Understanding Microbiome Science Through Big Data Analysis
The emerging disciplines of microbiome research and data science have offered countless promising innovations in human genetics. Alongside clinical information, the microbiome may be considered another dimension of patient clinical status. Over the past 1
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Understanding Microbiome Science Through Big Data Analysis Aditya Narayan, Ajeet Singh, and Shailesh Kumar
Abstract
The emerging disciplines of microbiome research and data science have offered countless promising innovations in human genetics. Alongside clinical information, the microbiome may be considered another dimension of patient clinical status. Over the past 15 years, the microbiome has become increasingly recognized as a moderator of interactions between both the external environment and our body, as well as between body systems themselves. These insights have led to an explosion in sequencing data, the key source of information upon which much of this research rests. To match this growing supply of information, there has been a corresponding increase in the number of tools that allow even nonprofessional individual access to data science methods. Such tools streamline the sequencing analysis process to make critical observations readily accessible. This chapter first aims to describe the historical significance of microbiome data science and the methods used to generate sequencing data. Following this, we offer a comprehensive guide to several commonly applied tools in microbiome data science. Keywords
Microbiome · Data science · High throughput sequencing
A. Narayan University of Virginia, Charlottesville, VA, USA e-mail: [email protected] A. Singh · S. Kumar (*) National Institute of Plant Genome Research (NIPGR), New Delhi, India e-mail: [email protected] # Springer Nature Singapore Pte Ltd. 2020 S. Singh (ed.), Metagenomic Systems Biology, https://doi.org/10.1007/978-981-15-8562-3_3
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3.1
Introduction
3.1.1
The Origin of the Term “Microbiome”
We as scientists are currently operating in a microbiome revolution. It is an era in which many of the most novel insights generated through research are associated with understanding the increasingly recognized “second genome” existing within our body - one that is acquired, rather than inherited. The term “microbiota” itself is largely attributed to Joshua Lederberg, microbiologist and Nobel Prize laureate who explained it to signify the community of symbiotic, commensal, and pathogenic organisms which shared our body and were understudied determinants of health. While the microbiota is the community of microorganisms itself, the microbiome may then be considered the entirety of genetic elements contained in the microbiota. The term “microbiota” even predates Lederberg, however, and was defined previously by Alan Logan in 1998. The biological link between microbiota and brain chemistry was demonstrated as early as 1986, with Linda Hegstrand and Roberta Hine exploring histamine levels in exposed vs germ-free animals (Prescott 2017). It is therefore evident that the research community has been familiar with the existence of this critical field of study for many years, though recent technological advances have fueled rapid advancements. In this chapter, we will discuss what insights we can glean about human health from the micro
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