دانلود رایگان مقاله انگلیسی ژنوم های میکروارگانیسم های غیر کشت شده - الزویر 2019

Future Outlook

The tremendous increase in genomes from uncultivated microorganisms (Fig. 1), including from candidate phyla with no cultivated representatives, provides an exciting foundation for the functional interrogation of this microbial dark matter. The down side of the data deluge, however, is the increasing gap in our ability to assign function to many of the newly discovered genes, proteins, and pathways (Fig. 4). Steps to fill the function gap are most commonly achieved by moving from sequence to function via designing experiments to validate sequence-based predictions of function; these experiments rely on technologies such as DNA synthesis and protein expression followed by a functional assay. An alternate approach is “function-driven” (meta)genomics. Here moving from function to sequence, prior to sequencing, cells or DNA from organisms are selected and enriched based on a particular phenotype. Function-driven single-cell genomics (Doud and Woyke, 2017) may target cells of general metabolic activity or highly specific activities, as demonstrated in a recent study by M. Martinez-Garcia and colleagues, where populations degrading the substrate laminarin were captured and genome sequenced following the addition of a fluorescently labeled form of laminarin. Analogous to these approaches is the application of stable isotope probing (SIP) to link microbial activity (function) to taxonomic identity within an environmental sample. This function-driven metagenomic approach relies on the incorporation of heavy isotopes (for example, 13C) into microbial DNA during growth on labeled substrates. Early successes of the technology include the identification of dimethyl sulphide (DMS) functional capacity within previously unknown bacterial groups by O. Eyice and colleagues, and most recently, the application of DNA-SIP for genome-resolved metagenomics by R. M. Ziels and colleagues. While a very promising approach, DNA-SIP is currently not widely utilized because it requires specialized laboratory equipment and technical expertise. However, we anticipate with advanced high-throughput protocols relying on robotic automation, along with improvements in depth of coverage for low-biomass samples, this technology will become more broadly accessible. While there is no magic bullet for validating function, and the aforementioned approaches are often rather custom, tedious and low throughput, it is important to continue making progress on the functional verification of genome sequence space. The integration of functional and phenotypic data with genomics will ultimately move us towards a better systems biology and ecosystem understanding of uncultivated bacterial and archaeal taxa.