Lactobacillus Genomics and Metabolic Engineering | Book
Caister Academic Press
Sandra M. Ruzal
Departamento de Química Biológica, IQUIBICEN-CONICET, Buenos Aires, Argentina
January 2019Buy book
GB £159 or US $319Ebook:
GB £159 or US $319
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Lactobacillus is a highly phylogenetically and metabolically diverse genus comprising more than 200 species. As food-grade microorganisms, lactobacilli have long been exploited in the feed, food and beverage industries, with applications ranging from extending the shelf-life of food products to their use as probiotics with health-promoting properties. In addition lactobacilli are also important producers of industrial chemicals such as lactic acid and gamma-aminobutyric acid.
The considerable commercial importance has stimulated a plethora of research projects studying the genomics, molecular biology and metabolic engineering of these bacteria and prompted the need for this concise book which provides a timely overview of the field. Topics covered include: the genomic perspective on niche adaptability; catabolic pathways of complex carbohydrates metabolism; the production of lactate; genetics, biology of the cell envelope and applications of the S-layer proteins; lactobacilli bacteriophage; DNA transfer into Lactobacillus species; recombinant gene expression and genomics of antibiotic resistance in Lactobacillus.
This book is an invaluable source of information and essential reading for everyone working with lactobacilli, lactic acid bacteria and probiotics, from the PhD student to the experienced scientist, in academia, the pharmaceutical or biotechnology industries and those working in clinical environments.
Table of contents
1. A Genomic Perspective on Niche Adaptability in Lactobacillus
Ewelina Stefanovic and Olivia McAuliffe
The Lactobacillus genus comprises more than 200 formally-recognised species characterized by a phylogenetic and metabolic diversity that exceeds that of a typical bacterial family. The widespread dissemination of members of the lactobacilli in different ecological niches testifies to their extraordinary niche adaptability. Advances in sequencing technologies has facilitated a comprehensive examination of the characteristics of the Lactobacillus genus through large-scale comparative genomics, and aided an understanding of the genomic background for the presence of lactobacilli in such a broad range of habitats. Comparative genomic analysis has revealed that adaptation to such highly variable environments is a result of genome evolution. Gene loss and acquisition, mainly driven by horizontal gene transfer, underlies the remarkable genomic diversity observed, resulting in species which may be considered either niche generalists or niche specialists. Larger genome sizes are associated with ecologically flexible species such as Lactobacillus casei and Lactobacillus plantarum. These niche generalists have typically acquired or retained the capacity to migrate between different habitats and have recently been described as nomadic. Niche specialists, or host-adapted species such as Lactobacillus sanfranciscensis, possess much smaller genomes, reflecting ecological specialisation. For many species, sufficient information to infer their real niche preferences remains elusive. In this chapter, we review the available genomic information for the Lactobacillus genus and the comparative genomic approaches that have been taken to evaluate strains or species found in different niches, which give an insight into niche adaptation within the genus.
2. Genetics and Genomics of Lactobacillus sakei and Lactobacillus curvatus
Lucrecia C. Terán, Raúl R. Raya, Monique Zagorec and Marie-Christine Champomier-Vergès
Lactobacillus sakei and Lactobacillus curvatus are two lactic acid bacteria widely used worldwide as starters for meat fermentation. They are phenotypically closely related species and have often been associated as a "sakei/curvatus" group in the past. These species have also been more recently described to be phylogenetically closely related to other Lactobacillus species such as L. fuchuensis and L. graminis. Genomic studies have contributed to a better characterization of each species and enlightened their specificities. L. sakei exhibits a high genomic diversity and several genomes are now available. Complete and draft genome sequences are also available from L. curvatus strains originating from various origins. This chapter will provide information on genomic repertoires of each species and illustrate their main common features.
3. Complex Oligosaccharide Utilization Pathways in Lactobacillus
Manuel Zúñiga, María Jesús Yebra and Vicente Monedero
Lactobacillus is the bacterial genus that contains the highest number of characterized probiotics. Lactobacilli in general can utilize a great variety of carbohydrates. This characteristic is an essential trait for their survival in highly competitive environments such as the gastrointestinal tract of animals. In particular, the ability of some strains to utilize complex carbohydrates such as milk oligosaccharides as well as their precursor monosaccharides, confer upon lactobacilli a competitive advantage. For this reason, many of these carbohydrates are considered as prebiotics. Genome sequencing of many lactobacilli strains has revealed a great variety of genes involved in the metabolism of carbohydrates and some of them have already been characterized. In this chapter, the current knowledge at the biochemical and genetic levels of the catabolic pathways of complex carbohydrates utilized by lactobacilli will be summarized.
4. Production of Lactate using Lactobacillus
Mariana C. Allievi, Maria Mercedes Palomino and Sandra M. Ruzal
Lactic acid is used in the food, cosmetic, textile, pharmaceutical and chemical industries. In the last decades, the interest of lactate production by the fermentation route has increased due to the prospects of environmental friendliness and the use of renewable sources instead of petroleum products. Recently, the enlarged manufacture of the biodegradable polylactic acid polymer (PLA) has increased the global interest in the production of L-lactic acid and D-lactic acid. In this chapter we will focus on the importance of lactic acid, and the main difficulties and the solutions that were designed to increase the production of lactic acid will be addressed. It will focus on the genetic engineering approaches to improve the producing strains of the genus Lactobacillus.
5. Modifications of Lactobacillus Surface Under Environmental Stress Conditions
Mariana C. Allievi, Sandra M. Ruzal and Maria Mercedes Palomino
Lactobacilli are a diverse group of food-grade microorganisms widely applied in the fermented food industry due to their technological and health-promoting properties; these bacteria have been extensively used as starter cultures and as probiotics. In this way, Lactobacillus is exposed to different stress factors during food fermentation. In this chapter we will discuss the ability of Lactobacillus to respond to environmental conditions, focusing on osmotic stress, by altering the nature of their cell wall for adaptation. We will describe their modification, in particular those related to the structure of peptidoglycan, secondary cell-wall polymers, named teichoic acids and surface-layer proteins.
6. S-Layer Proteins from Lactobacilli: Biogenesis, Structure, Functionality and Biotechnological Applications
Mariano Malamud, Patricia A. Bolla, Paula Carasi, Esteban Gerbino, Andrea Gómez-Zavaglia, Pablo Mobili and María de los Angeles Serradell
The S-layer is a (glyco)-proteinaceous envelope made up of subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea. The S-layer (glyco)-proteins have been shown to possess exceptional physicochemical properties which make them unique organizational structures with high potential application in different areas of biotechnology. It represents a very interesting model system for studying the processes involved in the synthesis, secretion and assembly of extracellular proteins. Among bacteria, its presence has been demonstrated in many species of lactobacilli, some of which could be considered as probiotic microorganisms. In this chapter, we will discuss the most relevant and updated concepts regarding genetics, structural features, cell wall- and self-assembly, functionality and biotechnological applications of the S-layer proteins from lactobacilli.
7. Bacteriophages of Lactobacillus species
María E. Dieterle and Mariana Piuri
Bacteriophages infecting lactic acid bacteria (LAB) are the main cause of fermentation failures leading to economic losses. Phages that infect Lactococcus and Streptococcus strains have been widely characterized in the literature mainly because of their relevance in industry. Despite the above, strains of Lactobacillus are particularly of interest because besides their contribution to the organoleptic properties of fermented products, several strains have purported probiotic properties and are part of commercial formulations. The use of these strains is the result of years of research that validated the claimed benefits in food products. Phage attack on these specifically chosen strains is particularly deleterious, as they cannot be easily replaced. Advances in phage genomics, virus-bacteria interactions, and new tools designed to avoid infection are described in this chapter.
8. DNA Transfer in Lactobacillus: An Overview
Maria Mercedes Palomino, Joaquina Fina Martin, Mariana C. Allievi, Marie Eugenia Dieterle, Carmen Sanchez-Rivas and Sandra M. Ruzal
An overview of the fundamental basis for the introduction of DNA into Lactobacillus species is given in this chapter. Natural ways for introducing DNA such as transformation, transduction or conjugation are reported in few strains. No evidence for natural competence is available in particular in probiotic Lactobacillus strains; although various components of natural gene transfer systems are present in various genomes. Protoplast fusion and transfection are also described. The most popular method used for introducing foreign DNA is electroporation, mostly based on cell-wall weakening prior to electroshock. The composition of the envelope, in particular the presence or not of an S-layer, and the content of endogenous plasmids in the different Lactobacillus species result in different transformation efficiencies. The use of ssRNA as donor and CRISPR-cas as the recombineering factor open the way for obtaining recombinants with the need of high efficiency DNA transfer systems to succeed in the genetic modifications.
9. Recombinant Gene Expression in Lactobacilli: Strategies and Applications
Clemens Peterbauer, Stefan Heinl, Aleš Berlec and Reingard Grabherr
Bacteria-based expression systems play a substantial role in industrial and medical biotechnology for the production of various proteins. In contrast to Gram negative bacteria such as Escherichia coli, Gram positive lactic acid bacteria possess a specific cell wall structure that allows for secretion of proteins directly into their environment. In spite of some limitations, this advantage and the fact that many of these bacteria have GRAS (generally recognized as safe) status made them into an attractive tool in biotechnology. In this chapter we give an overview of the potential of lactobacilli to be used for recombinant protein expression and their feasibility in various applications. In the past years lactobacilli have been used for the production of therapeutics, as vaccines, and as a platform for protein surface display. Many tools for genetic modification of lactobacilli have been developed and optimized. In addition, a great variety of gene regulatory elements have been isolated, characterized and established in the context of recombinant protein expression. We discuss the properties of different plasmids that may be used for the expression of intracellular or secreted target proteins. We describe the mechanisms of inducible and constitutive promoters, the influence of codon usage and ribosomal binding sites on protein expression levels, and strategies for stable integration of target genes into the genome of lactobacilli using modern technologies. Overall, there exists a high variety of different lactobacilli species and strains that are highly specialized and have adapted to specific ecological niches. Depending on the application, the desired product or the required process, genetic tools and regulatory elements often have to be tested, adapted and optimized individually.
10. Genomic Overview of Acquired Antibiotic Resistance Mechanisms in Lactobacillus
Cecilia Rodríguez, Lucía Petrelli, María Soledad Ramírez, Daniela Centrón, Elvira María Hebert and Lucila Saavedra
In recent years, the number of antibiotic-resistant bacteria prevalent in clinical settings has risen, alarming both scientists and government agencies. Studies on the emergence and spread of antibiotic resistance focused mainly on bacteria of clinical importance. However, commensal and environmental bacteria appear as a reservoir of the determinants of resistance to antibiotics found in bacteria of clinical origin. In particular, the food chain was proposed as the main route for the introduction of resistant bacteria associated with animals and the environment. The emergence of antibiotic resistance can be attributed to several factors, such as the overuse of antibiotics both within and outside of a clinical setting, random bacterial mutations leading to increased resistance, not completing the course of an antibiotic prescription, and the use of antibiotics in farming and agricultural. A summary of acquired antibiotic-resistance genes to tetracycline, erythromycin and aminoglycosides and a genomic overview of these resistance genes in Lactobacillus is described in this chapter.
How to buy this book
(EAN: 9781910190890 9781910190906 Subjects: [bacteriology] [microbiology] [molecular microbiology] [probiotics] )