Journal article
Insights from 20 years of bacterial genome sequencing
Oak Ridge National Laboratory1
Department of Systems Biology, Technical University of Denmark2
Agricultural and Environmental Proteomics, Department of Systems Biology, Technical University of Denmark3
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark4
Molecular Microbiology and Genomics Consultants5
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well.
Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced.
To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups.
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome.
The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families.
Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.
Language: | English |
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Publisher: | Springer Berlin Heidelberg |
Year: | 2015 |
Pages: | 141-161 |
ISSN: | 14387948 and 1438793x |
Types: | Journal article |
DOI: | 10.1007/s10142-015-0433-4 |
ORCIDs: | Lund, Ole |
Bacteria Bacterial genomes Comparative genomics Core-genome Metagenomics Next-generation sequencing Pan-genome SDG 3 - Good Health and Well-being
Animal Genetics and Genomics Bacterial Proteins Biochemistry, general Bioinformatics Biomedical and Life Sciences Cell Biology Codon Genetic Variation Genome Size Genome, Bacterial Genomics Life Sciences Microbial Genetics and Genomics Molecular Sequence Annotation Phylogeny Plant Genetics & Genomics Sequence Analysis, DNA