Abstract
The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.
Highlights
They should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution
Our ability to properly correlate environmental genomic data to currently charted bacteria is strongly hindered by the lack of whole-genome sequences for many of the microorganisms dispersed along the phylogenetic tree of life (Fig. 2)
Such cross-genome comparisons would allow the determination of the sizes of the pan-genomes across as many species per family and phylum as possible [1]. This type of analysis would facilitate a much improved interpretation of data from metagenomics projects through the specificity and increased understanding of the overall function of bacteria in natural milieus. The purpose of this opinion is to promote developments that will spur the generation of genome sequence data that are beneficial to the interpretation of the currently available and future metagenomics data sets [6, 23]
Summary
There is a current consensus that the technology is progressing so fast that a much required basis or background for the sound interpretation of the massive sequence information is lacking Key to this is the generally perceived lack of sufficient information on the genomes of representative taxa in each of the over 50 phyla that currently make up the bacterial tree of life [14, 16]. A clear example of this is the massive genome reduction in bacteria that adapts to a mutualistic/symbiotic lifestyle [cf 20], resulting in tiny, gene-dense genomes [5] It remains to be seen whether habitat-specific patterns can be distinguished among different genomes within the species. Our ability to properly correlate environmental genomic data to currently charted bacteria is strongly hindered by the lack of whole-genome sequences for many of the microorganisms dispersed along the phylogenetic tree of life (Fig. 2). On top of this, we lack information on the within-species diversity (defining the pan-genome) across both the poorly accessed as well as most of the well-
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