Genomes and Post-genome Technology
The beginning of the twenty-first century marks the genomic era in microbiology, where many genomes started being completely sequenced. The rate at which this kind of feat is now possible has increased drastically with the development of new sequencing te
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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 Application of Prokaryotic Intraspecies Genomic Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 Culture-Independent Exploitation of Microbial Genomes: Metagenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333 Single Cell Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 Using Genome and Post-genome Information to Make a Product . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337 DNA Sequencing and Bioinformatics . . . . . . . . . . . . . . . . . . . . . 338 Working with Large Amounts of Data . . . . . . . . . . . . . . . . . . 338 Analytical Pipelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340 Metagenomics Pipelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
Introduction Until a few years ago, microbial biotechnology was limited by the use of cultivated microorganisms. However, most of the microorganisms that can be seen through a microscope or be detected using molecular biology tools are labeled as non-cultivable (or not-yet-cultivated). Nowadays, this previously unreachable genomic information can be accessed without the need of having the microorganism in pure culture. Microbiology is at one of those inflection points in history, and it is expected that this newly accessible wealth of microorganisms will bring significant contributions to mankind over the next decades. This will be achieved by the development of new biotechnological products for plant and animal disease, diagnostics, management, and control. Furthermore, there will be significant contributions to improve the quality of crops and food production yields for an ever-growing human population, development of new biocatalysts, new processes, and applications for bioremediation and energy production. Although not absolutely necessary for biotechnological application, one of the first steps to study a microorganism is
its classification. DNA-DNA hybridization, 16S rRNA gene sequencing, multilocus house-keeping genes sequencing, and super-trees are the standards for bacterial classification. The first complete bacterial genome sequenced was that of Haemophilus influenza. This genome was published in the early 1990s (Fleischmann et al. 1995) and was undoubtedly a seminal achievement for the microbiology field. Now, with our access to whole genome information, even from ‘‘uncultivable’’ microbe representatives, we have a better understanding of what a microbe is capable of doing, its role in the microbial community, and its role in the environment. Access to individual genomes allowed comparison among genomes from different species, among genomes from different isolates from the same species (pan-genome), and
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