Thermotoga maritima, a rod-shaped bacterium belonging to the order Thermotogales, was originally isolated from geothermal heated marine sediment at Vulcano, Italy. The organism has an optimum growth temperature of 80 degrees C. T. maritima metabolizes many simple and complex carbohydrates including glucose, sucrose, starch, cellulose, and xylan. Through conversion to fuels such as hydrogen, both cellulose and xylan have great potential as renewable carbon and energy sources. T. maritima is also of evolutionary significance, because small-subunit ribosomal RNA phylogeny has placed this bacterium as one of the deepest and most slowly evolving lineages in the Eubacteria.

The genome of T. maritima MSB8 is a single circular chromosome consisting of 1,860,725 base pairs with an average G+C content of 46%. The genome contains 1,877 prediced coding regions, of which 1014 (54%) have functional assignments, and 863 (46%) are of unknown function. Genome analysis reveals numerous pathways involved in the degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Completion of the T. maritima genome has revealed a degree of similarity with the Archaea in terms of gene content and overall genome organization that was not previously appreciated. Although the core of T. maritima may be eubacterial, almost one quarter of the genome is archaeal in nature. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and the Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.