Pub Date : 2020-03-25DOI: 10.5772/intechopen.87949
W. Hozzein
Metagenomics can be defined as the techniques and procedures that are used for the culture-independent analysis of the total genomic content of microorganisms living in a certain environment [1]. It has many useful applications with very promising potential in both medical and environmental microbiology. The most common use of metagenomics in environmental microbiology is studying the diversity of microbial communities in particular environments through the analysis of rRNA genes and how these communities change in response to changes in physical and chemical properties of these environments [2]. Metagenomics also provides an opportunity to obtain and identify novel enzymes with industrial applications from extreme environments where unculturable extremophiles live. In such circumstances, functional metagenomics enables the isolation of genes coding for extremozymes, enzymes that are capable of being catalytically active in extreme conditions, or genes that will allow for better understanding of the mechanisms that make such organisms resistant to extreme environmental conditions [3]. Metagenomics has special importance when it comes to studying soil microbiology. It is estimated that the number of distinct microorganisms in 1 gram of soil exceeds the number of microbial species cultured so far [4]. Therefore, metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soil microorganisms and to study how this biodiversity is affected with continuously changing conditions.
{"title":"Introductory Chapter: Metagenomics and Metagenomic Approaches","authors":"W. Hozzein","doi":"10.5772/intechopen.87949","DOIUrl":"https://doi.org/10.5772/intechopen.87949","url":null,"abstract":"Metagenomics can be defined as the techniques and procedures that are used for the culture-independent analysis of the total genomic content of microorganisms living in a certain environment [1]. It has many useful applications with very promising potential in both medical and environmental microbiology. The most common use of metagenomics in environmental microbiology is studying the diversity of microbial communities in particular environments through the analysis of rRNA genes and how these communities change in response to changes in physical and chemical properties of these environments [2]. Metagenomics also provides an opportunity to obtain and identify novel enzymes with industrial applications from extreme environments where unculturable extremophiles live. In such circumstances, functional metagenomics enables the isolation of genes coding for extremozymes, enzymes that are capable of being catalytically active in extreme conditions, or genes that will allow for better understanding of the mechanisms that make such organisms resistant to extreme environmental conditions [3]. Metagenomics has special importance when it comes to studying soil microbiology. It is estimated that the number of distinct microorganisms in 1 gram of soil exceeds the number of microbial species cultured so far [4]. Therefore, metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soil microorganisms and to study how this biodiversity is affected with continuously changing conditions.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134019602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-02-26DOI: 10.5772/intechopen.86559
R. E. Valle-Gough, B. Y. Samaniego-Gámez, Javier Eduardo Apodaca-Hernández, M. L. Arena-Ortíz
Through millions of years, the multicellular organisms have coexisted and coevolved with the surrounding microorganisms, in an almost symbiotic relationship forming a complex entity known as holobiont. The composition and functions of these microbial communities were limited during many years to only a mere fraction, due to the use of culture-based techniques. The advent of molecular-based techniques allowed the identification of uncultured organisms in a culture-free manner. In recent years, the development of next generation sequencing techniques have allowed the high-throughput study of microbial communities allowing the identification and classification of otherwise uncultured microorganisms in a given environment, tissue or host through metagenomics. The next generation sequencing techniques have been used in the functional study of microbial assemblages and were able to identify the role of the microorganisms in biogeochemical cycles, pathogenic processes, metabolism and development, through metatranscriptomics. Taken together, the next generation sequencing based-studies have shown the existence of a complex metabolic network in different hosts and environments, with the microbial communities. This chapter will focus in different available bioinformatic tools that are suitable to study symbiosis and coevolution processes in a given sample.
{"title":"The Use of Bioinformatic Tools in Symbiosis and Co-Evolution Studies","authors":"R. E. Valle-Gough, B. Y. Samaniego-Gámez, Javier Eduardo Apodaca-Hernández, M. L. Arena-Ortíz","doi":"10.5772/intechopen.86559","DOIUrl":"https://doi.org/10.5772/intechopen.86559","url":null,"abstract":"Through millions of years, the multicellular organisms have coexisted and coevolved with the surrounding microorganisms, in an almost symbiotic relationship forming a complex entity known as holobiont. The composition and functions of these microbial communities were limited during many years to only a mere fraction, due to the use of culture-based techniques. The advent of molecular-based techniques allowed the identification of uncultured organisms in a culture-free manner. In recent years, the development of next generation sequencing techniques have allowed the high-throughput study of microbial communities allowing the identification and classification of otherwise uncultured microorganisms in a given environment, tissue or host through metagenomics. The next generation sequencing techniques have been used in the functional study of microbial assemblages and were able to identify the role of the microorganisms in biogeochemical cycles, pathogenic processes, metabolism and development, through metatranscriptomics. Taken together, the next generation sequencing based-studies have shown the existence of a complex metabolic network in different hosts and environments, with the microbial communities. This chapter will focus in different available bioinformatic tools that are suitable to study symbiosis and coevolution processes in a given sample.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"97 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125132939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-11DOI: 10.5772/intechopen.88958
Shrinivas N. Sabale, Padmaja P. Suryawanshi, Krishnaraj P.U.
Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein.
{"title":"Soil Metagenomics: Concepts and Applications","authors":"Shrinivas N. Sabale, Padmaja P. Suryawanshi, Krishnaraj P.U.","doi":"10.5772/intechopen.88958","DOIUrl":"https://doi.org/10.5772/intechopen.88958","url":null,"abstract":"Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125164025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-11DOI: 10.5772/intechopen.89944
Ahmed M. Shuikan, S. Alharbi, D. H. Alkhalifah, W. Hozzein
Metagenomic approaches are a growing branch of science and have many applications in different fields. Metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soils and to study how this biodiversity is affected with continuously changing conditions. In addition, its application in clinical and diagnostic approaches was reported. The emergence of several next-generation sequencing (NGS) strategies enriched the metagenomics. The combination between NGS and metagenomic approaches helped the investigators resolve several issues regarding the microbial diversity and the functions and relationships among different microbial flora. A number of NGS approaches were developed including Roche/454 pyrosequencing, Illumina/Solexa sequencing, and Applied Biosystems/SOLiD sequencing. In this chapter, different NGS platforms are discussed in terms of principle, advantages, and limitations. In addition, third-generation sequencing technologies are also addressed.
{"title":"High-Throughput Sequencing and Metagenomic Data Analysis","authors":"Ahmed M. Shuikan, S. Alharbi, D. H. Alkhalifah, W. Hozzein","doi":"10.5772/intechopen.89944","DOIUrl":"https://doi.org/10.5772/intechopen.89944","url":null,"abstract":"Metagenomic approaches are a growing branch of science and have many applications in different fields. Metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soils and to study how this biodiversity is affected with continuously changing conditions. In addition, its application in clinical and diagnostic approaches was reported. The emergence of several next-generation sequencing (NGS) strategies enriched the metagenomics. The combination between NGS and metagenomic approaches helped the investigators resolve several issues regarding the microbial diversity and the functions and relationships among different microbial flora. A number of NGS approaches were developed including Roche/454 pyrosequencing, Illumina/Solexa sequencing, and Applied Biosystems/SOLiD sequencing. In this chapter, different NGS platforms are discussed in terms of principle, advantages, and limitations. In addition, third-generation sequencing technologies are also addressed.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130893715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-10-09DOI: 10.5772/intechopen.89492
A. Sánchez-Reyes, J. Folch-Mallol
Phylogenetic relationships among microbial taxa in natural environments provide key insights into the mechanisms that shape community structure and functions. In this chapter, we address the current methodologies to carry out community structure profiling, using single-copy markers and the small subunit of the rRNA gene to measure phylogenetic diversity from next-generation sequencing data. Furthermore, the huge amount of data from metagenomics studies across the world has allowed us to assemble thousands of draft genomes, making necessary the comparison of whole genomes composites through phylogenomic approximations. Several computational tools are available to carry out these analyses with considerable success; we present a compendium of those open source tools, easy to use and with modest hardware requirements, with the aim that they can be applied by biologists non-specialists to study microbial diversity in a phylogenetic context.
{"title":"Metagenomics-Based Phylogeny and Phylogenomic","authors":"A. Sánchez-Reyes, J. Folch-Mallol","doi":"10.5772/intechopen.89492","DOIUrl":"https://doi.org/10.5772/intechopen.89492","url":null,"abstract":"Phylogenetic relationships among microbial taxa in natural environments provide key insights into the mechanisms that shape community structure and functions. In this chapter, we address the current methodologies to carry out community structure profiling, using single-copy markers and the small subunit of the rRNA gene to measure phylogenetic diversity from next-generation sequencing data. Furthermore, the huge amount of data from metagenomics studies across the world has allowed us to assemble thousands of draft genomes, making necessary the comparison of whole genomes composites through phylogenomic approximations. Several computational tools are available to carry out these analyses with considerable success; we present a compendium of those open source tools, easy to use and with modest hardware requirements, with the aim that they can be applied by biologists non-specialists to study microbial diversity in a phylogenetic context.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114552959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-06-05DOI: 10.5772/INTECHOPEN.86302
M. Tello, N. Valdés, R. Vargas, J. Rojas, M. Parra, G. Gajardo, Alex R. Gonzalez
Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish)microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.
{"title":"Application of Metagenomics to Chilean Aquaculture","authors":"M. Tello, N. Valdés, R. Vargas, J. Rojas, M. Parra, G. Gajardo, Alex R. Gonzalez","doi":"10.5772/INTECHOPEN.86302","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.86302","url":null,"abstract":"Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish)microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128313530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-03-20DOI: 10.5772/INTECHOPEN.84945
E. García-López, A. Moreno, C. Cid
Polar glaciers are inhabited by numerous microorganisms including representa-tives of bacteria, archaea, microeukaryotes, and viruses. Low temperature is a main factor when considering polar glaciers as extreme environments. However, desiccation, low nutrients availability, ultraviolet irradiation, and photoreactive chemistry do also significantly influence their challenging life. Glaciers are highly selective and confined habitats, which make them favorable environments for adaptation and speciation. Depending on the glacier area studied, microorganisms establish a vertical food chain, from the surface photosynthesizers in upper illuminated layers to chemoautotrophs and heterotrophs confined to the inner part. These regions are rich not only in biodiversity but also in new mechanisms of adaptation to the environment, since selection acts with a particular intensity. Glaciers are retreating in many areas of the world due to global warming. When glaciers have ultimately withdrawn, microorganisms play a main role, carrying out key processes in the development of soil and facilitating plant colonization. These features make them unique and interesting for the study and protection of the biological heritage. Metagenomics have allowed a deeper understanding of microbial ecology and function of polar glacier microbial communities. In this review, we present a complete analysis of the microbial diversity in these ecosystems and include a thorough overview of the metabolic potentials and biogeochemical cycles in polar glacier habitats.
{"title":"Microbial Community Structure and Metabolic Networks in Polar Glaciers","authors":"E. García-López, A. Moreno, C. Cid","doi":"10.5772/INTECHOPEN.84945","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.84945","url":null,"abstract":"Polar glaciers are inhabited by numerous microorganisms including representa-tives of bacteria, archaea, microeukaryotes, and viruses. Low temperature is a main factor when considering polar glaciers as extreme environments. However, desiccation, low nutrients availability, ultraviolet irradiation, and photoreactive chemistry do also significantly influence their challenging life. Glaciers are highly selective and confined habitats, which make them favorable environments for adaptation and speciation. Depending on the glacier area studied, microorganisms establish a vertical food chain, from the surface photosynthesizers in upper illuminated layers to chemoautotrophs and heterotrophs confined to the inner part. These regions are rich not only in biodiversity but also in new mechanisms of adaptation to the environment, since selection acts with a particular intensity. Glaciers are retreating in many areas of the world due to global warming. When glaciers have ultimately withdrawn, microorganisms play a main role, carrying out key processes in the development of soil and facilitating plant colonization. These features make them unique and interesting for the study and protection of the biological heritage. Metagenomics have allowed a deeper understanding of microbial ecology and function of polar glacier microbial communities. In this review, we present a complete analysis of the microbial diversity in these ecosystems and include a thorough overview of the metabolic potentials and biogeochemical cycles in polar glacier habitats.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"148 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132501177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-28DOI: 10.5772/INTECHOPEN.82707
T. Kenzaka
Understanding the dissemination of medically important microbiota is a significant public health necessity. Although modern bacteriology has advanced with improved culturing technology, several environmental bacteria occur in the “viable but nonculturable” state. By using next-generation sequencing (NGS) to comprehensively analyze the intestinal microbiota of migratory birds, research on microbial communities traveling over long distances has entered a new era and provides new insights that are valuable for the analysis of medical care, livestock industry, agriculture, and human health risks. The use of comprehensive analysis by NGS of not only intestinal microbiota but also diet biological communities may help elucidate the relationship between microbiological communities and the diet and succession of intestinal microbiota, including antibiotic-resistant bacteria, during migration and breeding. Here, we have described the current state and the future implications of studying intestinal microbiota associated with migratory birds.
{"title":"Dissemination of Intestinal Microbiota by Migratory Birds across Geographical Borders","authors":"T. Kenzaka","doi":"10.5772/INTECHOPEN.82707","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.82707","url":null,"abstract":"Understanding the dissemination of medically important microbiota is a significant public health necessity. Although modern bacteriology has advanced with improved culturing technology, several environmental bacteria occur in the “viable but nonculturable” state. By using next-generation sequencing (NGS) to comprehensively analyze the intestinal microbiota of migratory birds, research on microbial communities traveling over long distances has entered a new era and provides new insights that are valuable for the analysis of medical care, livestock industry, agriculture, and human health risks. The use of comprehensive analysis by NGS of not only intestinal microbiota but also diet biological communities may help elucidate the relationship between microbiological communities and the diet and succession of intestinal microbiota, including antibiotic-resistant bacteria, during migration and breeding. Here, we have described the current state and the future implications of studying intestinal microbiota associated with migratory birds.","PeriodicalId":286811,"journal":{"name":"Metagenomics - Basics, Methods and Applications","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114965132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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