Background: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.

The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome random sequencing. A total of 1738 predicted protein-coding genes were identified; however, only a minority of these (38 percent) could be assigned a putative cellular role with high confidence. Although the majority of genes related to energy production, cell division, and metabolism in M. jannaschii are most similar to those found in Bacteria, most of the genes involved in transcription, translation, and replication in M. jannaschii are more similar to those found in Eukaryotes.

rRNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an analysis and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives by using linear amplification-providing an assessment that is independent of a reverse primer-and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.The study of microbial communities is important on multiple levels, from describing nutrient cycling and elucidating novel metabolisms to understanding how ecosystems are maintained and how mixtures of microbes can promote and/or upset the health status of their harboring host. Our ability to evaluate aspects of microbial ecology depends to a large extent on correctly identifying community members and their relative contributions to the overall makeup of the ecosystem.The analysis of genes found in an environment as proxies for the organisms themselves has revolutionized our understanding of microbial communities (16). Studies of universal genes, especially the small-subunit rRNA (SSU rRNA), provide phylogenetic portraits of the communities, including organisms that have not yet been cultivated (10,16,32). These data increase in value with time, as newly cultivated species provide more anchor points that relate organismal phylogeny and physiology. Furthermore, communities are easily compared between locations and over time.An essential contribution to the utility of this approach is the interspersion of more-and less-conserved sequences within the rRNA genes. The more varied portions distinguish the phylogenetic groups, while the conserved portions provide universal (or nearly universal) sequences for PCR primer binding. This allows specific amplification of the genes of interest out of total community genome DNA (the metagenome). Nearly all studies of bacterial SSU rRNA genes rely on primers designed over 15 years ago (32, 35). Although several groups have warned of the limitations of these primers, this has had little impact on common practice (reviewed in reference 30). This might be of little consequence in studies that seek only a qualitative portrait of community diversity, but with the increasing application of rRNA genebased methods to analyze medical...

The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.