Protecting sausages with bacteria instead of salt

Assuming that sequencing of Haemophilus influenzae genome in 1995 marked the beginning of ‘genome era’, we have officially entered its second decade. Microbial genome sequencing has been progressing at a remarkably stable pace with the number of newly sequenced organisms nearly doubling every 2 years. This progress would become even more impressive if we count every sequenced genome of every bacterial strain, including seven genomes apiece for Staphylococcus aureus and Streptococcus pyogenes , not to mention nine nearly completed genomes of Bacillus anthracis . At first glance, repeated sequencing of the same pathogen might seem redundant, even excessive. However, one of the major insights afforded by complete genomes is the tremendous diversity of supposedly very closely related organisms. For example, a genome comparison of three different strains of Prochlococcus marinus showed that they share only ∼ 1000 genes, about half of their respective genomes (Hess, 2004). On one hand, these observations illuminate the need for additional measures of organism relatedness besides the 16S rRNA identity. Novel genome-based metrics have been developed that are based on the number of shared genes, conservation of gene order, alignments of ribosomal proteins and other approaches (Wolf et al ., 2001; 2002). Two recently proposed parameters, average nucleotide identity (for closely related organisms) and average amino acid identity (for distantly related organisms) seem to provide a basis for a reasonable and consistent taxonomy (Konstantinidis and Tiedje, 2005a, b). On the other hand, these observations illuminated the need for further genomic sequences of environmental microorganisms. This need is being fulfilled by the US DOE Joint Genome Institute (JGI) and other genome sequencing centres, which have been churning out complete genomes of environmentally important microorganisms at a rate of more than one genome per week. At such rates, reading certainly outpaces comprehension, so scientific descriptions of many fascinating genomes lag behind, if appear at all. The JGI now routinely releases new genomes with only an automated annotation (Table 1). This month’s crop includes such important environmental microorganisms as the sulfate-reducing bacterium Desulfovibrio desulfuricans and popular model organisms as Rhodospirillum rubrum , Moorella thermoacetica (formerly Clostridium thermoaceticum ) and Geobacter metallireducens (Table 1). While making these sequences available to the public is certainly a tremendous service to the community, the natural question is whether they could be trusted. Such questions have been constantly arising throughout the past 10 years and have been addressed in a variety of publications. The general consensus is that prokaryotic genome sequences are remarkably reliable, while eukaryotic genomes become reliable after certain manual effort. Indeed, post-genomic analysis verified a great majority of physiological predictions made on the basis of genome analysis: deduced proteins have been detected on twodimensional gels and by mass-spectrometry, new versions of supposedly missing enzymes have been successfully identified, and previously unsuspected growth capabilities have been verified in direct experiments.