Genome Project of Symbiobacterium thermophilum


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Nucleic Acids Res 32(16):4937-4944 (2004) (toll-free full text)


Symbiobacterium thermophilum IAM14863 (ST) is a rod-shaped thermophilic bacterium found in commensal submerged culture occurred from compost collected at Hiroshima, Japan (Suzuki, J Gen Microbiol 134:2353, 1988)(Ohno, 2000).  The unique features in Physiology, Taxonomy and Ecology indicate that this organism is an instance of uncultured microbe.  This web site provides information obtained from the complete nucleotide sequencing of its 3.57-mega base circular chromosome.


Physiology.  ST is characterised by the growth-dependence on microbial commensalism with Bacillus strain S, which was simultaneously isolated from compost (Suzuki, J Gen Microbiol 134:2353, 1988).  While ST alone shows no or significantly impaired growth under the standard culture condition, it effectively propagates up to 5x108 cells/ml when cocultured with Bacillus strain S (fig).  The dialysis cultures between ST and Bacillus strain S using the originally designed flask and jar fermentor established the pure growth of ST, which indicates that ST depends on dialisable substances generated by Bacillus strain S (Ohno, 1999)(Ueda, 2002).  Our recent studies have revealed that Bacillus strain S not only supplies but also eliminates multiple chemical factors to support the effective growth of ST.  These properties still prevent researchers to isolate ST and related organisms as evidenced by the poor 16S rDNA data submission in the public database.  [Return to top]



Taxonomy.  The traditional microbiological observations (table) indicated that ST is a Gram-negative bacterium, though electron micrograph showed a unique surface structure (Suzuki, J Gen Microbiol 134:2353, 1988).  The 16S rDNA-based phylogeny, however, revealed that ST is a Gram-positive bacterium not clustering to any other genera (fig) (Ohno, 2000).  Despite the high G+C content (68.7%), the overall feature of the ST genome is closest to that of Firmicutes, the group of low-G+C Gram-positive bacteria including Bacillae and Clostridiae.  ST is the first high G+C organism retaining the ability to form endospore.  ST is thus excluded from the categories of current bacterial systematics.  [Return to top]


Ecology.  Our screening study has shown that ST and related bacteria are widespread in natural environment.  They are frequently cultured from compost, soil, and feces, intestinal contents and feeds of animals (Ueda, 2001), and samples from marine environments such as shells and weeds (ms submitted).  16S rDNA-based phylogeny of the clones obtained from the Symbiobacterium-positive cultures revealed the potential diversity of the bacterial genus.  The result provides evidence for the presence of an uncultured microorganism, ubiquitous in nature but unknown because of the physiological properties.  Several Symbiobacterium-positive cultures contained Ureibacillius spp., which has an activity to support the growth of S. thermophilum.  [Return to top]