- Volume 46, Issue 1, 1996

We found that Thermosipho africanus was able to ferment d-glucose, d-ribose, Maltose, and starch, while d-galactose, fructose, and sucrose were utilized poorly. Acetate, H2, and CO2, as well as small amounts of ethanol and lactate, were end products of glucose metabolism in this organism. The presence of thiosulfate as an electron acceptor greatly improved growth and increased acetate production from the sugars. The genus Thermosipho is the only genus in the order Thermotogales that has been described as a non-carbohydrate fermenter. We propose that the description of the genus Thermosipho be emended because the only species in this genus, T. africanus, is a carbohydrate fermenter that is able to utilize thiosulfate as an electron acceptor.

Mycoplasma hyopneumoniae is the primary agent of mycoplasmal pneumonia in swine. In this study we performed an arbitrarily primed PCR (AP-PCR) analysis, in which low-stringency amplification with a single primer was used, to investigate genetic variability in M. hyopneumoniae strains and field isolates. We performed preliminary experiments to examine the efficacy of 40 different 10-mer oligonucleotides for priming an AP-PCR with M. hyopneumoniae JT (T = type strain) chromosomal DNA. On the basis of our results, we selected primers OPA-3, OPA-17, and OPB-10 for use in an analysis performed with 23 field isolates. The most informative results were obtained with primer OPA-3. A total of 21 of 23 clinical isolates produced multiband patterns with this primer, while 2 isolates failed to produce any detectable bands. Our data show that M. hyopneumoniae is genetically diverse and that M. hyopneumoniae strains can be divided into at least six epidemiological subgroups on the basis of AP-PCR results.

A DNA sequence analysis of the omp2 locus of Brucella type strains revealed nucleotide differences that can be used for species identification. We developed specific probes which were used to verify the observed differences among the type strains following PCR amplification of portions of the omp2 locus.

On the basis of partial 16S rRNA gene sequences and the results of Southern blot analyses, we confirmed the division of the genus Mobiluncus into the species Mobiluncus curtisii and Mobiluncus mulieris. Division of M. curtisii into M. curtisii subsp. curtisii and M. curtisii subsp. holmesii was not supported by our data.

The type strain of Lactobacillus casei subsp. casei (ATCC 393) exhibits low levels of DNA homology with other strains of L. casei subsp. casei (8 to 46%) and strains of Lactobacillus paracasei (30 to 50%), but exhibits a level of DNA similarity of 80% with Lactobacillus rhamnosus ATCC 15820, the original type strain of “Lactobacterium zeae” Kuznetsov 1959. Strains ATCC 393T (T = type strain) and ATCC 15820T are members of one protein profile cluster that is separate from the other Lactobacillus spp. The randomly amplified polymorphic DNA PCR profile of strain ATCC 393T is also different from the profiles obtained for the other species. L. casei ATCC 334T is genetically closely related to L. casei subsp. casei strains (71 to 97%) and L. paracasei strains (71 to 91%), is a member of the same protein profile cluster as these organisms, and shares several DNA amplicons with L. paracasei strains. On the basis of these results, we propose that L. casei subsp. casei ATCC 393T L. rhamnosus ATCC 15820 should be reclassified as members of Lactobacillus zeae nom. rev. (type strain, ATCC 15820), that strain ATCC 334 should be designated the neotype strain of L. casei subsp. casei, and that the name L. paracasei should be rejected.

In order to develop a PCR method to detect Fusobacterium prausnitzii in human feces and to clarify the phylogenetic position of this species, its 16S rRNA gene sequence was determined. The sequence described in this paper is different from the 16S rRNA gene sequence of F. prausnitzii in the GenBank database (accession number M58682). A PCR assay based on the new sequence is specific for F. prausnitzii, and the results of this assay confirmed that F. prausnitzii is the most common species in human feces. However, a PCR assay based on the original GenBank sequence was negative when it was performed with two strains of F. prausnitzii obtained from the American Type Culture Collection. A phylogenetic tree based on the new 16S rRNA gene sequence was constructed. On this tree F. prausnitzii was not a member of the Fusobacterium group but was closer to some Eubacterium spp. and located between Clostridium “clusters III and IV” (M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812–826, 1994).

“Candidatus Microthrix parvicella” is a filamentous bacterium that grows with great difficulty in cultures from the mixed liquor of activated sludge sewage treatment plants. It is gram positive, and the ultrastructure of its cell walls has been determined to be of the gram-positive type by electron microscopical examination. Phylogenetically, it is a deep-branching member of the subphylum actinomycetes within the gram-positive phylum of the domain Bacteria. As for phenotypic features, it is known that the organism contains polyphosphate inclusions and that it is catalase positive. In mixed cultures in activated sludge plants and in pure culture in the laboratory, it has a characteristic and distinctive winding filamentous morphology, with filaments hundreds of micrometers long.

The specific epithet of Halobacterium salinarium is a grammatically incorrect form for the genitive of salinae (salt works). Therefore, we propose that the name of the type species of the genus Halobacterium should be changed to Halobacterium salinarum nom. corrig. This species includes strains often designated Halobacterium halobium or Halobacterium cutirubrum.

The phylogenetic position of Methanopyrus kandleri has been difficult to determine because reconstructions of phylogenetic trees based on rRNA sequences have been ambiguous. The most probable trees determined by most algorithms place the genus Methanopyrus at the base of a group that includes the halobacteria and the methanogens and their relatives, although occasionally some algorithms place this genus near the eocytes (the hyperthermophilic, sulfur-metabolizing prokaryotes), suggesting that it may belong to this lineage. In order to resolve the phylogeny of the genus Methanopyrus, we determined the sequence of an informative region of elongation factor 1-alpha that contains an 11-amino-acid insertion in eocytes and eukaryotes which is replaced by a 4-amino-acid insertion in methanogens, halobacteria, and eubacteria. On the basis of the results of our elongation factor 1-alpha gene analysis, we concluded that the genus Methanopyrus diverged from the eocyte branch before the eukaryotic and eocyte lineages separated and therefore is not an eocyte.

Analyses of the sequences of the small-subunit (18S) rRNA gene and two internal transcribed spacers (ITSs), ITS1 and ITS2, revealed that members of the yeast genera Torulaspora and Zygosaccharomyces are phylogenetically intermixed. Despite some minor differences in 18S rRNA-, ITS1-, and ITS2-derived trees, in general the patterns of the relationships inferred from the three chronometers were in good agreement. The ITS sequences of Torulaspora and Zygosaccharomyces species exhibited far greater interspecies differences than the 18S rRNA sequences and were better than 18S rRNA sequences for measuring close genealogical relationships. Despite the existence of interstrain ITS sequence variation in some species, it is possible to identify conserved regions in both ITSs that are useful in species differentiation.

A study of DNA reassociation kinetics and electrophoretic karyotypes of several strains classified as Saccharomyces castellii, Saccharomyces dairensis, and Pachytichospora transvaalensis strains revealed that the group included members of at least five distinct species. Two of the four strains classified as P. transvaalensis exhibited very high levels of DNA sequence homology with the type strain of S. castellii, while the type strain and another strain demonstrated intermediate levels of relatedness to the type strains of the unrelated taxa S. castellii and S. dairensis. Five strains that were classified as S. diarensis strains were not related to the type strains of the taxa studied. Two of these strains exhibited intermediate relatedness (65% base sequence homology), while another pair exhibited a level of DNA reassociation of 97%. The remaining strain was distinct from all the other strains studied on the basis of both DNA base sequences and electrophoretic karyotype data.

The type strains and other strains of the phenotypically similar taxa Saccharomyces castellii Capriotti, Saccharomyces dairensis Naganishi, and Pachytichospora transvaalensis van der Walt were studied by comparing the ascospore morphologies of these organisms by examining ultrathin sections by transmission electron microscopy. The results of this study and another investigation of DNA base sequence homology demonstrated that the monotypic genus Pachytichospora van der Walt is invalid. We propose that the species Saccharomyces transvaalensis van der Walt should be reinstated.

Molecular and chemical taxonomic characteristics, including DNA base composition, electrophoretic karyotype, restriction fragment length polymorphism of genes coding for rRNA, cellular fatty acid composition, and ubiquinone systems, were studied for 19 strains of Candida boidinii Ramirez. Electrophoretic karyotype and restriction fragment length polymorphism demonstrated marked differences among these strains. A combination of molecular and chemical analyses can serve as a reliable tool for culture authentication and quality control of industrial strains.