Abstract
Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.
Highlights
The complete genome of an organism is obtained through 1) isolating and culturing the organism to obtain sufficient DNA mass, 2) extracting and amplifying DNA, 3) sequencing the genomes, 4) assembling them, and 5) annotating genes and regulatory elements
While recently published MEGAN software relies on BLAST for analysis, it attempts to address this problem by classifying DNA fragments based on a lowest common ancestor algorithm (LCA) [66]
Metagenomic data will produce a significant set of sequences that cannot be assigned to any known taxon, and the question arises how to estimate the number of unknown species
Summary
The complete genome of an organism is obtained through 1) isolating and culturing the organism to obtain sufficient DNA mass, 2) extracting and amplifying DNA, 3) sequencing the genomes, 4) assembling them, and 5) annotating genes and regulatory elements. There are a number of bacterial species that grow in such cultures, such as Escherichia coli Not coincidentally, such bacteria are the most well-studied and the first to be sequenced. The recent advent and application of high throughput generation sequencing methods have enabled a large increase in productivity [6, 7] This allows the decoding and assembly of multiple genomes from multiple species in communities. This becomes the field of metagenomics, where scientists must think on a broad-scale [8, 9], shifting their focus from “How does one organism work?” to “Who all is here and what are they doing?”. We highlight how tools for functional annotation have shed light on the coding capacities of natural bacterial communities, focusing on the potential harmful or beneficial consequences of these microbes from a human perspective
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