Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism

Kenji Ueda, Atsushi Yamashita, Jun Ishikawa, Masafumi Shamada, Tomo O. Watsuji, Kohji Morimura, Haruo Ikeda, Masahira Hattori, Teruhiko Beppu

Research output: Contribution to journalArticle

115 Citations (Scopus)

Abstract

Symbiobacterium thermophilium is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive bacteria. This provides evidence for the presence of an undefined category in the Gram-positive bacterial group. The presence of both spo and related genes and microscopic observation indicate that S.thermophilum is the first high G + C organism that forms endospores. The S.thermophilum genome is also characterized by the widespread insertion of class C group II introns, which are oriented in the same direction as chromosomal replication. The genome has many membrane transporters, a number of which are involved in the uptake of peptides and amino acids. The genes involved in primary metabolism are largely identified, except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also has a variety of respiratory systems including Nap nitrate reductase, which has been found only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is adaptable to and thus lives in various environments, such that its growth requirement could be a substance or a physiological condition that is generally available in the natural environment rather than a highly specific substance that is present only in a limited niche. The genomic information from S.thermophilum offers new insights into microbial diversity and evolutionary sciences, and provides a framework for characterizing the molecular basis underlying microbial commensalism.

Original languageEnglish
Pages (from-to)4937-4944
Number of pages8
JournalNucleic Acids Research
Volume32
Issue number16
DOIs
Publication statusPublished - 2004
Externally publishedYes

Fingerprint

Symbiosis
Genome
Bacteria
Organism Forms
Nitrate Reductase
Carbonic Anhydrases
Membrane Transport Proteins
Base Composition
Gram-Positive Bacteria
Phylogeny
Ribosomal DNA
Gram-Negative Bacteria
Respiratory System
Introns
Genes
Soil
Amino Acids
Peptides
Enzymes
Growth

ASJC Scopus subject areas

  • Genetics

Cite this

Ueda, K., Yamashita, A., Ishikawa, J., Shamada, M., Watsuji, T. O., Morimura, K., ... Beppu, T. (2004). Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Research, 32(16), 4937-4944. https://doi.org/10.1093/nar/gkh830

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. / Ueda, Kenji; Yamashita, Atsushi; Ishikawa, Jun; Shamada, Masafumi; Watsuji, Tomo O.; Morimura, Kohji; Ikeda, Haruo; Hattori, Masahira; Beppu, Teruhiko.

In: Nucleic Acids Research, Vol. 32, No. 16, 2004, p. 4937-4944.

Research output: Contribution to journalArticle

Ueda, K, Yamashita, A, Ishikawa, J, Shamada, M, Watsuji, TO, Morimura, K, Ikeda, H, Hattori, M & Beppu, T 2004, 'Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism', Nucleic Acids Research, vol. 32, no. 16, pp. 4937-4944. https://doi.org/10.1093/nar/gkh830
Ueda, Kenji ; Yamashita, Atsushi ; Ishikawa, Jun ; Shamada, Masafumi ; Watsuji, Tomo O. ; Morimura, Kohji ; Ikeda, Haruo ; Hattori, Masahira ; Beppu, Teruhiko. / Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. In: Nucleic Acids Research. 2004 ; Vol. 32, No. 16. pp. 4937-4944.
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