Abstract
High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.
Highlights
The development of next-generation sequencing (NGS) platforms for DNA samples has grown exponentially in recent years [1,2,3]
The analysis of microbial diversity is becoming a crucial component in several fields of scientific research, and bioaerosols is no exception
Many of the bioinformatics tools used to study microbial diversity were developed for researchers comfortable with a command line environment
Summary
The development of next-generation sequencing (NGS) platforms for DNA samples has grown exponentially in recent years [1,2,3]. Vincent and Charette tried to answer the question “Who qualifies as a bioinformatician?” by suggesting that the status should be reserved for experts who develop bioinformatics algorithms and tools (software) and for those who design architectural models to maintain databases [37] This definition did not elicit unanimity amongst the scientists who do not develop algorithms, but who use bioinformatics tools on a daily basis to analyze data, generate results and solve problems [38]. While this distinction is important as it allows universities, human resources and governments to accurately recognize and certify students, employees and others as bioinformatics experts, it is important to remember that using computers to understand biological concepts is as important and necessary as using any other laboratory tool/equipment. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field
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