Microbiology in the post-genomic era

doi:10.1038/NRMICRO1901

Open AccessJournal ArticleDOI

Microbiology in the post-genomic era

Duccio Medini, +8 more

- 01 Jun 2008 -

Nature Reviews Microbiology

- Vol. 6, Iss: 6, pp 419-430

TLDR

The evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments are reviewed, and the implications of the genomic era for the future of microbiology are addressed.

Abstract:

Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.

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Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower, +253 more

- 14 Jun 2012 -

Nature

TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.

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Journal Article

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower, +247 more

- 01 Jun 2012 -

PubMed Central

TL;DR: The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding 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.

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Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Anna Klindworth, +6 more

- 01 Jan 2013 -

Nucleic Acids Research

TL;DR: The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

Chen-Shan Chin, +11 more

- 01 Jun 2013 -

Nature Methods

TL;DR: This work presents a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.

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Inferring Correlation Networks from Genomic Survey Data

Jonathan Friedman, +2 more

- 20 Sep 2012 -

PLOS Computational Biology

TL;DR: SparCC as mentioned in this paper is a new approach that is capable of estimating correlation values from compositional data, which is used to infer a rich ecological network connecting hundreds of interacting species across 18 sites on the human body.

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References

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Journal ArticleDOI

DNA sequencing with chain-terminating inhibitors

Frederick Sanger, +2 more

- 01 Dec 1977 -

Proceedings of the National Academy of S...

TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.

...read moreread less

Journal ArticleDOI

An obesity-associated gut microbiome with increased capacity for energy harvest

Peter J. Turnbaugh, +5 more

- 21 Dec 2006 -

Nature

TL;DR: It is demonstrated through metagenomic and biochemical analyses that changes in the relative abundance of the Bacteroidetes and Firmicutes affect the metabolic potential of the mouse gut microbiota and indicates that the obese microbiome has an increased capacity to harvest energy from the diet.

...read moreread less

Journal ArticleDOI

Genome sequencing in microfabricated high-density picolitre reactors

Marcel Margulies, +55 more

- 15 Sep 2005 -

Nature

TL;DR: A scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments with 96% coverage at 99.96% accuracy in one run of the machine is described.

...read moreread less

Journal ArticleDOI

Diversity of the human intestinal microbial flora.

Paul B. Eckburg, +10 more

- 10 Jun 2005 -

Science

TL;DR: A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms, and significant intersubject variability and differences between stool and mucosa community composition were discovered.

...read moreread less