Genome, Bacterial

Publication Title: 
Proceedings of the National Academy of Sciences of the United States of America

One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune deficiencies. Here we report the complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them to infections by this pathogen. The comparison of the genomes of the two CF strains with those of other P.

Mathee, Kalai
Narasimhan, Giri
Valdes, Camilo
Qiu, Xiaoyun
Matewish, Jody M.
Koehrsen, Michael
Rokas, Antonis
Yandava, Chandri N.
Engels, Reinhard
Zeng, Erliang
Olavarietta, Raquel
Doud, Melissa
Smith, Roger S.
Montgomery, Philip
White, Jared R.
Godfrey, Paul A.
Kodira, Chinnappa
Birren, Bruce
Galagan, James E.
Lory, Stephen
Publication Title: 
PloS One

The genomes of four Lactobacillus reuteri strains isolated from human breast milk and the gastrointestinal tract have been recently sequenced as part of the Human Microbiome Project. Preliminary genome comparisons suggested that these strains belong to two different clades, previously shown to differ with respect to antimicrobial production, biofilm formation, and immunomodulation.

Saulnier, Delphine M.
Santos, Filipe
Roos, Stefan
Mistretta, Toni-Ann
Spinler, Jennifer K.
Molenaar, Douwe
Teusink, Bas
Versalovic, James
Publication Title: 
Nucleic Acids Research

The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria.

Van Pijkeren, Jan-Peter
Britton, Robert A.
Publication Title: 
Proceedings of the National Academy of Sciences of the United States of America

The human microbiome plays a key role in human health and is associated with numerous diseases. Metagenomic-based studies are now generating valuable information about the composition of the microbiome in health and in disease, demonstrating nonneutral assembly processes and complex co-occurrence patterns. However, the underlying ecological forces that structure the microbiome are still unclear.

Levy, Roie
Borenstein, Elhanan
Publication Title: 
PLoS genetics

The molecular chaperone Hsp90 is essential in eukaryotes, in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients. In contrast, Hsp90 is not essential in bacteria, and a broad characterization of its molecular and organismal function is lacking. To enable such characterization, we used a genome-scale phylogenetic analysis to identify genes that co-evolve with bacterial Hsp90.

Press, Maximilian O.
Li, Hui
Creanza, Nicole
Kramer, Günter
Queitsch, Christine
Sourjik, Victor
Borenstein, Elhanan
Publication Title: 
PLoS computational biology

Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa.

Carr, Rogan
Shen-Orr, Shai S.
Borenstein, Elhanan
Publication Title: 
Proceedings of the National Academy of Sciences of the United States of America

Nitrogen acquisition and assimilation is a primary concern of insects feeding on diets largely composed of plant material. Reclaiming nitrogen from waste products provides a rich reserve for this limited resource, provided that recycling mechanisms are in place. Cockroaches, unlike most terrestrial insects, excrete waste nitrogen within their fat bodies as uric acids, postulated to be a supplement when dietary nitrogen is limited.

Sabree, Zakee L.
Kambhampati, Srinivas
Moran, Nancy A.
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