Using Metagenomics to Connect Microbial Community Biodiversity and Functions

Abstract

Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India

“…The present research was designed to identify bioremediation bacteria and fungi species of commercial importance and their relations with different riverine ecosystems using high-throughput sequencing and computational metagenomics. The sensitive taxonomical classification was used for the identification of microbial community biodiversity and their functions ( Mendes et al, 2017 ). A large number of bioremediation bacteria and fungal species (Bacteria: 45 genera and 92 species; fungi: 13 genera and 24 species) ( Supplementary Tables S1 , S2 ) were found including pesticide degrading domains in the Ganga and Yamuna river sediments.…”

Dynamics of archaeal community in soil with application of composted tannery sludge

“…The knowledge about the factors driving the composition of microbial community in soil after application of waste is important to predict the potential effects on soil functioning since soil microorganisms play important roles in soil ecosystem 7 . Archaea community plays some fundamental ecological functions in the soil, including oxidation or reduction of metals and alteration of chemical conditions in the environment 8 .…”

Conserve the germs: the gut microbiota and adaptive potential

“…Even more recently, NGS technology has allowed the characterization of whole communities of microorganisms from various sample types using taxa-specific markers ('metataxonomics'; Marchesi and Ravel 2015), with rapid parallel development of appropriate field collection methods (Hale et al 2016;Song et al 2016) and bioinformatic analyses (e.g. Callahan et al 2017;Jiménez and Sommer 2017;Mendes et al 2017).…”