Metagenomics for Microbiology

Jacques Izard, Maria Rivera

• Publisher: Academic Press
• Year: 2014
• Print ISBN: 9780124104723
• eBook ISBN: 9780124105089
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications.With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future.- Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies- Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose- Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Chapter 1

Steps in Metagenomics: Let’s Avoid Garbage in and Garbage Out

Jacques Izard

Abstract

New technological advances come with their limitations, biases, and drastic improvements on how we can observe life. Metagenomics is no different. This overview focuses on some of the elements that need to be taken into account prior to planning a sequencing experiment. From students and traditional researchers to those involved in citizen science, there are a few things to keep in mind.

Keywords

Metagenomics

metatranscriptomics

whole shotgun sequencing

WGS

DNA-Seq

16S rRNA gene

RNA-Seq

Why metagenomics?

Is metagenomics a revolution or a new fad? Metagenomics is tightly associated with the availability of next-generation sequencing in all its implementations. The key feature of these new technologies, moving beyond the Sanger-based DNA sequencing approach, is the depth of nucleotide sequencing per sample.¹ Knowing much more about a sample changes the traditional paradigms of “What is the most abundant?” or “What is the most significant?” to “What is present and potentially significant that might influence the situation and outcome?”

Let’s take the case of identifying proper biomarkers of disease state in the context of chronic disease prevention. Prevention has been deemed as a viable option to avert human chronic diseases and to curb healthcare management costs.² The actual implementation of any effective preventive measures has proven to be rather difficult. In addition to the typically poor compliance of the general public, the vagueness of the successful validation of habit modification on the long-term risk, points to the need of defining new biomarkers of disease state.

Scientists and the public are accepting the fact that humans are super-organisms, harboring both a human genome and a microbial genome, the latter being much bigger in size and diversity, and key for the health of individuals.^3,4 It is time to investigate the intricate relationship between humans and their associated microbiota and how this relationship modulates or affects both partners.⁵ These remarks can be expanded to the animal and plant kingdoms, and holistically to the Earth’s biome. By its nature, the evolution and function of all the Earth’s biomes are influenced by a myriad of interactions between and among microbes (planktonic, in biofilms or host associated) and the surrounding physical environment.

The general definition of metagenomics is the cultivation-independent analysis of the genetic information of the collective genomes of the microbes within a given environment based on its sampling. It focuses on the collection of genetic information through sequencing that can target DNA, RNA, or both. The subsequent analyses can be solely focused on sequence conservation, phylogenetic, phylogenomic, function, or genetic diversity representation including yet-to-be annotate...

Table of contents

• Cover
• Title page
• Table of Contents
• Copyright
• List of Contributors
• Preface
• Chapter 1: Steps in Metagenomics: Let’s Avoid Garbage in and Garbage Out
• Chapter 2: Long-Read, Single Molecule, Real-Time (SMRT) DNA Sequencing for Metagenomic Applications
• Chapter 3: Ribosomal RNA Removal Methods for Microbial Transcriptomics
• Chapter 4: High-Throughput Sequencing as a Tool for Exploring the Human Microbiome
• Chapter 5: Computational Tools for Taxonomic Microbiome Profiling of Shotgun Metagenomes
• Chapter 6: Hypothesis Testing of Metagenomic Data
• Chapter 7: Longitudinal Microbiome Data Analysis
• Chapter 8: Metagenomics for Bacteriology
• Chapter 9: Toward the Understanding of the Human Virome
• Chapter 10: Promises and Prospects of Microbiome Studies
• Glossary
• Index