Preface
Page: ii-ii (1)
Author: Prakash M. Halami and Aravind Sundararaman
DOI: 10.2174/9789815165678124010002
Recent Advances in CRISPR-Cas Genome Engineering: An Overview
Page: 1-17 (17)
Author: Angelina Job Kolady, Aritra Mukherjee, Ranjith Kumavath*, Sarvepalli Vijay Kumar and Pasupuleti Sreenivasa Rao*
DOI: 10.2174/9789815165678124010004
PDF Price: $15
Abstract
Bacteria is one of the most primitive organisms on earth. Its high
susceptibility to bacteriophages has tailored them to use specific tools to edit their
genome and evade the bacteriophages. This defense system has been developed to be
the most specific genome editing technology of this current period. Previously, various
other tools such as restriction enzymes (RE), zinc finger nucleases (ZNF), and
transcription activator-like effector nucleases (TALENS) were utilized. Still, its major
limitations led to exploiting the bacterial defense system to edit the genome. CRISPR
technology can be applied in various microbiology, pathology, cancer biology,
molecular biology, and industrial biotechnology, but its limitations, such as off-target
effects due to unspecific alterations, are a major concern. In the future, this effective
gene alteration technology will be developed to treat inherited rare genetic disorders.
This chapter highlights the discovery, components, applications, limitations, and future
prospects of CRISPR-Cas.
Overview and Applications of CRISPR/Cas9 Based Genome Editing in Industrial Microorganisms
Page: 18-44 (27)
Author: Kiran Dindhoria, Vivek Manyapu, Ashif Ali, Aman Kumar and Rakshak Kumar*
DOI: 10.2174/9789815165678124010005
PDF Price: $15
Abstract
CRISPR-Cas technology has reshaped the field of microbiology. It has
improved the microbial strains for better industrial and therapeutic utilization. In this
chapter, we have tried to provide an overview of this technology with special reference
to its associated applications in the various fields of interest. We have discussed the
origin, classification, and different genome editing methods of CRISPR-Cas to
understand its historical significance and the basic mechanism of action. Further,
different applications in the area of agriculture, food industry, biotherapeutics, biofuel,
and other valuable product synthesis were also explained to highlight the advancement
of this system in industrial microbes. We have also tried to review some of the
limitations offered by CRISPR and insights into its future perspective.
Modulating the Gut Microbiome through Genome Editing for Alleviating Gut Dysbiosis
Page: 45-61 (17)
Author: Atul R. Chavan, Maitreyee Pathak, Hemant J. Purohit and Anshuman A. Khardenavis*
DOI: 10.2174/9789815165678124010006
PDF Price: $15
Abstract
One of the components of the emerging lifestyle shows an exponential rise
in the consumption of packaged or high-calorie food. This has caused an increase in the
incidences of diseases which are considered to be a consequence of the changing
lifestyle. It has been observed that these clinical conditions are linked with gut
dysbiosis, and hence it has been proposed that by modulation of the composition of gut
microbiota, the risk of such diseases can be lowered. Prebiotics and probiotics, in
combination, possess tremendous potential for maintaining the homeostasis in
individuals. In this chapter, a comparative assessment of CRISPR-mediated genome
editing technique has been discussed with conventional omics tools and modelling
approaches. These techniques substantially simplify the modification of target genome
in complex microbial communities and could enhance their prebiotic and probiotic
potential. The synthetic biology approach to microbiome therapies such as additive,
subtractive, and modulatory therapies for curing gut dysbiosis are also discussed. The
chapter is aimed at developing a better understanding about the role of CRISPR/Cas as
a reliable technology that may be employed as a diagnostic tool for infectious disease
diagnosis as well as its treatment. Although, the tool has already demonstrated its use
in a wide range of genome editing and genetic engineering applications, additional
study into its use in human genome editing and diagnostics is needed considering any
potential side effects or ambiguities.
Bifidobacterial Genome Editing for Potential Probiotic Development
Page: 62-87 (26)
Author: Kriti Ghatani*, Shankar Prasad Sha, Subarna Thapa, Priya Chakraborty and Sagnik Sarkar
DOI: 10.2174/9789815165678124010007
PDF Price: $15
Abstract
Genome editing is a promising tool in the era of modern biotechnology that
can alter the DNA of many organisms. It is now extensively used in various industries
to obtain the well-desired and enhanced characteristics to improve the yield and
nutritional quality of products. The positive health attributes of Bifidobacteria, such as
prevention of diarrhoea, reduction of ulcerative colitis, prevention of necrotizing
enterocolitis, etc., have shown promising reports in many clinical trials. The potential
use of Bifidobacteria as starter or adjunct cultures has become popular. Currently,
Bifidobacterium bifidum, B. adolescentis, B. breve, B. infantis, B. longum, and B. lactis
find a significant role in the development of probiotic fermented dairy products.
However, Bifidobacteria, one of the first colonizers of the human GI tract and an
indicator of the health status of an individual, has opened new avenues for research
and, thereby, its application. Besides this, the GRAS/QPS (Generally Regarded as
Safe/Qualified Presumption of Safety) status of Bifidobacteria makes it safe for use.
They belong to the subgroup (which are the fermentative types that are primarily found
in the natural cavities of humans and animals) of Actinomycetes. B. lactis has been used
industrially in fermented foods, such as yogurt, cheese, beverages, sausages, infant
formulas, and cereals. In the present book chapter, the authors tried to explore the
origin, health attributes, and various genetic engineering tools for genome editing of
Bifidobacteria for the development of starter culture for dairy and non-dairy industrial
applications as well as probiotics.
Metabolic Engineering of Bifidobacterium sp. Using Genome Editing Techniques
Page: 88-105 (18)
Author: Aravind Sundararaman and Prakash M. Halami*
DOI: 10.2174/9789815165678124010008
PDF Price: $15
Abstract
The gut microbiome is significant in maintaining human health by
facilitating absorption and digestion in the intestine. Probiotics have diverse and
significant applications in the health sector, so probiotic strains require an
understanding of the genome-level organizations. Probiotics elucidate various
functional parameters that control their metabolic functions. Gut dysbiosis leads to
inflammatory bowel disease and other neurological disorders. The application of
probiotic bacteria to modulate the gut microbiota prevents diseases and has gained
large interest. In a recent decade, the development of modern tools in molecular
biology has led to the discovery of genome engineering. Synthetic biology approaches
provide information about diverse biosynthetic pathways and also facilitate novel
metabolic engineering approaches for probiotic strain improvement. The techniques
enable engineering probiotics with the desired functionalities to benefit human health.
This chapter describes the recent advances in probiotic strain improvement for
diagnostic and therapeutic applications via CRISPR-Cas tools. Also, the application of
probiotics, current challenges, and future perspectives in disease treatment are
discussed.
Lactic Acid Bacteria as Starter Cultures in Food: Genome Characterization and Comparative Genomics
Page: 106-139 (34)
Author: Md Minhajul Abedin, Srichandan Padhi, Rounak Chourasia, Loreni Chiring Phukon, Puja Sarkar, Sudhir P. Singh and Amit Kumar Rai*
DOI: 10.2174/9789815165678124010009
PDF Price: $15
Abstract
Fermented food products are consumed by about 30% of the world's
population due to their high nutritional value and health properties. The use of LAB in
the fermentation process has resulted in a variety of fermented food products derived
from both plant and animal sources. LAB have been used as starter cultures for food
fermentation both traditionally and industrially, having certain specific characteristics
such as rapid growth, product yield, higher biomass and also unique organoleptic
properties, and are employed in food fermentation. The advancement of highthroughput genome sequencing methods has resulted in a tremendous improvement in
our understanding of LAB physiology and has become more essential in the field of
food microbiology. The complete genome sequence of Lactococcus lactis in 2001
resulted in a better understanding of metabolic properties and industrial applications of
LAB. Genes associated with β-galactosidase, antimicrobial agents, bile salt hydrolase,
exopolysaccharide, and GABA producing LAB have received a lot of attention in
recent years. Genome editing techniques are required for the development of strains for
novel applications and products. They can also play an important part as a research
method for acquiring mechanistic insights and identifying new properties. The genome
editing of lactic acid bacterial strains has a lot of potential applications for developing
functional foods with a favourable influence on the food industries.
L. Plantarum of Vegetable Origin - Genome Editing and Applications
Page: 140-155 (16)
Author: Sudeepa E. S.* and A. Sajna
DOI: 10.2174/9789815165678124010010
PDF Price: $15
Abstract
Lactobacillus plantarum is a widespread, versatile bacterium that plays a
vital role in the preservation of innumerable fermented foods. These strains are
commonly employed as silage additives and starter cultures of fermented goods.
Genome editing could provide an added benefit by improving the fermentation profile
and quality, as well as the accompanying therapeutic benefits.
Genome editing of various strains of L. plantarum can be used commercially to
produce L-ribulose or succinic acid, direct lactic acid production, and increased ethanol
production. L. plantarum strains or recombinant strains can help restore intestinal flora
homeostasis, reduce the number of pathogenic organisms, and could even be employed
as vaccine carriers. Food products such as raw and fermented vegetables, olives, and
cereals inoculated with probiotic microbes have shown encouraging benefits as people
now seek non-dairy based probiotics. L. plantarum of vegetable or plant origin, as well
as applications of genome edited strains, are discussed in this book chapter.
Genome Editing in Bacillus Licheniformis: Current Approaches and Applications
Page: 156-180 (25)
Author: Steji Raphel and Prakash M. Halami*
DOI: 10.2174/9789815165678124010011
PDF Price: $15
Abstract
Bacillus licheniformis has been regarded as an exceptional microbial cell
factory for the production of biochemicals and enzymes. The complete genome
sequencing and annotation of the genomes of industrially-relevant Bacillus species has
uplifted our understanding of their properties and helped in the progress of genetic
manipulations in other Bacillus species. The genome sequence analysis has given
information on the different genes and their functional importance. Post-genomic
studies require simple and highly efficient tools to enable genetic manipulation. With
the developments of complete genome sequences and simple genetic manipulation
tools, the metabolic pathways of B. licheniformis could be rewired for the efficient
production of interest chemicals. However, gene editing (such as gene knockout) is
laborious and time consuming using conventional methods. Recently, useful tools for
the genetic engineering of Bacillus species have emerged from the fields of systems
and synthetic biology. The recent progress in genetic engineering strategies as well as
the available genetic tools that have been developed in Bacillus licheniformis species,
has conveniently enabled multiple modifications in the genomes of Bacillus species
and thereby improved its use in the industrial sector.
Subject Index
Page: 181-186 (6)
Author: Prakash M. Halami and Aravind Sundararaman
DOI: 10.2174/9789815165678124010012
Introduction
This reference is a comprehensive review of genome editing in bacteria. The multi-part book meticulously consolidates research findings and insights on the applications of bacteria across several industries, including food processing and pharmaceutical development. The book covers four overarching themes for readers: a historical perspective of genome editing, genome editing in probiotics, applications of genome editing in agricultural microbiology and genetic engineering in environmental microbiology. The editors have also compiled chapters that provide an in-depth analysis of gene regulation and metabolic engineering through genome editing tools for specific bacteria. Key topics in part 1: - An Overview of advances in CRISPR-CAS research - Applications of CRISPR/CAS9-based genome editing for industrial microorganisms - Gut microbiome modulation to address gut dysbiosis - Bifidobacterium genome editing for probiotic development and metabolic engineering. - Insights into the use of lactic acid bacteria as starter cultures in the food - Genome editing of vegetable-derived L. Plantarum - Genome editing in Bacillus Licheniformis Genome Editing in Bacteria is a definitive reference for scholars, researchers and industry professionals navigating the forefront of bacterial genomics.