An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists
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...
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| Format: | Article |
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MDPI AG
2020-09-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/10/9/185 |
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| author | Hamza Mbareche Nathan Dumont-Leblond Guillaume J. Bilodeau Caroline Duchaine |
| author_facet | Hamza Mbareche Nathan Dumont-Leblond Guillaume J. Bilodeau Caroline Duchaine |
| author_sort | Hamza Mbareche |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T16:28:23Z |
| format | Article |
| id | doaj.art-273507c21660405d8d329e8c20162280 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T16:28:23Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-273507c21660405d8d329e8c201622802023-11-20T13:01:12ZengMDPI AGLife2075-17292020-09-0110918510.3390/life10090185An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for MicrobiologistsHamza Mbareche0Nathan Dumont-Leblond1Guillaume J. Bilodeau2Caroline Duchaine3Sunnybrook Research Institute, Toronto, ON M4N 3M5, CanadaCentre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, CanadaPathogen Identification Research Lab, Canadian Food Inspection Agency (CFIA), Ottawa, ON K2J 1G3, CanadaCentre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, CanadaHigh-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.https://www.mdpi.com/2075-1729/10/9/185bioaerosolsbioinformaticsmicrobial ecology |
| spellingShingle | Hamza Mbareche Nathan Dumont-Leblond Guillaume J. Bilodeau Caroline Duchaine An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists Life bioaerosols bioinformatics microbial ecology |
| title | An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists |
| title_full | An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists |
| title_fullStr | An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists |
| title_full_unstemmed | An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists |
| title_short | An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists |
| title_sort | overview of bioinformatics tools for dna meta barcoding analysis of microbial communities of bioaerosols digest for microbiologists |
| topic | bioaerosols bioinformatics microbial ecology |
| url | https://www.mdpi.com/2075-1729/10/9/185 |
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