The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

By Alejandra Escobar-Zepeda, Arturo Vera-Ponce de León, A. Sánchez-Flores. Frontiers in Genetics, 2015

304 citations recorded by the source corpus.

The study of microorganisms that pervade each and every part of this planet has encountered many challenges through time such as the discovery of unknown organisms and the understanding of how they interact with their environment. The aim of this review is to take the reader along the timeline and major milestones that led us to modern metagenomics. This new and thriving area is likely to be an important contributor to solve different problems. The transition from classical microbiology to modern metagenomics studies has required the development of new branches of knowledge and specialization. Here, we will review how the availability of high-throughput sequencing technologies has transformed microbiology and bioinformatics and how to tackle the inherent computational challenges that arise from the DNA sequencing revolution. New computational methods are constantly developed to collect, process, and extract useful biological information from a variety of samples and complex datasets, but metagenomics needs the integration of several of these computational methods. Despite the level of specialization needed in bioinformatics, it is important that life-scientists have a good understanding of it for a correct experimental design, which allows them to reveal the information in a metagenome.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cca5e74bf5303d9504e78bc58d61d9fe653d160d

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Citations in the corpus

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, background): “As the field of WMG expands, comprehensive and accessible software for unified analysis of metagenomic data is needed [7, 11].”
Current knowledge of interactions between Drosophila suzukii and microbes, and their potential utility for pest management (2016, methodology): “Indeed, the whole meta-genome shotgun sequencing technique has been validated and bioinformatic procedures have been developed to answer taxonomic and metabolic profiling questions (Segata et al. 2013; Escobar-Zepeda et al. 2015).”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, methodology): “, 2016) and should be used in conjunction with standard quality control pipelines for sequence quality, including chimeric removal (Smyth et al., 2010; Teeling and Glöckner, 2012; Zhou et al., 2014; Escobar-Zepeda et al., 2015; Jeon et al., 2015).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “Specifically, we summarise methods associated with the analysis of short DNA fragments, or ‘amplicons’, amplified for taxonomic purposes, which is often referred to as ‘metabarcoding’ (Escobar-Zepeda et al. 2015) and is distinct from metagenomics approaches.”