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Phylogenetic Placement of Sarcina Ventriculi and Sarcina Maxima

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Phylogenetic Placement of Sarcina Ventriculi and Sarcina Maxima INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1994, p. 591-593 Vol. 44, No. 3 0020-7713/94/$04.00+ 0 Phylogenetic Placement of Sarcina ventriculi and Sarcina maxima within Group I Clostridium, a Possible Problem for Future Revision of the Genus Clostridium Request for an Opinion A. WILLEMS" AND M. D. COLLINS Microbiology Department, Reading Laboratory, Institute of Food Research, Earley Gate, Reading RG6 2EF, United Kingdom The 16s rRNA gene sequences of Sarcinu ventriculi DSM 286T (T = type strain) and Sarcina maxima DSM 31(iT were determined. Phylogenetic analysis revealed that these two species are closely related to each other and belong to group I Clostridium (sensu Johnson and Francis). The implications of these phylogenetic findings for future revision of the genus Clostridiurn are discussed. In 1842 Goodsir described some bundle-shaped organisms peptone, 5 g of yeast extract, 30 g of glucose, 1 liter of H,O; pH observed in the stomach fluid of a patient with digestive tract 6.0) at 37"C, and chromosomal DNAs were prepared as problems and named these organisms Sarcina ventriculi (12). described by Lawson et al. (14). The 16s rRNA genes were This obligately anaerobic microorganism was first cultured by amplified by a PCR, purified, and sequenced directly as Beijerinck (1, 2) and has since been isolated from human and described previously (19). The sequences which we determined animal stomach contents and feces, soil, and the surfaces of were aligned with sequences of reference organisms obtained cereal seeds (5). After the original description of S. ventriculi, from the EMBL data library by using the PILEUP, PRETTY, many other mostly aerobic, packet-forming cocci were assigned and UGLY programs of the Genetics Computer Group Se- to the genus Sarcina as separate species. The morphological quence Analysis package (7) and a VAX computer. A contin- criterion of packet formation, however, proved to be unsuit- uous stretch of 1,343 bases was used in the analysis. Distances able for genus delineation as studies in the 1960s to 1970s were calculated by using the DNADIST program of the revealed major phenotypic heterogeneity within the genus. Phylogeny Inference package (9), and a bootstrapped phylo- Most Sarcina species have now been placed in other genera (i.e., the genus Micrococcus for some aerobic nonsporing species; the genus Sporosarcina for aerobic sporing species; the 100 C. limosum genus Methanosarcina for anaerobic methane fermenters; and c. histolyticum the genus Halococcus for obligate halophiles [3, 4]), and currently only two species, S. ventriculi and Sarcina maxima, are retained in the genus Sarcina (5). Studies in which Fox et C. cellulovorans al. (11) used 16s rRNA oligonucleotide cataloging revealed a possible phylogenetic affinity between S. ventriculi and some Clostridla 100 Group I species of the anaerobic spore-forming genus Clostridium (SAB [see reference 10 for definition] with Clostridium butyricum [the type species], Clostridiurn scatologenes, and Clostridium pasteurianum, 0.5 to 0.65). Oligonucleotide cataloging has in recent years been largely superseded by complete or partial 16s rRNA (or rRNA gene) sequencing. Complete (or nearly C. botulinum type E complete) sequences provide far more precision for determin- ing phylogenetic relationships (20). A large number of clos- tridial 16s rRNA sequences have been published in recent years (15,17,18), and these sequences now make it possible to C. mllagenovorans determine more precisely the phylogenetic affinities of the C. estertheticum sarcinas. In this paper we describe the 16s rRNA gene sequences of the type strains of S. ventriculi and S. maxima and the results of a comprehensive phylogenetic analysis of these organisms and the clostridia. S. ventriculi DSM 286T (T = type strain) and S. maxima - C. kluyveri DSM 316T were grown anaerobically in Sarcina broth (5 g of C. tetanomorphurn C. oceaniwm C. botulinum type A C. cochlearium * Corresponding author. Mailing address: Department of Microbi- C. malenominatum ology, Institute of Food Research, Earley Gate, Whiteknights Road, Reading RG6 2EF, Berkshire, United Kingdom. Phone: 44 734 FIG. 1. Unrooted phylogenetic tree showing the positions of S. 357224. Fax: 44 734 267917. Electronic mail address: willems@arcb. ventriculi and S. maxima within group I Clostridium. Bootstrap values afrc.ac.uk. greater than 90% are given at the branching points. 1591 592 REQUEST FOR AN OPINION INT. J. SYST.BACTERIOL. TABLE 1. Similarity values for the 16s rRNA genes of Sarcina species and their closest relatives % Similarity with: t w EMBL E Taxon accession .u .Y E no. 4 s f f 3 5 g 5 8 8 Sarcina ventriculi X76649 98.5 Clostridium acetobutylicum X68182 92.9 92.7 Clostridium aurantibutyricum X68183 92.9 92.3 95.9 Clostridium beijerinckii X68179 93.0 93.1 99.2 95.8 Clostridium botulinum type E X68170 92.9 92.8 95.8 95.0 96.6 Clostridium butyricum X68 177 93.3 93.3 97.4 95.2 97.6 96.2 Clostridium camis M59091 94.1 93.3 95.1 95.7 95.3 95.3 95.0 Clostridium paraperj%ngens M59102 94.4 94.0 95.3 96.3 95.3 95.1 95.7 96.0 Clostridium paraputnficum x73445 93.9 93.8 95.3 97.1 95.9 95.8 96.0 96.4 98.8 Clostridium perfrangens M59103 93.3 93.3 93.4 92.8 93.6 93.5 93.0 94.2 93.8 93.8 Clostridium puniceum x73444 93.4 93.2 97.1 94.5 97.4 96.0 96.9 95.3 95.1 94.4 93.0 The EMBL accession number of S. maxima is X76650. genetic tree (Fig. 1) was produced by using the NEIGHBOR, 1842 (12) and as such has nomenclatural priority over the DNABOOT, and CONSENSE programs of the same package. genus Clostridium (Prazmowski), which was described in 1880 The 16s rRNA gene sequences which we determined were (16). There is no question that nomenclatural rules are neces- deposited in the EMBL data library under accession numbers sary and should be followed in most cases. However, strict X76649 and X76650. adherence to nomenclatural priority would in this case result in The partial 16s rRNA gene sequences of S. ventriculi and S. the loss of the name Clustridium, with all Clustridium species maxima consisted of 1,461 and 1,399 nucleotides, respectively, becoming Sarcina species! Such a change would, in our opin- and exhibited 98.5% similarity (corresponding to 20 nucleotide ion, be quite unacceptable to the scientific community, as the differences). Sequence similarity calculations revealed that S. name Clostridium is widely used and the genus contains several ventriculi and S. maxima were highly related to group I important human and animal pathogens (e.g., Clustridium Clustridium of Johnson and Francis (13) (approximate 16s botulinum, Clustridium perfnngens, and Clostridium tetani). rRNA sequence similarity range, 89 to 94%). The similarity Abandoning the name Clustridium also makes no phenotypic values obtained with the closest relatives of both Sarcina sense and would cause unnecessary confusion as clostridial species, as calculated by using the GAP program of the species lack the typical parcel shape implied by the name Genetics Computer Group package, are shown in Table 1. Sarcina. Significantly lower levels of sequence relatedness (<85%) rRNA (or gene) sequencing is revolutionizing microbial were obtained with other clostridial lineages (data not shown). systematics and provides an immensly powerful method for The results of distance matrix analyses confirmed these affin- elucidating phylogenetic relationships. It is important that ities, with the two Sarcina species clustering well within the taxonomists capitalize on this revolution and do not shirk from confines of this major Clostridium group (Fig. 1). constructing more phylogenetically meaningful classification The genus Clustridium, as presently constituted, contains schemes. As the results of rRNA sequence analysis fundamen- more than 100 species and is phylogenetically extremely het- tally challenge many currently accepted classifications (includ- erogeneous. 16s rRNA sequencing has revealed that members ing our perception of which phenotypic traits are good indica- of the genus Clostridium belong to several major lines of tors of relatedness), a more pragmatic interpretation of the descent, some of which almost certainly represent new or rules of priority may become necessary in order to minimize distinct genera (15, 17, 18). Almost one-half of all currently nomenclatural confusion. We believe that a more phylogeneti- described clostridial species are members of a single clade, cally based classification of the clostridia is an achievable goal referred to as group I Clustridium of Johnson and Francis (13). for the next few years, with the group I organisms forming the The genus Clostridium is clearly in need of extensive taxonomic basis of a redefined genus Clostridium.From a purely practical revision, and there is a growing view (6, 15) that group I point of view, we feel that if this occurs, the rule of priority Clustridium, which includes the type species, C. butyricum, should be set aside and Sarcina species should be included in could form the nucleus of a redefined genus. Restricting the an emended genus Clustridium. We therefore request an genus Clostridium to the group I organisms would result in a opinion from the Judicial Commission as to whether it would genealogically coherent, albeit deep, genus and would do much be an acceptable option to conserve the generic name Clus- to resolve the phylogenetic absurdity of the present system. tridium Prazmowski 1880 (type species, C. butyricum Praz- Placement of S. ventriculi, the type species of the genus mowski 1880). Sarcina, in group I Clustridium, however, presents a serious After the submission of the manuscript for this paper, the nomenclatural problem for any such future proposed generic rRNA gene sequence of S. ventriculi GIFU 7886 was published emendation. The genus Sarcina (Goodsir) was proposed in by Ezaki et al.
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