Blog
About

240
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Insights from 20 years of bacterial genome sequencing

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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.

          Related collections

          Most cited references 192

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          The RAST Server: Rapid Annotations using Subsystems Technology

          Background The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. Conclusion By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Structure, Function and Diversity of the Healthy Human Microbiome

            Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              A human gut microbial gene catalogue established by metagenomic sequencing.

              To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
                Bookmark

                Author and article information

                Contributors
                (865) 574-8201 , usserydw@ornl.gov
                Journal
                Funct Integr Genomics
                Funct. Integr. Genomics
                Functional & Integrative Genomics
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                1438-793X
                1438-7948
                27 February 2015
                27 February 2015
                2015
                : 15
                : 2
                : 141-161
                Affiliations
                [ ]Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
                [ ]Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996 USA
                [ ]Department of Microbiology, University of Tennessee, Knoxville, TN 37996 USA
                [ ]Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
                [ ]Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
                [ ]Molecular Microbiology and Genomics Consultants, Tannenstr 7, 55576 Zotzenheim, Germany
                [ ]Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
                Article
                433
                10.1007/s10142-015-0433-4
                4361730
                25722247
                © The Author(s) 2015

                Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

                Categories
                Review
                Custom metadata
                © Springer-Verlag Berlin Heidelberg 2015

                Comments

                Comment on this article