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Contents
Contributors xi
About the editors xv
Preface xvii
Acknowledgment xix
1. Role of bioinformatics tools in microbial prospectives and its future
Ananya Nayak, Maheswata Sahoo, Swayamprabha Sahoo, Ayushman Gadnayak, Jatindra Nath Mohanty, Shivani Dave, Padmaja Mohanty, Sushma Dave, and Jayashankar Das
1.1 Introduction 1
1.2 Overview of the role of bioinformatics in microbiology 2
1.3 Prokaryotic genome sequencing 2
1.4 Prokaryotic genome annotation 4
1.5 Microbial profiling 4
1.6 Metagenomics and microbiome 5
1.7 Analysis of the human microbiome with the 16s rRNA gene 5
1.8 Phylogenetic microchips 6
1.9 Bacterial genetic barcode and their uses 6
1.10 NGS in microbial metabolism 6
1.11 The role of genomics in finding microbes 8
1.12 Genome scale metabolic reconstruction 9
1.13 Summary 10
References 11
2. Recent trends in genomic approaches for microbial bioprospecting
R. Nabil, M. Chamundeeswari, and K. Tamilarasan
2.1 Introduction 13
2.2 Overall scheme for genome-based bioprospecting 14
2.3 Culture-independent methods 14
2.4 Bioprospecting through RT-PCR 16
2.5 Heterologous expression of secondary metabolite biosynthesis gene 17
2.6 DNA microarrays 18
2.7 PCR-independent amplification techniques 19
2.8 Shift to metagenomic approach 19
2.9 Synthetic biology approaches to hetero-expression of new gene clusters 22
2.10 Conclusion 23
Acknowledgment 23
Conflict of Interest 23
References 24
3. Revolution in microbial bioprospecting via the development of omics-based technologies
Megha Bansal, Neha Tiwari, and Jai Gopal Sharma
3.1 Introduction 27
3.2 Loopholes in microbial cultivation and emergence of culture-independent methods 30
3.3 Development of “omics-based” approaches for microbial cultivation 32
3.4 Potential applications of “omics” technology in microbial bioprospecting 41
3.5 Conclusion 41
Competing Interests 42
References 43
4. Microbial assisted production of alcohols, acetone and glycerol
21.3 Bioactive antiviral compounds from seaweeds 459
21.4 Bioactive compounds from seaweeds with a beneficial role in general human health and immunity 462
21.5 Bioactive compounds from seaweeds controlling secondary infections 462
21.6 Potential role of seaweed-derived bioactive compounds as a therapeutic agent in COVID-19 disease management 463
21.7 Conclusion 464
Conflict of interest 464
Acknowledgments 465
References 465
22. Bioprospecting of extremophiles for industrial enzymes
Rehan Deshmukh and Sharmili Jagtap
22.1 Introduction 471
22.2 Extremozymes and their industrial significance 472
22.3 Extremozymes from thermophiles 474
22.4 Extremozymes from psychrophiles 476
22.5 Conclusion and future challenges 478
Competing interests 480
References 480
23. Bioenergy: An overview of bioenergy as a sustainable and renewable source of energy
Sangeeta Singh, Pradip Sarkar, and Kasturi Dutta
23.1 Introduction 483
23.2 Bioethanol 485
23.3 Biodiesel 487
23.4 Biogas and biohydrogen 490
23.5 Advance bioenergy 493
23.6 Challenges 496
23.7 Conclusion 497
Acknowledgments 497
Competing interests 497
References 498
24. Microbial diversity and bioprospecting potential of Phragmites rhizosphere microbiome through genomic approaches
Stiti Prangya Dash, Madhusmita Mohapatra, and Gurdeep Rastogi
24.1 Introduction 503
24.2 Structure and function of Phragmites
microbiome 506
24.3 P. karka rhizosphere microbiome: An unexplored niche for bioprospecting 517
24.4 Conclusions and perspectives 523
Acknowledgment 524
References 524
Index 529
Contributors
Tanmai Agasam Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Chetan Aware Department of Biotechnology, Shivaji University, Kolhapur, Maharashtra, India
Megha Bansal Department of Biotechnology, Delhi Technological University, Delhi, India
Tushar Bharadwaj Department of Life Sciences, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
M. Chamundeeswari Department of Biotechnology, St. Joseph’s College of Engineering, Chennai, India
Ram Chandra Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, India
P.S. Chandrashekharaiah Reliance Industries Ltd, Jamnagar, India
P.D. Charan Department of Environmental Science, M.G.S. University, Bikaner, India
J. Chitra Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
Pooja Dange Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Michael K. Danquah Chemical Engineering Department, University of Tennessee, Chattanooga, TN, United States
Jayashankar Das Centre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
Santanu Dasgupta Reliance Industries Ltd, Reliance Corporate Park, Mumbai, India
Stiti Prangya Dash Wetland Research and Training Centre, Chilika Development Authority, Balugaon, India
Shivani Dave MBM Engineering College, JIET, Jodhpur, India
Sushma Dave Jodhpur Institute of Engineering and Technology, Jodhpur, India
Dishant Desai Reliance Industries Ltd, Jamnagar, India
Rehan Deshmukh Department of Microbiology, School of Life-Sciences, Pondicherry University, Kalapet, Puducherry; Biomedical Engineering Laboratory, Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai; School of Biology, Faculty of Science, MIT World Peace University, Pune, India
Kasturi Dutta National Institute of Technology Rourkela, Rourkela, India
Vinay Dwivedi Reliance Industries Ltd, Jamnagar, India
Ayushman Gadnayak Centre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
B. Gopal Samy Department of Biotechnology, Roever Engineering College, Perambalur, Tamil Nadu, India
Piyush K. Gupta Department of Life Sciences, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
Rukmani Hansdah Department of Botany and Biotechnology, Ravenshaw University, Cuttack, Odisha, India
Jyoti Jadhav Department of Biotechnology; Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra, India
Contributors
Sharmili Jagtap Department of Microbiology, School of Life-Sciences, Pondicherry University, Kalapet, Puducherry, India
J. Jeba Mercy Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
Jaison Jeevanandam CQM—Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, Funchal, Portugal
J. Jeyakanthan Structural Biology and BioComputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
Abhipsa Kar Department of Biotechnology, Centre of Biotechnology, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, India
Ashraf Y.Z. Khalifa Biological Sciences Department, College of Science, King Faisal University, Hofuf, Kingdom of Saudi Arabia; Botany and Microbiology Department, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
Santosh Kodgire Reliance Industries Ltd, Jamnagar, India
Richa Kothari Department of Environmental Sciences, Central University of Jammu, Rahya Suchani, (Bagla) Samba, J&K, India
Adarsh Kumar Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, India
Saroj Kumar Department of Environmental Sciences, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, India
G. Mahendran Department of Electrical and Electronics Engineering, Kathir College of Engineering, Coimbatore, Tamil Nadu, India
N. Manikandan WASH Institute, Dindigul, Tamil Nadu, India
Gautam Kumar Meghwanshi Department of Microbiology, M.G.S. University, Bikaner, India
Jatindra Nath Mohanty Centre for Genomics and Molecular Therapeutics, IMS and SUM
Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
Padmaja Mohanty Department of Botany, Bioinformatics and Climate change, University School of Sciences, Gujarat University, Ahmedabad, India
Madhusmita Mohapatra Wetland Research and Training Centre, Chilika Development Authority, Balugaon, India
R. Nabil Department of Biotechnology, St. Joseph’s College of Engineering, Chennai, India
Ananya Nayak Centre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
Vinod Kumar Nigam Department of BioEngineering, Birla Institute of Technology Mesra, Ranchi, India
Sharadwata Pan TUM School of Life Sciences, Technical University of Munich, Freising, Germany
Soumya Pandit Department of Life Sciences, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
Dinesh Prasad Birla Institute of Technology, Mesra, Ranchi, India
Jay Kishor Prasad Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
N.K. Prasanna Kumari CSIR-NISCAIR, New Delhi, India
Praveen Purohit Department of Chemistry, Engineering College, Bikaner, India
Marzuqa Quraishi Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Richa Raghuwanshi Department of Botany, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
Shubham Raina Department of Environmental Sciences, Central University of Jammu, Rahya Suchani, (Bagla) Samba, J&K, India
S. Rajendren CSIR—Central Electrochemical Research Institute, Karaikudi, Tamil Nadu, India
Gurdeep Rastogi Wetland Research and Training Centre, Chilika Development Authority, Balugaon, India
Shruti Rawat Department of Agri Business Management, Symbiosis Institute of International Business, Symbiosis International University, Pune, Maharashtra, India
Ayush Singha Roy Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Uma Shankar Sagaram Reliance Industries Ltd, Reliance Corporate Park, Mumbai, India
Maheswata Sahoo Centre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
Swayamprabha Sahoo Centre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
Muthu Kumar Sampath Birla Institute of Technology Mesra, Ranchi, India
A. Sankaranarayanan C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat; Department of Life Sciences, Sri Sathya Sai University for Human Excellence, Kamalapur, Kalaburagi, Karnataka, India
Debanjan Sanyal Reliance Industries Ltd, Jamnagar, India
Angana Sarkar Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
Debapriya Sarkar Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
Pradip Sarkar National Institute of Technology Rourkela, Rourkela, India
T. Savitha Department of Microbiology, Tiruppur Kumaran College for Women, Tiruppur, Tamil Nadu, India
Nishit Savlab Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Nishant Saxena Reliance Industries Ltd, Jamnagar, India
Masirah Zahid Shah Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Abhishek Sharma C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat, India
Jai Gopal Sharma Department of Biotechnology, Delhi Technological University, Delhi, India
Ajay Kumar Singh Department of Environmental Microbiology, School of Earth and Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, India
Har Mohan Singh School of Energy Management, Shri Mata Vaishno Devi University, Katra, J&K, India
Sangeeta Singh National Institute of Technology Rourkela, Rourkela, India
Sunita Singh Reliance Industries Ltd, Jamnagar, India
Varsha Vasantrao Sonkamble School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
Pulkit Srivastava Birla Institute of Technology, Mesra, Ranchi, India
K. Tamilarasan Department of Chemical Engineering, SRM Institute of Science and Technology, Chennai, India
Neha Tiwari Department of Biotechnology, Delhi Technological University, Delhi, India
V.V. Tyagi School of Energy Management, Shri Mata Vaishno Devi University, Katra, J&K, India
Abhishek Vashishtha Department of Microbiology, M.G.S. University, Bikaner, India
Nilesh Shirish Wagh Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, India
Prashant Rajesh Wagh Modern College of Arts, Science, and Commerce (Autonomous), Pune, Maharashtra, India
Anjali Yadav Department of Microbiology, M.G.S. University, Bikaner, India
About the editors
Prof. Pradeep Verma completed his PhD from Sardar Patel University Gujarat, India, in 2002. In the same year he was selected as UNESCO fellow and joined Czech Academy of Sciences Prague, Czech Republic. He later moved to Charles University, Prague, to work as Post-Doctoral Fellow. In 2004 he joined as a visiting scientist at UFZ Centre for Environmental Research, Halle, Germany. He was awarded a DFG fellowship which provided him another opportunity to work as a Post-Doctoral Fellow at Gottingen University, Germany. He moved to India in 2007 where he joined Reliance Life Sciences, Mumbai, and worked extensively on biobutanol production which attributed few patents to his name. Later he was awarded with JSPS PostDoctoral Fellowship Programme and joined Laboratory of Biomass Conversion, Research Institute of Sustainable Humanosphere (RISH), Kyoto University, Japan. He is also a recipient of various prestigious awards such as Ron-Cockcroft award by Swedish society, UNESCO Fellow ASCR Prague.
Prof. Verma began his independent academic career in 2009 as a Reader and Founder Head at the Department of Microbiology at Assam University. In 2011 he moved to Department of Biotechnology at Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, and served as an Associate professor till 2013. He is currently working as Professor (former Head and Dean, School of Life Sciences) at Department of Microbiology, CURAJ. He is a member of various national and international societies/academies. He has completed two collaborated projects worth 150 million INR in the area of microbial diversity and bioenergy. Prof. Verma is a Group leader of Bioprocess and Bioenergy laboratory at Department of Microbiology, School of Life Sciences, CURAJ. His area of expertise involves Microbial Diversity, Bioremediation, Bioprocess Development, Lignocellulosic and Algal Biomass-based Biorefinery. He also holds 12 international patents in the field of microwave-assisted biomass pretreatment and biobutanol production. He has more than 60 research articles in peer reviewed international journals and contributed in several book chapters (28 published; 15 in press) in different edited books. He has also edited 3 books in international publishers such as Springer and Elsevier. He is a Guest editor to several journals such as Biomass Conversion and Biorefinery (Springer), Frontier in Nanotechnology (Frontiers), and International Journal of Environmental Research and Public Health (mdpi). He is also an editorial board member for the journal Current Nanomedicine (Bentham Sciences). He is acting as reviewer for more than 40 journals in different publication houses such as Springer, Elsevier, RSC, ACS, Nature, Frontiers, mdpi, etc.
Dr. Maulin P. Shah is an active researcher and scientific writer in his field for over 20 years. He received a BSc degree (1999) in Microbiology from Gujarat University, Godhra (Gujarat), India. He also earned his PhD degree (2005) in Environmental Microbiology from Sardar Patel University, Vallabh Vidyanagar, (Gujarat) India. He is Chief Scientist and Head of the Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India. His work focuses on the impact of industrial pollution on the microbial diversity of wastewater following cultivation dependent
and cultivation independent analysis. His major work involves isolation, screening, identification, and genetically engineering high-impact microbes for the degradation of hazardous materials. His research interests include Biological Wastewater Treatment, Environmental Microbiology, Biodegradation, Bioremediation, and Phytoremediation of Environmental Pollutants from Industrial Wastewaters. He has published more than 250 research papers in national and international journals of repute on various aspects of microbial biodegradation and bioremediation of environmental pollutants. He is the editor of more than 50 books of international repute (Elsevier, Springer, RSC, and CRC Press). He is an active editorial board member in top-rated journals. He is on the Advisory Board of CLEAN—Soil, Air, Water (Wiley); editor of Current Pollution Reports (Springer Nature), Environmental Technology and Innovation (Elsevier), Current Microbiology (Springer Nature), Journal of Biotechnology and Biotechnological Equipment (Taylor & Francis), Ecotoxicology (Microbial Ecotoxicology) (Springer Nature), and Current Microbiology (Springer Nature); and associate editor of GeoMicrobiology (Taylor & Francis) and Applied Water Science (Springer Nature).
Preface
Microbes are considered as reservoirs of different industrially important biomolecules such as enzymes, therapeutic compounds, alcohols, etc. Thus, the bioprospecting of microbes becomes very critical. As a result, several technologies have been developed for the bioprospecting of the microbes to identify its potential to produce bioactive compounds. These bioactive compounds find its application in several industries such as food processing, paper and pulp, pharmaceuticals, and essential biochemical production through greener methods. Naturally, microorganisms play a vital role in agriculture, as these microbes or microbe-based products play a key role in improving the agricultural yields by acting as biopesticides and biofertilizers, etc. The ability of the microbes in remediation of different environment pollutants has also been greatly exploited in recent past. Therefore, there is need to understand the progress made in the field of microbial bioprospecting and its anticipated application in industrial and agriculture production as well as environment protection.
Thus, the book will focus on potential of microbes for the industrial-scale production of different bioactive compounds, with special emphasis on its recovery and its application in different economically and environmentally important sectors. The content of this book is designed keeping in mind the academic and research requirements around the globe. The current book will provide the reader with basic and advance knowledge on
each technological aspect and applications of microbe-based products in various industries, environment and agricultural sectors. Conventional methods for the microbial bioprospecting are usually tedious and time consuming. This book is an attempt to highlight some of the advanced bioinformatics-based genomics and proteomics technologies that revolutionized the microbial bioprospecting. This book made an attempt to integrate information on microbial production and recovery of the several biomolecules such as alcohol, acetone, glycerol, enzymes, etc. Several chapters highlighted the microbialassisted production of chemotherapeutics and medicinal compounds in controlling serious diseases such as COVID. The book consists of chapters highlighting major research findings on application of microbial system in agriculture (biofertilizers, rhizospheres) and environmental pollution control (biosensors, biofuels, heavy metal recovery, etc.). This book encompasses highly updated information and will also provide future directions to young researchers and scientists, who are working in the field of microbial bioprospecting with targeted application in industries, agriculture, or environment. This book will find its readerships in academics as well as several environmental engineers, scientists, environmental consultants, policy makers, industry persons, and doctoral-level students who aspire to work in the area of microbial bioprospecting.
Pradeep Verma Maulin P. Shah
Acknowledgment
First of all, we convey deep sense of gratitude toward Elsevier for accepting our proposal to act as editors for the current book. The support from all the researchers and academicians who contributed to the book has made this book a reality. The contributors supported us immensely right from accepting our invitation and their quick response during the revision stage made this book possible, therefore we are thankful to all the contributors. The contributors supported us immensely right from accepting our invitation and their quick response during the revision stage made this book possible, therefore we are thankful to all the contributors. Editors are thankful to Mr. Bikash Kumar (PhD Scholar, Department of Microbiology, Central University of Rajasthan, Ajmer) for his contributions during review/editing
process and technical support during the entire stage of book development. Prof. Pradeep Verma is also thankful to Central University of Rajasthan (CURAJ), Ajmer, India, for providing infrastructural support, suitable teaching and research environment. The work experience of Prof Pradeep Verma and Dr. Maulin at academic and industrial setup provided with the necessary understanding of the current needs of students, researchers, academicians, and industrial setup. This understanding is greatly helpful during the development of the book and need to be acknowledged. We are always thankful to god and parents for their blessings. We also express our deep sense of gratitude toward our family for their support during the development of the book and in life.
Role of bioinformatics tools in microbial prospectives and its future
aCentre for Genomics and Molecular Therapeutics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
bMBM Engineering College, JIET, Jodhpur, India
cDepartment of Botany, Bioinformatics and Climate change, University School of Sciences, Gujarat University, Ahmedabad, India
dJodhpur Institute of Engineering and Technology, Jodhpur, India
1.1 Introduction
Understanding the molecular sequence, identification, and phylogenetic analysis of microorganisms is crucial in many more areas of the life sciences. When several microorganisms are found, it is necessary to understand their origin, origin and distribution. Therefore, phenotypic, epidemiological, screening and metagenomic studies of the diversity of microbes are important (Pevsner, 2015). The genomic DNA sequence data generation from various species, including microorganisms, needs bioinformatic analysis (Choudhuri, 2014). Tools of bioinformatics, including MSA, BLAST, etc., are used to analyze DNA, RNA, and protein sequences for phylogenetic affiliation (Niu et al., 2018). The main areas of comparative and phylogenetic genomics require a broad knowledge and thorough understanding of calculation methods in order to be able to process the extensive data they contain. Sequence data analysis includes (Kim, 2018):
1. Selection of molecules
2. Acquisition of molecular sequences
3. Multiple sequence alignment
4. Phylogenetic evaluation
This chapter shows how the molecular sequences from any microorganism are used for identification or detection using bioinformatics tools.
1.2 Overview of the role of bioinformatics in microbiology
Next-generation data bioinformatics (NGS) tools and techniques are increasingly being used to diagnose and monitor infectious diseases. To review the bioinformatics tools application, databases that are commonly used, and the NGS data used in clinical microbiology is somehow interesting, with an emphasis on molecular identification, genotype studies, microbiome, analysis of antibiotic resistance, and detection of unknown disease-related pathogens, in clinical trials. In addition, bioinformatics tools are widely used to identify, characterize, and type all types of pathogens (Carriço, Sabat, Friedrich, & Ramirez, 2013; Markowitz et al., 2009).
Bioinformatics is used to identify pathogens, detect virulence factors, and analyze resistance and strain types. Next-generation sequencing (NGS) decides the DNA sequence of the whole bacterial genome in one sequence (Aloy & Russell, 2004; Apweiler et al., 2000). This information gives data on resistance and virulence, just as helpful data as a prologue to outbreak investigations (Altschul, Gish, Miller, Myers, & Lipman, 1990).
The focus in bioinformatics is on the collection of accumulated DNA (genome), RNA (transcripts), and protein sequences (proteomes). These billions of molecular sequences present enormous opportunities and challenges. This is a hallmark of bioinformatics: biological problems can be solved from individual genes and proteins to cell lines and tissues (Altschul et al., 1997) (Fig. 1.1).
1.3 Prokaryotic genome sequencing
Annotating the genome is an important step in extracting useful information from the genome. The available annotations still face serious problems in spite of intensive efforts for decades to refine annotation tools and to also achieve new experimental results (Azad & Borodovsky, 2004).
Prokaryotic gene prediction usually involves evaluating the potential of a genome segment that is bounded by the nucleotide motifs that are conserved. The mostly used gene detection programs build genetic models based on the traits of sequences that are the real genes. This model is used to estimate a particular segment that will encode a gene. With this method, it is easier to remove the genes with an abnormal sequence composition (Bader, Chaudhuri, Rothberg, & Chant, 2004; Bairoch, 1992).
There is another popular method of gene localization to compare genome segments with gene sequence databases found in other organisms. If sequences are maintained across the genome (statistically significant similarity), the segments to be recorded will most likely be coding genes (this is a "similarity technique") (Bairoch, 2000; Baker & Sali, 2001).
1.3.1 Finding genome variants with the help of bioinformatics
Genotype analysis and variant detection differ between variant variants and all three designs, but all workflows share the following four characteristics.
(1) Detection: Align sequence readings with the reference genome and recognize expected areas or regions where at least one sample varies from the reference sequence (Mardis, 2008a).
(2) Filtration: Uses quality control measures to remove candidate websites that are likely to have false positives (Mardis, 2008b).
(3) Genotype: evaluation of alleles present in different locations or regions in each individual;
FIG. 1.1 Different applications of bioinformatics in the microbiology sectors.
(4) Verification: Analysis of a subset of newfound variants utilizing a free innovation that can be utilized to survey the false detection rate (FDR). Independent data sources were utilized to survey the genotype precision of the offspring (Sanger, Nicklen, & Coulson, 1977).
Variable call quality is impacted by numerous elements, including the standard mistake rate figured for successive measurements, the accuracy of metric local alignment, and individual genotype strategy. To start with, the baseline quality measurements detailed by the picture handling programming are eliminated observationally by estimating extents that don't coordinate the reference sequence (in non-dbSNP locations) as an element of revealed quality factors, understanding positions, and different properties (Voelkerding, Dames, & Durtschi, 2009). Second, the local correction of all indications in all samples is carried out simultaneously at the possible point of deviation, which allows alternative alleles to indel. This reconfiguration step significantly reduces errors, as local inconsistencies, especially with indeles, can be a major cause of errors when invoking variations (Dunne, Westblade, & Ford, 2012).
1.4 Prokaryotic genome annotation
With the development of next-generation sequencing technology, now researchers can easily obtain millions of sequence readings from the prokaryotic genomes of their choice. This sequence made it possible to extract a large part of the genome from overlapping sequences of measured values. However, the assembly is somehow difficult because of the brief sequence readings and the genome contains the segments that are internally repeated which can confuse a full reconstruction of the genome because of the reading of its constituent parts (Bhoyar et al., 2020). There are several approaches to addressing this challenge, including more complex assembly tools, genome reference sequences, and target sequences. In any case of the strategy used, many steps and programs are required and the final results must be recorded and interpreted based on certain deficiencies in data and methods (Lata et al., 2020). Annotated microbial genome sequences are sent/collected from important archival stores to public data sequences such as Genbank which reviews genomic data to ensure consistency in form and content (Tu, Shen, Wen, Zong, & Li, 2020). Secondary public resources such as RefSeq from NCBI further process microbial genome data from primary sources to obtain the most up-to-date view of the microbial genome sequence and to gradually improve the quality and completeness of the associated functional annotations through manual computation. In addition to primary and secondary public resources, microbial genome records are included in various tertiary resources such as SEED and IMG, which review additional microbial genome records that may be inaccurate and scarce (Mohanty et al., 2020).
1.5 Microbial profiling
Microorganisms are essential for the proper functioning of all the ecosystems. It is mainly because they exist in huge numbers and have a broad mass and cumulative activity. In this, we mainly focus on one of the two families of genomic methods for studying natural microbial
1.7
5 populations and communities: fingerprint technology. First of all, we bring up different techniques of fingerprinting and discuss their pros and cons. Second, we study the structure of phylogenetic trees and use various multidimensional tools to interpret the patterns of diverse microbial communities. Finally, we discuss the unsolved problems and the prospects of microbial ecology (Sharma et al., 2020).
1.6 Metagenomics and microbiome
The determination of metagenomics is to assess the composition of the organism and the metabolic potential encoded in the genetic material of the microbial community. Its main objective is to compare genetic information with specific environmental/host metadata to identify genetic biomarkers of disease, health, and environmental change/adaptation (Vezina, Rehm, & Smith, 2020). Direct culture sequencing applications have been used to study entire microbial communities in combination with increasingly efficient sequencing technologies (DeLong, 2004). For linking microbiota to serious disease and environmental changes, metagenomics and metatranscriptomic approaches are mostly used. Numerous investigations have been utilized to look at the functional and taxonomic profiles of microbiota in environments or individuals. While most metagenomic breaks down spotlight on species-level profiles, a few investigations use metagenomic strain rate examination to analyze the connection between explicit strains and certain conditions (Roumpeka, Wallace, Escalettes, Fotheringham, & Watson, 2017). Metatranscriptomic examination gives another significant perspective on gene activity by looking at levels of gene expression in the microbiota. Along these lines, a mix of metagenomic and metatranscriptomic measures assists with understanding the action or aggregation of a specific arrangement of genes as drug-resistant genes among the microbiome tests. Here we sum up existing bioinformatics tools for breaking down metagenomic information and automated meta-transcripts that analysts can use to recognize reasonable tools for their microbiome research (Pontiroli et al., 2013).
1.7 Analysis of the human microbiome with the 16s rRNA gene
Various strategies are utilized today to derive various degrees of data about the microbiome. The strategies incorporate 16S ribosomal RNA (rRNA) analysis, whole-genome sequencing (WGS; metagenome), and intact transcript analysis (meta-record). 16S rRNA analysis is one of the most well known and moderately economical techniques for profiling the generic composition of the microbiota. 16S rRNA analysis utilized moderating the 16S rRNA gene to identify microorganisms (Rahfeld et al., 2019). The WGS analysis utilizes data on all genes to decipher microbial character down to the species or strain level (Navarro-Muñoz et al., 2020). The total analysis of the tissue transcripts permits the perception of gene expression patterns and the usefulness of the microbial network. Analysis of complete metabolites gives an extensive list of chemical substances in the medium of interest and permits us to contrast microbial levels and downstream chemicals. Utilizing the 16S rRNA gene sequence to comprehend microbial taxonomy and phylogeny is one of the most well-known methodologies for a few reasons (Pishchany, 2020; Zarins-Tutt et al., 2016).
