Chapter 5 Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Vartul Sangal , Leena Nieminen , Nicholas P. Tucker , Paul A. Hoskisson Next-generation sequencing has revolutionized modern research in all life sciences. It has been applied in studying evolution, global transmission and local adaptation of pathogens, microbial ecology, genetics and physiology. In this chapter, we have provided a brief summary of recent advances in sequencing technologies and easy to use bioinformatic tools to analyse sequence data, with a focus on prokaryotic biology. We have emphasized the importance of routinely applyi...
Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research
Chapter 4 16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Mincheol Kim , Jongsik Chun 16S ribosomal RNA sequences have been used extensively in the classification and identification of Bacteria and Archaea. The comparison of almost complete 16S rRNA gene sequences has been widely used to establish taxonomic relationships between prokaryotic strains, with 98.65% similarity currently recognized as the cutoff for delineating species. The comparison of the 16S rRNA gene sequence of an isolate against sequences of type strains of all prokaryotic species provides an accurate and convenient way to routinel...
Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research
Chapter 3 The All-Species Living Tree Project
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Pablo Yarza , Raul Munoz The All-Species Living Tree Project (LTP) is an international initiative for the creation and maintenance of highly curated 16S rRNA and 23S rRNA gene sequence databases, alignments and phylogenetic trees for all the type strains of Archaea and Bacteria. These small but taxonomically representative SSU and LSU datasets may be used as a reference for classification and identification purposes in several fields of application. The complete package tool, including the full database, alignment, metadata and tree, is freel...
Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research
Chapter 2 An Introduction to Phylogenetics and the Tree of Life
We present an introduction to experimental design and hypothesis testing in phylogenetics, guiding the reader through the series of steps that are generally involved in making phylogenetic trees. These include choosing a phylogenetic question, selecting the appropriate sequences to analyse, aligning sequences and assessing the quality of sequence alignments, choosing the appropriate phylogenetic methods and interpreting the results. We provide a brief introduction to the freely available, open source software and Web services that can be used to perform these tasks and discuss the difficulties most frequently encountered w...
Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research
Chapter 1 The Need for Change Embracing the Genome
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): William B. Whitman With the development of Next-Generation Sequencing techniques, genomic sequencing of prokaryotes has become inexpensive enough to become a routine tool in the research laboratory. For systematics, genome sequences will provide valuable insights into the phylogeny of prokaryotes and a wealth of information about their genealogy. By providing more reliable and complete data, it will allow the formation of more accurate groupings of taxa. As important, it will provide new understandings of the evolutionary processes within prok...
Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research
16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): Mincheol Kim , Jongsik Chun 16S ribosomal RNA sequences have been used extensively in the classification and identification of Bacteria and Archaea. The comparison of almost complete 16S rRNA gene sequences has been widely used to establish taxonomic relationships between prokaryotic strains, with 98.65% similarity currently recognized as the cutoff for delineating species. The comparison of the 16S rRNA gene sequence of an isolate against sequences of type strains of all prokaryotic species provides an accurate and convenie...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
The Need for Change: Embracing the Genome
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): William B. Whitman With the development of Next-Generation Sequencing techniques, genomic sequencing of prokaryotes has become inexpensive enough to become a routine tool in the research laboratory. For systematics, genome sequences will provide valuable insights into the phylogeny of prokaryotes and a wealth of information about their genealogy. By providing more reliable and complete data, it will allow the formation of more accurate groupings of taxa. As important, it will provide new understandings of the evolutionary pro...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): Volker Gürtler , Gangavarapu Subrahmanyam , Malathi Shakar , Biswajit Maiti , Indrani Karunasagar The rrn operon is the basic building block of all bacteria found in 1–15 copies per bacterial genome in all bacteria. All bacterial genomes contain rrn operons that contain four basic components: (i) 16S rRNA gene; (ii) 16S–23S intergenic transcribed spacer (ITS); (iii) 23S rRNA gene; (iv) 5S rRNA gene. The chapter “Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer ...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): Olga K. Kamneva , Naomi L. Ward Bacterial genome content varies greatly, even between closely related species, due to processes such as gene duplication, loss, and horizontal gene transfer (HGT). New genes derived from duplication or HGT give rise to new molecular functions within microbial genomes. Therefore, an in-depth understanding of gene family evolution is fundamental to bacterial genome annotation and gene function prediction. The genomic content of ancestral bacterial species is also of interest. This unit provides ...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
Whole-Genome Analyses: Average Nucleotide Identity
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): David R. Arahal Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA–DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and approaches that can be derived from comparative genomic data and used for taxonomic purposes. Here, an overview about the impact and current usage of ANI values is giv...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways
Publication date: Available online 13 November 2014 Source:Methods in Microbiology Author(s): Simon R. Harris , Chinyere K. Okoro The advent of DNA sequencing technologies with the capability to sequence the entire genomes of large numbers of bacteria in clinically relevant timescales has opened up the opportunity of using whole-genome sequencing as an epidemiological tool. With costs of sequencing also reducing, we are on the verge of a genomic epidemiology revolution that will provide a method that is both more widely applicable and more detailed than any other current bacterial typing technique. However, the wealt...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level
Publication date: Available online 15 November 2014 Source:Methods in Microbiology Author(s): Xiaoying Rong , Ying Huang Multi-locus sequence analysis (MLSA) is now established as a powerful phylogenetic approach for defining the taxonomic structure and evolutionary history of diverse bacteria, and for exploring population parameters that shape speciation. In this chapter, the emphasis is on practical procedures, notably MLSA schemes designed to clarify relationships within specific genera. MLSA uses data retrieved from fragmented nucleotide sequences of housekeeping genes (normally five to seven) spread across the c...
Source: Methods in Microbiology - November 15, 2014 Category: Microbiology Source Type: research
12 Characterization of Pigments of Prokaryotes and Their Use in Taxonomy and Classification
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Aharon Oren A great diversity of pigments is produced by different groups of prokaroytes. Some pigments serve to convert light energy into biologically available energy: chlorophyll a for oxygenic photosynthesis in cyanobacteria, bacteriochlorophylls in anoxygenic phototrophs, retinal pigments such as bacteriorhodopsin and xanthorhodopsin. Phototrophic prokaryotes generally also contain accessory pigments involved in light harvesting: the phycobiliproteins of the cyanobacteria, carotenoid pigments in all oxygenic and anoxygenic phototrophs. Ca...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
11 Polyamines
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Hans-Jürgen Busse Polyamines are essential components of almost all bacterial cells. Their ubiquitous distribution and the variability of polyamine patterns make them an excellent tool to supplement the set of chemotaxonomic approaches for classification of bacteria because usually they reflect phylogenetic relationships quite well. The suitability of the polyamine approach has been demonstrated for several major lines of descent. Within the classes Alphaproteobacteria and Gammaproteobacteria, numerous families and even some closely related g...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
10 Detection and Characterization of Mycolic Acids and Their Use in Taxonomy and Classification
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Atteyet-Alla Fetouh Yassin Mycolic acids are high molecular weight α-alkyl-branched β-hydroxy fatty acids found in the cell wall lipids of acid-fast bacteria. Mycobacterial mycolic acids are among the longest chain (contain between 60 and 90 carbon atoms) and usually occur as complex mixtures of structurally related molecules having oxygen functions such as carboxy, epoxy, keto or methoxy groups in addition to the 3-hydroxy unit and combinations of cis or trans double bonds or cyclopropane rings, methyl branches also being encountered. Mycol...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
