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
Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks
TL;DR: This study reveals an extensive (and previously undescribed) sharing of AR genes between Actinobacteria and Gammaproteobacteria, suggesting that the former might represent an important reservoir ofAR genes for the latter.
Comparative genomics of Lactobacillaceae from the gut of honey bees, Apis mellifera, from the Eastern United States
Emma Bradford,Noah Wax,Emma K. Bueren,Jenifer B. Walke,Richard D. Fell,Lisa K. Belden,David C. Haak +6 more
TL;DR: In this paper , the authors completed whole-genome sequencing of 3 unique Lactobacillaceae isolates collected from hives in Virginia, USA and assessed the phylogenetics of the 3 isolates.
Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
Patrick S. G. Chain,Patrick S. G. Chain,Ping Hu,Stephanie Malfatti,Stephanie Malfatti,Lyndsay Radnedge,Frank W. Larimer,Frank W. Larimer,Lisa M. Vergez,Lisa M. Vergez,Patricia L. Worsham,May C. Chu,Gary L. Andersen +12 more
TL;DR: In this paper, the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516, were compared with the corresponding features in Yersinia pseudotuberculosis, and the results showed that grouping Y. pestis strains based strictly on the classical definition of biovars does not accurately reflect the phylogenetic relationships within this species.
Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis.
Hirokazu Yano,Hirokazu Yano,Tomotada Iwamoto,Yukiko Nishiuchi,Chie Nakajima,Daria Starkova,Igor Mokrousov,Olga Narvskaya,Shiomi Yoshida,Kentaro Arikawa,Noriko Nakanishi,Ken Osaki,Ichiro Nakagawa,Manabu Ato,Yasuhiko Suzuki,Fumito Maruyama +15 more
TL;DR: In this paper, the authors assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study.
Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation
TL;DR: The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect and a large number of genes gained are associated with carbohydrate transport and metabolism, indicating that the evolution of glycometabolism is a key factor for the environmental adaptability of Paanibacilli species.
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