Journal Article10.1016/J.GDE.2005.09.006
The microbial pan-genome
1.2K
TL;DR: A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed and the pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome", might be orders of magnitude larger than any single genome.
read more
About: This article is published in Current Opinion in Genetics & Development. The article was published on 01 Dec 2005. The article focuses on the topics: Minimal genome & Bacterial genome size.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Complete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates
Yuwei Zhang,FenFen Lv,Yan Su,Huan Zhang,Baojiang Zhang +4 more
TL;DR: Findings show that genetic exchange across S. equi strains influences the development of the donkey S.equi genome, offering important genetic insights for future epidemiological studies of S. Equi infection.
Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates
TL;DR: In this paper , the authors performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulenceassociated genes (VAGs) of S suis.
Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features
J. Rusakovica,J. Hallinan,A. Wipat,P. Zuliani +3 more
TL;DR: Probabilistic Latent Semantic Analysis (PLSA) is applied to whole bacterial genomes to identify common genomic features, revealing hidden patterns in methicillin-resistant Staphylococcus aureus and Bacillus subtilis, shedding light on the genomic basis of pathogenicity.
Quantitative and Theoretical Microbial Population Biology
Martin F. Polz,William P. Hanage +1 more
TL;DR: Researchers aim to define and identify microbial populations, challenging traditional species concepts due to horizontal gene transfer and sampling difficulties, yet crucial for understanding ecology, evolution, and community dynamics in bacteria and archaea.
More than planetary-scale feedback self-regulation: A Biological-centred approach to the Gaia Hypothesis
Sergio Rubin,Michel Crucifix +1 more
TL;DR: This study reinterprets the Gaia Hypothesis, shifting focus from self-regulation by feedback mechanisms to a biological-centred approach, proposing a relational and systemic theory of life at the planetary scale through autopoiesis and (M,R)-system formalism.
References
Diversity of the human intestinal microbial flora.
Paul B. Eckburg,Elisabeth M. Bik,Charles N. Bernstein,Elizabeth Purdom,Les Dethlefsen,Michael Sargent,Steven R. Gill,Karen E. Nelson,David A. Relman,David A. Relman,David A. Relman +10 more
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.
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”
Hervé Tettelin,Vega Masignani,Michael J. Cieslewicz,Claudio Donati,Duccio Medini,Naomi L. Ward,Samuel V. Angiuoli,Jonathan Crabtree,Amanda L. Jones,A. Scott Durkin,Robert T. DeBoy,Tanja M. Davidsen,Marirosa Mora,Maria Scarselli,Immaculada Margarit Y Ros,Jeremy Peterson,Christopher R. Hauser,Jaideep P. Sundaram,William C. Nelson,Ramana Madupu,Lauren M. Brinkac,Robert J. Dodson,M. J. Rosovitz,Steven A. Sullivan,Sean C. Daugherty,Daniel H. Haft,Jeremy D. Selengut,Michelle L. Gwinn,Liwei Zhou,Nikhat Zafar,Hoda Khouri,Diana Radune,George Dimitrov,Kisha Watkins,Kevin J. B. O'Connor,Shannon Smith,Teresa Utterback,Owen White,Craig E. Rubens,Guido Grandi,Lawrence C. Madoff,Dennis L. Kasper,John L. Telford,Michael R. Wessels,Rino Rappuoli,Claire M. Fraser +45 more
TL;DR: The genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans, was generated and Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactic pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
2.5K
Mobile elements: drivers of genome evolution.
TL;DR: Mobile elements within genomes have driven genome evolution in diverse ways and are becoming useful tools for learning more about genome evolution and gene function.
1.9K
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
TL;DR: The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework to demonstrate that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving.
1.7K