insight into the difference of gal-lac operons in these two strains. Comparative genomics analysis showed that gene order and individual gene size of gal-lac operons are conserved in AR333 and S-3. The DNA sequence of gal operon responsible for galactose utilization between AR333 and S-3 is almost identical except that galK promoter of S-3 possesses single base pair mutation (G to A substitution) at -9 box galK region. Moreover, the expression of red fluorescent protein can be activated by galK promoter of S-3, but cannot by galK promoter of AR333 in galactose medium, suggesting that gal operon is silent in AR333 and active in S-3 under galactose-containing medium. Overall, our results indicated that single point mutation at -9 box in the galK promoter can significantly affect the expression of gal operon and is largely responsible for the Gal+ phenotype of S. thermophilus.
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Affiliation(s)
- Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Ling-Hui Kong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hai-Lin Meng
- Bioengineering Research Center, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Jin-Ming Cui
- Bioengineering Research Center, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Yong-Jun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Shi-Jie Wang
- Shijiazhuang Junlebao Dairy Co. Ltd., Shijiazhuang, 050211, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
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Kigel N, Melnik I, Naumenko O. STUDY OF THE BIOTECHNOLOGICAL POTENTIAL OF SELECTED LACTIC ACID BACTERIA CULTURES. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.15673/fst.v12i4.1176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fermenting microflora has been selected by biotechnological activity markers, with various methodological approaches used, namely: directional selection, selection of bacteriophage-insensitive mutants, protoplast regeneration. The experimental data show a significant biotechnological potential of the selected lactic acid bacteria. They are characterized by high milk-clotting activity and yield, the ability to form aromatic compounds and/or viscous components, excellent organoleptic qualities of clots fermented by them, antago-nistic activity against pathogenic and opportunistic pathogenic microorganisms, and phage-resistance to species-specific virulent phages. The collection of industrial microorganisms of Institute of Food Resources of National Academy of Agrarian Sciences (IFR NAAS) has been supplemented with new bioactive strains, in particular, the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactoba-cillus rhamnosus and Lactococcus lactis. Four bacterial compositions have been created. Three of them (Iprovit-LB-R; Iprovit-LB-A, and Iprovit-ST) are supposed to be used as functional enrichers for dry foodstuffs or as biologically active supplements. The bacterial prepara-tion Iprovit-Bifidolux is a universal composition. It can be introduced both as a fermenting culture for milk fermentation and as an enricher for dry and liquid foodstuffs. Biotechnologies for the production of dry bacterial preparations on the basis of selected strains have been field-proven at the State Research Enterprise of Starter Cultures that belongs to the IFR NAAS. The data on a wide range of clinical and therapeutic effects of the bacterial preparation Iprovit-Bifidolux allow recommending it for manufacturing functional foods.
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Bintsis T. Lactic acid bacteria as starter cultures: An update in their metabolism and genetics. AIMS Microbiol 2018; 4:665-684. [PMID: 31294241 PMCID: PMC6613329 DOI: 10.3934/microbiol.2018.4.665] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022] Open
Abstract
Lactic acid bacteria (LAB) are members of an heterogenous group of bacteria which plays a significant role in a variety of fermentation processes. The general description of the bacteria included in the group is gram-positive, non-sporing, non-respiring cocci or rods. An overview of the genetics of lactococci, Streptococcus thermophilus, lactobacilli, pediococci, leuconostocs, enterococci and oenococciis presented with special reference to their metabolic traits. The three main pathways in which LAB are involved in the manufacture of fermented foods and the development of their flavour, are (a) glycolysis (fermentation of sugars), (b) lipolysis (degradation of fat) and (c) proteolysis (degradation of proteins). Although the major metabolic action is the production of lactic acid from the fermentation of carbohydrates, that is, the acidification of the food, LAB are involved in the production of many beneficial compounds such as organic acids, polyols, exopolysaccharides and antimicrobial compounds, and thus have a great number of applications in the food industry (i.e. starter cultures). With the advances in the genetics, molecular biology, physiology, and biochemistry and the reveal and publication of the complete genome sequence of a great number of LAB, new insights and applications for these bacteria have appeared and a variety of commercial starter, functional, bio-protective and probiotic cultures with desirable properties have marketed.
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Affiliation(s)
- Thomas Bintsis
- Department of Agricultural Technology, TEI of West Macedonia, 53100 Florina, Greece
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Aleem B, Rashid MH, Zeb N, Saqib A, Ihsan A, Iqbal M, Ali H. Random mutagenesis of super Koji (Aspergillus oryzae): improvement in production and thermal stability of α-amylases for maltose syrup production. BMC Microbiol 2018; 18:200. [PMID: 30486793 PMCID: PMC6264608 DOI: 10.1186/s12866-018-1345-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 11/16/2018] [Indexed: 01/26/2023] Open
Abstract
Background Alpha-amylases hydrolyze 1,4 α-glycosidic bonds of starch and produce malto-oligosaccharides. It is an important enzyme generally applied in textile, food and brewing industries. Enhancement in thermal stability and productivity of enzymes are the two most sought after properties for industrial use. The Aspergillus oryzae (Koji) has Generally Recognized as Safe (GRAS) status and safe for use in food industry. Hence, Koji strain’s development for the screening of potent mutants, hyper producer of thermostable α-amylases, with desired attributes is the need of the time. Results A process has been developed to improve super Koji (A. oryzae cmc1) strain through γ-rays treatment. The doses i.e. 0.60, 0.80, 1.00, 1.20 & 1.40 KGy gave more than 3.0 log kill. Initially, 52 Koji mutants resistant to 1% (w/v) Triton X-100 were selected. 2nd screening was based on α-amylases hyper production and 23 mutants were sorted out by measuring clearing zones index (CI). Afterwards nine potent mutants, resistant to 2-deoxy D-glucose, were screened based on CI. These were further analyzed for thermal stability and productivity of α-amylase under submerged conditions. The mutants’ M-80(10), M-100(6) & M-120(5) gave about four fold increases in α-amylases productivity. The half life of M-100(6) α-amylase at 55 °C was 52 min and was highest among the mutants. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis confirmed that mutants did not produce aflatoxins. Field Emission Scanning Electron Microscopy (FESEM) of Koji mycelia depicted that exposure to gamma rays increased rigidity of the mycelium. The potent Koji mutant M-100(6) was grown on soluble starch in 10L fermenter and produced 40.0 IU ml-1 of α-amylases with specific activity of 2461 IU mg-1 protein. Growth kinetic parameters were: μ = Specific growth rate= 0.069 h-1, td = Biomass doubling time= 10.0 h, Yp/x = Product yield coefficient with respect to cell mass = 482 U g-1; qp= Specific rate of product formation= 33.29 U g-1 h-1. Conclusion It was concluded that the developed five step screening process has great potential to generate potent mutants for the hyper production of thermostable enzymes through γ-rays mediated physical mutagenesis. The developed thermostable α-amylases of super Koji mutantM-100(6) has immense potential for application in saccharification process for maltose syrup production. Moreover, the developed five step strain’s development process may be used for the simultaneous improvement in productivity and thermal stability of other microbial enzymes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bushra Aleem
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamaabd, Pakistan
| | - Muhammad Hamid Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan. .,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamaabd, Pakistan.
| | - Neelam Zeb
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Anam Saqib
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Ayesha Ihsan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Mazhar Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
| | - Hazrat Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P. O. Box 577, Faisalabad, Pakistan
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Cell Wall Glycans Mediate Recognition of the Dairy Bacterium Streptococcus thermophilus by Bacteriophages. Appl Environ Microbiol 2018; 84:AEM.01847-18. [PMID: 30242010 PMCID: PMC6238053 DOI: 10.1128/aem.01847-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/14/2018] [Indexed: 01/21/2023] Open
Abstract
Streptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants. Receptors on the cell surfaces of bacterial hosts are essential during the infection cycle of bacteriophages. To date, the phage receptors of the industrial relevant dairy starter bacterium Streptococcus thermophilus remain elusive. Thus, we set out to identify cell surface structures that are involved in host recognition by dairy streptococcal phages. Five industrial S. thermophilus strains sensitive to different phages (pac type, cos type, and the new type 987), were selected to generate spontaneous bacteriophage-insensitive mutants (BIMs). Of these, approximately 50% were deselected as clustered regularly interspaced short palindromic repeat (CRISPR) mutants, while the other pool was further characterized to identify receptor mutants. On the basis of genome sequencing data, phage resistance in putative receptor mutants was attributed to nucleotide changes in genes encoding glycan biosynthetic pathways. Superresolution structured illumination microscopy was used to visualize the interactions between S. thermophilus and its phages. The phages were either regularly distributed along the cells or located at division sites of the cells. The cell wall structures mediating the latter type of phage adherence were further analyzed via phenotypic and biochemical assays. Altogether, our data suggested that phage adsorption to S. thermophilus is mediated by glycans associated with the bacterial cell surface. Specifically, the pac-type phage CHPC951 adsorbed to polysaccharides anchored to peptidoglycan, while the 987-type phage CHPC926 recognized exocellular polysaccharides associated with the cell surface. IMPORTANCEStreptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants.
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López-González MJ, Escobedo S, Rodríguez A, Neves AR, Janzen T, Martínez B. Adaptive Evolution of Industrial Lactococcus lactis Under Cell Envelope Stress Provides Phenotypic Diversity. Front Microbiol 2018; 9:2654. [PMID: 30455679 PMCID: PMC6230721 DOI: 10.3389/fmicb.2018.02654] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/17/2018] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis is widely used as a starter in the manufacture of cheese and fermented milk. Its main role is the production of lactic acid, but also contributes to the sensory attributes of cheese. Unfortunately, the diversity of suitable strains to be commercialized as dairy starters is limited. In this work, we have applied adaptive evolution under cell envelope stress (AE-CES) as means to provide evolved L. lactis strains with distinct physiological and metabolic traits. A total of seven strains, three of industrial origin and four wild nisin Z-producing L. lactis, were exposed to subinhibitory concentrations of Lcn972, a bacteriocin that triggers the cell envelope stress response in L. lactis. Stable Lcn972 resistant (Lcn972R) mutants were obtained from all of them and two mutants per strain were further characterized. Minimal inhibitory Lcn972 concentrations increased from 4- to 32-fold compared to their parental strains and the Lcn972R mutants retained similar growth parameters in broth. All the mutants acidified milk to a pH below 5.3 with the exception of one that lost the lactose plasmid during adaptation and was unable to grow in milk, and two others with slower acidification rates in milk. While in general phage susceptibility was unaltered, six mutants derived from three nisin Z producers became more sensitive to phage attack. Loss of a putative plasmid-encoded anti-phage mechanism appeared to be the reason for phage susceptibility. Otherwise, nisin production in milk was not compromised. Different inter- and intra-strain-dependent phenotypes were observed encompassing changes in cell surface hydrophobicity and in their autolytic profile with Lcn972R mutants being, generally, less autolytic. Resistance to other antimicrobials revealed cross-protection mainly to cell wall-active antimicrobials such as lysozyme, bacitracin, and vancomycin. Finally, distinct and shared non-synonymous mutations were detected in the draft genome of the Lcn972R mutants. Depending on the parental strain, mutations were found in genes involved in stress response, detoxification modules, cell envelope biogenesis and/or nucleotide metabolism. As a whole, the results emphasize the different strategies by which each strain becomes resistant to Lcn972 and supports the feasibility of AE-CES as a novel platform to introduce diversity within industrial L. lactis dairy starters.
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Affiliation(s)
- María Jesús López-González
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | - Susana Escobedo
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
| | | | | | - Beatriz Martínez
- DairySafe Group, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
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43
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Dijkstra AR, Starrenburg MJC, Todt T, van Hijum SAFT, Hugenholtz J, Bron PA. Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11. Front Microbiol 2018; 9:2418. [PMID: 30374338 PMCID: PMC6196286 DOI: 10.3389/fmicb.2018.02418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/20/2018] [Indexed: 11/20/2022] Open
Abstract
The viability of starter cultures is essential for an adequate contribution to the fermentation process and end-product. Therefore, robustness during processing and storage is an important characteristic of starter culture strains. For instance, during spray drying cells are exposed to heat and oxidative stress, generally resulting in loss of viability. In this study, we exposed the industrially relevant but stress-sensitive Lactococcus lactis strain SK11 to two cycles of heat stress, with intermediate recovery and cultivation at moderate temperatures. After these two cycles of heat exposure, the abundance of robust derivatives was increased as compared with the original culture, which enabled isolation of heat-resistant subpopulations displaying up to 1,000-fold enhanced heat stress survival. Moreover, this heat-resistant subpopulation demonstrated an increased survival during spray drying. Derivatives from two independent lineages displayed different transcriptome changes as compared with the wild type strain, indicating that the increased robustness within these lineages was established by different adaptive strategies. Nevertheless, an overlap in differential gene expression in all five derivatives tested in both lineages included three genes in an operon involved in zinc transport. The link between zinc homeostasis and heat stress survival in L. lactis was experimentally established by culturing of the wild type strain SK11 in medium with various levels of zinc ions, which resulted in alterations in heat stress survival phenotypes. This study demonstrates that robust derivatives of a relatively sensitive L. lactis strain can be isolated by repeated exposure to heat stress. Moreover, this work demonstrates that transcriptome analysis of these robust derivatives can provide clues for improvement of the robustness of the original strain. This could boost the industrial application of strains with specific desirable traits but inadequate robustness characteristics.
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Affiliation(s)
- Annereinou R Dijkstra
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, Netherlands.,Nederlands Instituut Voor Zuivel Oonderzoek (NIZO), Ede, Netherlands.,Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, Netherlands
| | | | - Tilman Todt
- Centre for Molecular and Biomolecular Informatics, Radboud umc, Nijmegen, Netherlands
| | - Sacha A F T van Hijum
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, Netherlands.,Nederlands Instituut Voor Zuivel Oonderzoek (NIZO), Ede, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud umc, Nijmegen, Netherlands
| | - Jeroen Hugenholtz
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, Netherlands
| | - Peter A Bron
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, Netherlands.,Nederlands Instituut Voor Zuivel Oonderzoek (NIZO), Ede, Netherlands
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44
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Hatti-Kaul R, Chen L, Dishisha T, Enshasy HE. Lactic acid bacteria: from starter cultures to producers of chemicals. FEMS Microbiol Lett 2018; 365:5087731. [DOI: 10.1093/femsle/fny213] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/29/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Rajni Hatti-Kaul
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Lu Chen
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Tarek Dishisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62511 Beni-Suef, Egypt
| | - Hesham El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81 310 Skudai, Johor, Malaysia
- City of Scientific Research and Technology Applications, New Burg Al Arab, Alexandria, Egypt
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45
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López-González MJ, Campelo AB, Picon A, Rodríguez A, Martínez B. Resistance to bacteriocin Lcn972 improves oxygen tolerance of Lactococcus lactis IPLA947 without compromising its performance as a dairy starter. BMC Microbiol 2018; 18:76. [PMID: 30029618 PMCID: PMC6053707 DOI: 10.1186/s12866-018-1222-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Lactococcus lactis is the main component of the mesophilic starters used in cheese manufacture. The success of milk fermentation relies on the viability and metabolic activity of the starter bacteria. Therefore, robust strains able to withstand the harsh conditions encountered during cheese manufacture and starter production are demanded. In this work, we have applied adaptive evolution under cell envelope stress imposed by the cell wall active bacteriocin Lcn972 to evolve strains with more robust phenotypes. Results Consecutive exposure of the starter strain L. lactis IPLA947 to Lcn972 yielded a stable mutant, L. lactis R5, with enhanced survival when challenged with hydrogen peroxide. L. lactis R5 exhibited faster growth rates in aerobic fermentations in broth and was able to acidify milk to a lower pH in aerated milk cultures. The improved behavior of L. lactis R5 in the presence of oxygen did not translate into a better performance in the presence of heme (i.e. respiration metabolism) or into higher survival during storage at cold temperatures or after freeze-drying compared to the wild type L. lactis IPLA947. L. lactis R5 retained the same milk acidification rate and no changes in the consumption of lactose and production of organic acids were noticed. However, the profile of volatile compounds revealed a significant increase in 3-hydroxy-2-butanone (acetoin) in curds manufactured with L. lactis R5. Conclusions Based on our results, L. lactis R5 can be proposed as a suitable dairy starter with improved survival under oxidative stress and enhanced metabolic traits. The results support the notion that adaptive evolution under cell envelope stress might be useful to generate strain diversity within industrial L. lactis strains.
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Affiliation(s)
- María Jesús López-González
- Dairy Safe group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Paseo Río Linares, s/n 33300, Villaviciosa, Asturias, Spain
| | - Ana Belén Campelo
- Dairy Safe group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Paseo Río Linares, s/n 33300, Villaviciosa, Asturias, Spain
| | - Antonia Picon
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - Ana Rodríguez
- Dairy Safe group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Paseo Río Linares, s/n 33300, Villaviciosa, Asturias, Spain
| | - Beatriz Martínez
- Dairy Safe group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Paseo Río Linares, s/n 33300, Villaviciosa, Asturias, Spain.
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46
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Constraint-based modeling in microbial food biotechnology. Biochem Soc Trans 2018; 46:249-260. [PMID: 29588387 PMCID: PMC5906707 DOI: 10.1042/bst20170268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/19/2022]
Abstract
Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM.
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47
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Johansen E. Future access and improvement of industrial lactic acid bacteria cultures. Microb Cell Fact 2017; 16:230. [PMID: 29268733 PMCID: PMC5738899 DOI: 10.1186/s12934-017-0851-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/15/2017] [Indexed: 11/25/2022] Open
Abstract
Industrial fermentations based on micro-organisms such as the lactic acid bacteria (LAB) play an important role in several industries globally and represent multi-billion Euro/dollar businesses. LAB provide a natural way to produce safe, sustainable, and environmentally friendly products for a variety of industries. Product innovation is a key requirement for these industries to survive and grow globally. However, the development of new products may be affected by two man-made constraints; the Nagoya Protocol on benefit sharing and the opposition to the use of modern biotechnology for strain improvement. An expert workshop was held in Amsterdam, May 10-11, 2017 to discuss these challenges; a number of conclusions and recommendations were formulated and will be presented herein.
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Affiliation(s)
- Eric Johansen
- Chr Hansen A/S, 10-12 Bøge Allé, Dk2970, Hørsholm, Denmark.
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48
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Mills S, Griffin C, O'Connor PM, Serrano LM, Meijer WC, Hill C, Ross RP. A Multibacteriocin Cheese Starter System, Comprising Nisin and Lacticin 3147 in Lactococcus lactis, in Combination with Plantaricin from Lactobacillus plantarum. Appl Environ Microbiol 2017; 83:e00799-17. [PMID: 28476774 PMCID: PMC5494623 DOI: 10.1128/aem.00799-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/02/2017] [Indexed: 12/31/2022] Open
Abstract
Functional starter cultures demonstrating superior technological and food safety properties are advantageous to the food fermentation industry. We evaluated the efficacies of single- and double-bacteriocin-producing starters of Lactococcus lactis capable of producing the class I bacteriocins nisin A and/or lacticin 3147 in terms of starter performance. Single producers were generated by mobilizing the conjugative bacteriophage resistance plasmid pMRC01, carrying lacticin genetic determinants, or the conjugative transposon Tn5276, carrying nisin genetic determinants, to the commercial starter L. lactis CSK2775. The effect of bacteriocin coproduction was examined by superimposing pMRC01 into the newly constructed nisin transconjugant. Transconjugants were improved with regard to antimicrobial activity and bacteriophage insensitivity compared to the recipient strain, and the double producer was immune to both bacteriocins. Bacteriocin production in the starter was stable, although the recipient strain proved to be a more efficient acidifier than transconjugant derivatives. Overall, combinations of class I bacteriocins (the double producer or a combination of single producers) proved to be as effective as individual bacteriocins for controlling Listeria innocua growth in laboratory-scale cheeses. However, using the double producer in combination with the class II bacteriocin producer Lactobacillus plantarum or using the lacticin producer with the class II producer proved to be most effective for reducing bacterial load. As emergence of bacteriocin tolerance was reduced 10-fold in the presence of nisin and lacticin, we suggest that the double producer in conjunction with the class II producer could serve as a protective culture providing a food-grade, multihurdle approach to control pathogenic growth in a variety of industrial applications.IMPORTANCE We generated a suite of single- and double-bacteriocin-producing starter cultures capable of generating the class I bacteriocin lacticin 3147 or nisin or both bacteriocins simultaneously via conjugation. The transconjugants exhibited improved bacteriophage resistance and antimicrobial activity. The single producers proved to be as effective as the double-bacteriocin producer at reducing Listeria numbers in laboratory-scale cheese. However, combining the double producer or the lacticin-producing starter with a class II bacteriocin producer, Lactobacillus plantarum LMG P-26358, proved to be most effective at reducing Listeria numbers and was significantly better than a combination of the three bacteriocin-producing strains, as the double producer is not inhibited by either of the class I bacteriocins. Since the simultaneous use of lacticin and nisin should reduce the emergence of bacteriocin-tolerant derivatives, this study suggests that a protective starter system produced by bacteriocin stacking is a worthwhile multihurdle approach for food safety applications.
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Affiliation(s)
- S Mills
- CSK Food Enrichment, Ede, The Netherlands
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - C Griffin
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- CSK Food Enrichment, Ede, The Netherlands
| | - P M O'Connor
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | | | - W C Meijer
- CSK Food Enrichment, Ede, The Netherlands
| | - C Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R P Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
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49
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Bachmann H, Molenaar D, Branco dos Santos F, Teusink B. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol Rev 2017. [DOI: 10.1093/femsre/fux024] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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50
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Finding the Needle in the Haystack-the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria. mBio 2017; 8:mBio.00526-17. [PMID: 28559484 PMCID: PMC5449655 DOI: 10.1128/mbio.00526-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient screening technologies aim to reduce both the time and the cost required for identifying rare mutants possessing a phenotype of interest in a mutagenized population. In this study, we combined a mild mutagenesis strategy with high-throughput screening based on microfluidic droplet technology to identify Lactococcus lactis variants secreting vitamin B2 (riboflavin). Initially, we used a roseoflavin-resistant mutant of L. lactis strain MG1363, JC017, which secreted low levels of riboflavin. By using fluorescence-activated droplet sorting, several mutants that secreted riboflavin more efficiently than JC017 were readily isolated from the mutagenesis library. The screening was highly efficient, and candidates with as few as 1.6 mutations per million base pairs (Mbp) were isolated. The genetic characterization revealed that riboflavin production was triggered by mutations inhibiting purine biosynthesis, which is surprising since the purine nucleotide GTP is a riboflavin precursor. Purine starvation in the mutants induced overexpression of the riboflavin biosynthesis cluster ribABGH. When the purine starvation was relieved by purine supplementation in the growth medium, the outcome was an immediate downregulation of the riboflavin biosynthesis cluster and a reduction in riboflavin production. Finally, by applying the new isolates in milk fermentation, the riboflavin content of milk (0.99 mg/liter) was improved to 2.81 mg/liter, compared with 0.66 mg/liter and 1.51 mg/liter by using the wild-type strain and the original roseoflavin-resistant mutant JC017, respectively. The results obtained demonstrate how powerful classical mutagenesis can be when combined with droplet-based microfluidic screening technology for obtaining microorganisms with useful attributes. The food industry prefers to use classical approaches, e.g., random mutagenesis followed by screening, to improve microorganisms used in food production, as the use of recombinant DNA technologies is still not widely accepted. Although modern automated screening platforms are widely accessible, screening remains as a bottleneck in strain development, especially when a mild mutagenesis approach is applied to reduce the chance of accumulating unintended mutations, which may cause unwanted phenotypic changes. Here, we incorporate a droplet-based high-throughput screening method into the strain development process and readily capture L. lactis variants with more efficient vitamin secretion from low-error-rate mutagenesis libraries. This study shows that useful mutants showing strong phenotypes but without extensive mutations can be identified with efficient screening technologies. It is therefore possible to avoid accumulating detrimental mutations while enriching beneficial ones through iterative mutagenesis screening. Due to the low mutation rates, the genetic determinants are also readily identified.
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