Ten simple rules for investigating (meta)genomic data from environmental ecosystems

Le résumé fourni par la source

Metagenomics is the sequencing and study of DNA directly from environmental samples and is an approach used in microbial ecology to explore the diversity and functions of microbial communities [1].The study of the metagenome presents an avenue to investigate environmental microorganisms in-situ through culture-independent techniques, which facilitates the discovery and analysis of the metabolic potential of hitherto uncultured taxa [2].Expanding our reach into the once obscure facets of microbial life has yielded further insights into the ecological activity of microorganisms, uncovering a trove of novel metabolic products and pathways with a wide range of biotechnical applications in many industries [3,4].Data obtained from metagenomes have also been pivotal in directing strategies for the cultivation of novel microorganisms [5].The benefit of metagenomics is that it forms a wide-reaching preliminary approach that can provide contextual information to direct further downstream research for microorganisms in the wet lab.Microbial ecology has developed to a stage where "big data" is often the norm.Through advances in sequencing and computational technologies, we have experienced an unprecedented level of progress in the field of microbial ecology, improving our understanding of the many global ecosystems [6].Metagenomics draws many parallels when compared to data science-environmental sequence data presents a large volume of information that must be sifted through and sorted to make sense of underlying ecological and taxonomic patterns [7].The amount of information that needs to be processed, however, can be daunting for those starting out and often still pose challenges even for those familiar to the field.The inspiration behind this writing is from a recommendation to a PLOS Ten Simple Rules article on command-line bioinformatics [8].The article provided a lot of information on tools and concepts used by bioinformaticians and it would have been a valuable source of guidance for many.This paper styled in the typical format of a Ten Simple Rules article, presents a guide on the basics of metagenomic-based research aimed at environmental settings.We will explore the concepts, tools, and resources utilized in metagenomics and how these can potentially help the progress of a researcher beginning their studies (Fig 1).The 10 simple rules format is a casual one and people are often busy, so at the end of each rule is a TL; DR (too long; didn't read) that summarizes the point we are trying to make if you want to skim through (although we do hope you'll stick around and read the paper in depth!).

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