Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method.

Draft genome sequence of the rubber tree Hevea brasiliensis.

Background: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876.

Results: Here, we report the draft genome sequence of H.

Genomics for key players in the N cycle from guinea pigs to the next frontier.

While sequencing methods were available in the late 1970s, it was not until the human genome project and a significant influx of funds for such research that this technology became high throughput. The fields of microbiology and microbial ecology, among many others, have been tremendously impacted over the years, to such an extent that the determination of complete microbial genome sequences is now commonplace. Given the lower costs of next-generation sequencing platforms, even small laboratories from around the world will be able to generate millions of base pairs of data, equivalent to entire genomes worth of sequence information.

Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria.

Globin-coupled sensors are heme-binding signal transducers in Bacteria and Archaea in which an N-terminal globin controls the activity of a variable C-terminal domain. Here, we report that BpeGReg, a globin-coupled diguanylate cyclase from the whooping cough pathogen Bordetella pertussis, synthesizes the second messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP) upon oxygen binding. Expression of BpeGReg in Salmonella typhimurium enhances biofilm formation, while knockout of the BpeGReg gene of B.

Cloning, expression, and purification of the N-terminal heme-binding domain of globin-coupled sensors.

Globin-coupled sensors (GCSs) are multidomain proteins, consisting of an N-terminal globin domain fused to a variety of C-terminal transmitter domains. Functional classification of GCSs is based on the transmitter domain(s) they possess, broadly falling under either aerotaxis or gene regulation. This chapter describes methods and strategies for cloning, expression, and purification of GCSs for spectroscopic analysis and determination of the minimum heme-binding domain, together with bioinformatic approaches for database searching and examination of domain architectures.

Globin-coupled sensors, protoglobins, and the last universal common ancestor.

The strategy for detecting oxygen, carbon monoxide, nitric oxide, and sulfides is predominantly through heme-based sensors utilizing either a globin domain or a PAS domain. Whereas PAS domains bind various cofactors, globins bind only heme. Globin-coupled sensors (GCSs) were first described as regulators of the aerotactic responses in Bacillus subtilis and Halobacterium salinarum.

Ancestral hemoglobins in Archaea.

Hemoglobins are ubiquitous in Eukarya and Bacteria but, until now, have not been found in Archaea. A phylogenetic analysis of the recently revealed microbial family of globin-coupled heme-based sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (Pgb). Here, we report the discovery and characterization of two Pgbs from the Archaea: ApPgb from the obligately aerobic hyperthermophile Aeropyrum pernix, and MaPgb from the strictly anaerobic methanogen Methanosarcina acetivorans.

The diversity of globin-coupled sensors.

The recently discovered globin-coupled sensors (GCSs) are heme-containing two-domain transducers distinct from the PAS domain superfamily. We have identified an additional 22 GCSs with varying multi-domain C-terminal transmitters through a search of the complete and incomplete microbial genome datasets. The GCS superfamily is composed of two major subfamilies: the aerotactic and gene regulators.