Strain RHS 1^T (= DSM 20476 = ATCC 29202 = JCM 14554) is the type strain of the species Slackia heliotrinireducens and was originally described by Lanigan in 1976 as Peptococcus heliotrinreducans (sic) [1] and validly published following an orthographic correction as Peptococcus heliotrinreducens in 1983 [2,3]. The strain was later transferred to the genus Peptostreptococcus on the basis of its G+C content [4]. 16S rRNA gene sequence analysis indicated that it should not be assigned to the genus Peptostreptococcus and therefore the strain was subsequently allocated to the novel genus Slackia as S. heliotrinireducens [5,6]. The three species of the genus Slackia, S. exigua, S. faecicanis, and S. heliotrinireducens form a distinct cluster within the Coriobacteriaceae, located in the neighborhood to the genera Cryptobacterium and Collinsella.

Five additional strains identified as S. heliotrinireducens based on their proteolytic enzyme profiles have been isolated from human polymicrobial abscesses [7], but these strains were dissimilar from the type strain as shown by pyrolysis mass spectrometry [8]. With 94% sequence identity (16S rRNA gene), S. exigua, the type strain of the closest related species represents the only meaningful (>91%) hit in nucleotide sequence database searches, indicating a complete lack of cultivated and even uncultivated relatives of strain RHS 1^T in accessible microbiological diversity. Screening of environmental samples and surveys reported at NCBI BLAST server indicated no closely related phylotypes that can be linked to the species (as of July 2009). Here we present a summary classification and a set of features for S. heliotrinireducens RHS 1^T Together with the description of the complete genomic sequencing and annotation.

Classification and features

Figure 1 shows the phylogenetic neighborhood of S. heliotrinireducens strain RHS 1^T in a 16S rRNA based tree. The sequence of one of the two 16S rRNA genes differs in two nucleotides from the other copy and from the previously published 16S rRNA sequence generated from ATCC 29202 (AF101241).

Figure 1 Phylogenetic tree highlighting the position of S. heliotrinireducens RHS 1T relative to other type strains within the family Coriobacteriaceae. The tree was inferred from 1,422 aligned 16S rRNA characters [9,10] under the maximum likelihood criterion [11], and rooted with type strains of the genera Collinsella and Coriobacterium. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates, if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] are shown in blue, published genomes in bold, e.g. the recently published GEBA genomes from Cryptobacterium curtum [13], and Eggerthella lenta [14].

S. heliotrinireducens is Gram-positive, nonmotile, obligatly anaerobic, and does not produce endospores (Table 1). Strain RHS 1 forms cocci or coccobacilli (Figure 2) with a diameter of 0.3 to 0.6 µm and 0.8 x 1.2 µm, respectively [5,6]. The strain grows very slowly on blood agar and forms small translucent, glistening colonies, up to 1 mm in diameter after extensive incubation. It does not utilize carbohydrates, but reduces nitrates and pyrrolizidine alkaloids [5,6]. Reductive cleavage of pyrrolizidines (heliotrine, europine, heleurine, supinine and lasiocarpine) occurs by using hydrogen gas or formate as hydrogen donor [1]. Ammonia is formed from tryptone, yeast extract, adenine, uracil and arginine. Nitrates are completely reduced to ammonia if an appropriate electron donor (H₂, formate) is present [19]. The strain is bile-sensitive, indole-negative, hydrolyses arginine but not esculin. Does not produce catalase or urease, but is able to dissimilate arginine. Growth is generally stimulated by addition of 0.5% arginine. Metabolic products from S. heliotrinireducens grown in prereduced PYG broth are acetic acid, isovaleric acid, and butyric acid in trace amounts [4].

Figure 2 Scanning electron micrograph of S. heliotrinireducens RHS 1T

Almost nothing is known about the chemotaxonomy of strain RHS 1^T, except that its predominant cellular fatty acid is C18:1 [4].

The genome is 3,165,038 bp long and comprises one main circular chromosome with a 60.2% GC content (Table 3 and Figure 3). Of the 2,858 genes predicted, 2,798 were protein coding genes, and 60 RNAs; 33 pseudogenes were also identified. The majority of the protein-coding genes (70.6%) were assigned with a putative function, while those remaining were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. The distribution of genes into COGs functional categories is presented in Table 4, and a cellular overview diagram is presented in Figure 4, followed by a summary of metabolic network statistics shown in Table 5.

Figure 3 Graphical circular map of the genome. 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 4 Schematic cellular overview diagram of all pathways of the S. heliotrinireducens RHS 1T metabolism. Nodes represent metabolites, with shape indicating class of metabolite (see key to right). Lines represent reactions.