Journal ArticleDOI
Lateral gene transfer and the nature of bacterial innovation
TLDR
Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms.Abstract:
Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.read more
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Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke,Patrick Schwientek,Alexander Sczyrba,Alexander Sczyrba,Natalia Ivanova,Iain Anderson,Jan Fang Cheng,Aaron E. Darling,Aaron E. Darling,Stephanie Malfatti,Brandon K. Swan,Esther A. Gies,Jeremy A. Dodsworth,Brian P. Hedlund,Georgios Tsiamis,Stefan M. Sievert,Wen Tso Liu,Jonathan A. Eisen,Steven J. Hallam,Nikos C. Kyrpides,Ramunas Stepanauskas,Edward M. Rubin,Philip Hugenholtz,Tanja Woyke +23 more
TL;DR: This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
Journal ArticleDOI
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Michael McClelland,Kenneth E. Sanderson,John Spieth,Sandra W. Clifton,Phil Latreille,Laura Courtney,Steffen Porwollik,Johar Ali,Mike Dante,Feiyu Du,Shunfang Hou,Dan Layman,Shawn Leonard,Christine Nguyen,Kelsi Scott,Andrea Holmes,Neenu Grewal,Elizabeth Mulvaney,Ellen E. Ryan,Hui Sun,Liliana Florea,Liliana Florea,Webb Miller,Tamberlyn Stoneking,Michael Nhan,Robert H. Waterston,Richard K. Wilson +26 more
TL;DR: The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A and Klebsiella pneumoniae as mentioned in this paper.
Journal ArticleDOI
Role of the normal gut microbiota
Sai Manasa Jandhyala,Rupjyoti Talukdar,Chivkula Subramanyam,Harish Vuyyuru,Mitnala Sasikala,D. Nageshwar Reddy +5 more
TL;DR: The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens.
Journal ArticleDOI
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.
Jinshui Zheng,Stijn Wittouck,Elisa Salvetti,Charles M. A. P. Franz,Hugh M. B. Harris,Paola Mattarelli,Paul W. O'Toole,Bruno Pot,Peter Vandamme,Jens Walter,Koichi Watanabe,Sander Wuyts,Giovanna E. Felis,Michael G. Gänzle,Michael G. Gänzle,Sarah Lebeer +15 more
TL;DR: This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences and proposed reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties.
Journal ArticleDOI
The role of hybridization in evolution
TL;DR: Fisher’s model of stabilizing selection on multiple traits, under which reproductive isolation evolves as a side‐effect of adaptation in allopatry, confirms a priori arguments that while recombinant hybrids are less fit on average, some gene combinations may be fitter than the parents, even in the parental environment.
References
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Journal ArticleDOI
Lysogenic conversion by a filamentous phage encoding cholera toxin.
TL;DR: The emergence of toxigenic V. cholerae involves horizontal gene transfer that may depend on in vivo gene expression, and is shown here to be encoded by a filamentous bacteriophage (designated CTXΦ), which is related to coliphage M13.
Origins and evolution of antibiotic resistance
TL;DR: This review presents the salient aspects of antibiotic resistance development over the past half-century, with the oft-restated conclusion that it is time to act.
Journal ArticleDOI
Phylogenetic Classification and the Universal Tree
TL;DR: Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.
Journal ArticleDOI
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
Karen E. Nelson,Rebecca A. Clayton,Steven R. Gill,Michelle L. Gwinn,Robert J. Dodson,Daniel H. Haft,Erin Hickey,Jeremy Peterson,William C. Nelson,Karen A. Ketchum,Lisa McDonald,Teresa Utterback,Joel A. Malek,Katja D. Linher,Mina M. Garrett,Ashley M. Stewart,Matthew D. Cotton,Matthew S. Pratt,Cheryl Phillips,Delwood Richardson,John F. Heidelberg,Granger G. Sutton,Robert D. Fleischmann,Jonathan A. Eisen,Owen White,Steven L. Salzberg,Hamilton O. Smith,J. Craig Venter,Claire M. Fraser +28 more
TL;DR: Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea.
Journal ArticleDOI
Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution
TL;DR: Bacteriophage attachment sites and cryptic genes on Pais indicate that these particular genetic elements were previously able to spread among bacterial populations by horizontal gene transfer, a process known to contribute to microbial evolution.
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