Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

Abstract

Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1(T), and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1(T) with its 1,866 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: GEBA; Gram-negative; Sphaerochaeta; Spirochaetaceae; chemoorganotrophic; di- and oligosaccharide-degrading; mesophilic; non-motile; obligately anaerobic; termite hindgut.

Figure 1

Phylogenetic tree highlighting the position of S. coccoides relative to the other type strains within the family Spirochaetaceae. The tree was inferred from 1,360 aligned characters [9,10] of the 16S rRNA gene sequence under the maximum likelihood criterion [11]. Rooting was done initially using the midpoint method [12] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 500 ML bootstrap replicates [13] (left) and from 1,000 maximum parsimony bootstrap replicates [14] (right) if larger than 60% if. Lineages with type strain genome sequencing projects registered in GOLD [15] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks (see [16-19], CP002696 for Treponema brennaborense, CP002903 for S. thermophila, and CP002868 for S. caldaria). Also, genomes that are finished but are missing a second asterisk are S. africana CP003282, S. pleomorpha CP003155 and S. globosa CP002541.

Figure 2

Graphical map of the chromosome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3

Phylogenetic tree inferred from completely sequenced genomes of the Spirochaeta type strains. The tree was inferred from 140,413 aligned amino acid characters under the maximum likelihood (ML) criterion and rooted with Leptospira. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches are bootstrapping support values (if larger than 60%) from (i) maximum-likelihood supermatrix analysis; (ii) maximum-parsimony supermatrix analysis; (iii) maximum-likelihood gene-content analysis; (iv) maximum-parsimony gene-content analysis. INSDC accession numbers are given in square brackets. Note that the placement of Borrelia is probably caused by long-branch attraction. For further details see the text.