Search

The best-known acetone-butanol (solvent)-producing bacterium is the Weizmann organism, Clostridium acetobutylicum, which was used for starch-based industrial fermentation. In the past two decades, cultures of "C. acetobutylicum" from various culture collections have included organisms that were isolated for sugar (molasses)-based industrial solvent production. Recent biochemical and genetic studies have revealed significant differences among some of these "C. acetobutylicum" strains. We used DNA-DNA reassociation to analyze 39 cultures of "C. acetobutylicum" and phenotypically similar organisms from major collections. The results of this study clearly identified four groups intergroup reassociation values of less than 30%. All of the intragroup values except the value for one strain were 68% or more, which supported species status for each group. The C. acetobutylicum group (with ATCC 824 as the type strain) consisted of 17 cultures and had average reassociation values of 10% with the other three groups. All strains of C. acetobutylicum produced riboflavin in milk, and the cultures were bright yellow, which is useful for differentiating this species from the other three groups. The Clostridium beijerinckii group (with VPI 5481 [= ATCC 25752] as the type strain) consisted of 16 cultures and included strains NCIMB 8052 and NCP 270. Strains NCP 262 and NRRL B643 constituted the third group, whereas strain N1-4 ("Clostridium saccharoperbutylacetonicum") and its derivative, strain N1-4081, formed the fourth group. At present, the last two groups are each represented by only one independent strain; definitive descriptions of these two groups as two new or revived species will require further phenotypic characterization, as well as identification of additional strains. C. beijerinckii NCP 270, Clostridium sp. strain NRRL B643, and "C. saccharoperbutylacetonicum" were used in industrial solvent production from molasses, which confirms that the new organisms used for the sugar-based processes are distinct from C. acetobutylicum.

DNAs of type strains and representative members of Actinomyces groups from the human periodontal flora and from other habitats were compared by using the S1 nuclease procedure to determine their genetic relatedness. One rather common group from the human periodontal flora, previously called “Actinomyces D08,” is phenotypically distinct from, and genetically unrelated to, previously described species. We propose the name Actinomyces georgiae for this organism; the type strain is strain ATCC 49285. Another common group from the human periodontal flora is Actinomyces israelii serotype II, which was found to be genetically distinct from the type strain of A. israelii (serotype I) and from other previously described species of Actinomyces. We propose the name Actinomyces gerencseriae for this organism; the type strain is strain ATCC 23860. A. naeslundii serotype I strains were distinct from the other strains studied. A separate genospecies which included strains of A. naeslundii serotypes II and III and A. viscosus serotype II was delineated. Strains of Actinomyces serotype WVA 963 constitute an additional distinct genospecies. Because there are no reliable phenotypic tests, other than serological analyses, to differentiate Actinomyces serotype WVA 963 and the two genospecies of A. naeslundii, no taxonomic changes are proposed for these three genospecies.

Bacillus sphaericus strains isolated on the basis of pathogenicity for mosquito larvae and strains isolated on the basis of a reaction with a B. sphaericus DNA homology group IIA 16S rRNA probe were analyzed for DNA similarity. All of the pathogens belonged to homology group IIA, but this group also contained nonpathogens. It appears inappropriate to designate this homology group a species based solely upon pathogenicity.

Clostridium putrificum (Trevisan 1889) Reddish and Rettger 1922; Clostridium botulinum (van Ermengem 1896) Bergey, Harrison, Breed, Hammer, and Huntoon 1923; and Clostridium sporogenes (Mechnikoff 1908) Bergey, Harrison, Breed, Hammer, and Huntoon 1923 are genetically related at the species level. We propose rejection of the name C. putrificum (which has priority) and conservation of the name C. botulinum on the basis of Rules 23a and 56a of the International Code of Nomenclature of Bacteria and conservation of the name C. sporogenes for nontoxigenic strains according to Rules 23a and 56b.

The type strain of Selenomonas sputigena (Flugge) Boskamp 1922, 70, the type species of the genus Selenomonas, is strain VPI 10068 (= ATCC 33150). This strain was a reference strain that was arbitrarily designated as the type strain on the 1980 Approved Lists of Bacterial Names before adequate documentation of its characteristics. It is not an original strain of the author of the species; subsequent examination has indicated that it almost certainly is not representative of the species described by Boskamp or by Flugge (P =

Deoxyribonucleic acid homology studies of 66 strains formerly classified as Bacteroides melaninogenicus subsp. intermedius showed two distinct groups with negligible intergroup homology. The larger group, with homology to the type strain of B. melaninogenicus subsp. intermedius, is designated Bacteroides intermedius, and the description of the taxon is emended. The other deoxyribonucleic acid homology group, which includes strains that differ from B. intermedius in not fermenting sucrose or producing indole, is designated Bacteroides corporis sp. nov.; ATCC 33547T (= VPI 9342) is the type strain. Strains of B. intermedius and B. corporis do not ferment lactose, as strains of B. melaninogenicus, Bacteroides loescheii, and Bacteroides denticola do. Strain ATCC 29147T is designated the type strain of Bacteroides levii sp. nov. This organism is a pigmenting bacteroides whose strains have been isolated from cattle and include the LEV strain (previously called B. melaninogenicus or “B. melaninogenicus subsp. levii”). Phenotypic characteristics useful in differentiating among nine species that formerly have been included in or identified as B. melaninogenicus are listed.

We determined the levels of ribosomal ribonucleic acid similarity among 30 Bacteroides species. The ribosomal ribonucleic acid homology values (determined by using the membrane competition method and both 16S and 23S ribosomal ribonucleic acid subunits) ranged from 100 to 4%. The organisms presently placed in the genus Bacteroides represent a major phylogenetic unit, as shown by the sequence diversity of the ribosomal ribonucleic acid cistrons among the species. There were three major clusters of species, which had intercluster homology values of 20 to 30%. The first cluster consisted of Bacteroides fragilis and nine other saccharolytic species which are common fecal organisms. The second cluster contained Bacteroides melanogenicus and 11 other moderately saccharolytic species, many of which are commonly isolated from human oral cavities. The third, rather heterogeneous cluster contained Bacteroides asaccharolyticus and four other mostly asaccharolytic species.

Bacteroides disiens sp. nov. and Bacteroides bivius sp. nov., both isolated from human clinical specimens, are described. They are species of obligately anaerobic, nonsporeforming, nonmotile, nonpigmenting, gram-negative rods that produce succinic and acetic acids (often with traces of isobutyric, isovaleric, and lactic acids) from peptone-yeast-glucose cultures. Gelatin, milk, casein, and meat are digested. Glucose, maltose, and starch, but not sucrose, are fermented. Most strains of B. bivius also ferment lactose. Hemin is required for growth. Strains of these species are phenotypically similar to those of B. melaninogenicus subsp. intermedius except that they do not form pigmented colonies. However, they do not show a high level of deoxyribonucleic acid/deoxyribonucleic acid homology with B. melaninogenicus subsp. intermedius or with each other. ATCC 29426 (= VPI 8057) is designated the type strain of B. disiens, and ATCC 29303 (= VPI 6822) is designated the type strain of B. bivius.

The phylogenetic relationships among seven strains of methylotrophic methane-producing bacteria were determined by ribosomal ribonucleic acid hybridization and deoxyribonucleic acid homology techniques. The strains tested had deoxyribonucleic acid guanine-plus-cytosine contents of 39 to 43 mol% and represented a diversity of phenotypic characteristics. Our results indicate that these strains should be divided into six species within the genera Methanosarcina, Methanolobus, and Methanococcoides. The genus Methanosarcina includes Methanosarcina barkeri strains MS and 227, Methanosarcina sp. strain TM-1, Methanosarcina acetivorans strain C2A, and Methanosarcina mazei strain S-6. The genus Methanolobus is represented by Methanolobus tindarius strain Tindari 3, and the genus Methanococcoides is represented by Methanococcoides methylutens strain TMA-10. Despite phenotypic similarities between Methanolobus tindarius and Methanococcoides methylutens, we propose that these species remain in separate genera based on differences in ribosomal ribonucleic acid homology and fractional differences in midpoint temperatures. The divisions indicated by deoxyribonucleic acid homology experiments complemented the ribosomal ribonucleic acid hybridization results. Phenotypic characteristics were consistent with these phylogenetic divisions; an apparent exception was cell wall composition, which is a conserved trait. Methanosarcina acetivorans had only a thin protein cell wall, but all other strans of Methanosarcina previously studied have been reported to have heteropolysaccharide cell walls. We present evidence which indicates that a protein component may be associated with the heteropolysaccharide cell wall of Methanosarcina barkeri strain 227.

Five new species of motile and nonsporeforming anaerobic gram-negative rods that have deoxyribonucleic acids with guanine-plus-cytosine contents of 56 to 58 mol%, produce major amounts of propionic and acetic acids, and were isolated from the human gingival crevice are described: Selenomonas noxia with ATCC 43542 as the type strain, Selenomonas flueggei with ATCC 43531 as the type strain, Selenomonas infelix with ATCC 43532 as the type strain, Selenomonas dianae with ATCC 43527 as the type strain, and Selenomonas artemidis with ATCC 43528 as the type strain.

The genetic relatedness of 62 strains of Bacillus sphaericus, 4 strains of B. pasteurii, 6 strains of B. brevis, and 1 strain each of B. globisporus and B. aminovorans was examined by deoxyribonucleic acid (DNA) homology. Five homology groups were identified, and they contained all but 12 of the B. sphaericus strains. Intergroup homologies ranged from about 20 to 40% except for groups III and IV, which had 50 to 60% intergroup homology. Although a few strains within some groups had 63 to 69% homology to the reference strain, most strains were in the 70 to 90% range. Homology group I contained the type of strain of B. sphaericus, ATCC 14577, and three other strains. Homology group II was subdivided into groups IIA and IIB, the former containing all of the strains found to be pathogenic for mosquito larvae. Although none of the physiological characteristics or combination of characteristics examined allowed the complete differentiation of strains into the appropriate homology groups, the strains of group I could be distinguished from those of group IIA-IIB. The strains of group IIA could be distinguished from all others by mosquito pathogenicity. The B. pasteurii strains formed a distinct homology group, although the guanine plus cystosine contents of their DNAs fell within the range of 34 to 37 mol% found for the 45 strains of B. sphaericus examined for this property. The B. brevis strains possessed a higher guanine plus cystosine content, and their DNAs were unrelated to the DNAs of the B. sphaericus reference strains tested.

The phylogenetic relationships of all species in the genus Campylobacter, Wolinella succinogenes, and other gram-negative bacteria were determined by comparison of partial 16S ribosomal ribonucleic acid sequences. The results of this study indicate that species now recognized in the genus Campylobacter make up three separate ribosomal ribonucleic acid sequence homology groups. Homology group I contains the following true Campylobacter species: Campylobacter fetus (type species), Campylobacter coli, Campylobacter jejuni, Campylobacter laridis, Campylobacter hyointestinalis, Campylobacter concisus, Campylobacter mucosalis, Campylobacter sputorum, and “Campylobacter upsaliensis” (CNW strains). “Campylobacter cinaedi,” “Campylobacter fennelliae,” Campylobacter pylori, and W. succinogenes constitute homology group II. Homology group III contains Campylobacter cryaerophila and Campylobacter nitrofigilis. We consider the three homology groups to represent separate genera. However, at present, easily determinable phenotypic characteristics needed to clearly differentiate them are not apparent. The three homology groups are only distantly related to representatives of the alpha, beta, and gamma branches of the purple bacteria, indicating that these bacteria do not belong to any previously defined branch of this phylum.

Seven strains of Campylobacter sputorum subsp. mucosalis, reference strains of Campylobacter fetus, Campylobacter jejuni, Campylobacter coli, Campylobacter laridis, “Campylobacter hyointestinalis,” “Campylobacter fecalis,” C. sputorum subsp. sputorum, C. sputorum subsp. bubulus, and Campylobacter nitrofigilis, aerotolerant Campylobacter sp. strain 02790, and catalase-negative or weakly catalase-positive strain CG-1 were compared with C. sputorum subsp. mucosalis type strain NCTC 11000 in deoxyribonucleic acid hybridization experiments. Strain NCTC 11000T(T = type strain) showed a high level of deoxyribonucleic acid homology with all of the C. sputorum subsp. mucosalis strains tested, but no significant homology with any of the other reference strains used, including C. sputorum subsp. sputorum and C. sputorum subsp. bubulus strains. Based on these observations, we propose that C. sputorum subsp. mucosalis be reclassified as Campylobacter mucosalis comb. nov.

Strains of the genus Veillonella were compared by ribosomal ribonucleic acid homology (16S and 23S). The strains examined represented all species in the genus, as well as several unnamed organisms which had negligible deoxyribonucleic acid homology with each other or with any of the named species. The organisms which we studied formed three clusters with average intracluster homology values of 90 to 100% and an average intercluster homology value of 60 to 70%. Veillonella parvula, Veillonella dispar, Veillonella atypica, Veillonella rodentium, and Veillonella caviae belonged to one cluster. Veillonella ratti, Veillonella criceti, and strains VPI 12095, VPI 1148B, and VPI 7944 belonged to a second cluster, whereas the two strains belonging to the “3312A” homology group represented the third cluster. Although some of the Veillonella species, as defined by deoxyribonucleic acid homology, are associated with specific host animals, this relationship does not appear to extend to the ribosomal ribonucleic acid homology clusters. For example, strains of V. rodentium and V. criceti were isolated exclusively from hamsters but belonged to separate ribosomal ribonucleic acid homology clusters.

The family Bacteroidaceae is emended to include bacteria that are monotrichous or lophotrichous. The genus Butyrivibrio is emended to include lophotrichous bacteria. Desulfomonas, a new genus of nonmotile, nonsporeforming, gram-negative, anaerobic, sulfate-reducing rods, and 10 new species of anaerobes, Desulfomonas pigra, Butyrivibrio crossotus, Ruminococcus gnavus, R. lactaris, R. obeum, Eubacterium dolichum, E. hadrum, E. ramulus, E. siraeum, and Clostridium leptum, are described. These species have been isolated from human intestinal contents or from human feces. The type strains of these species are ATCC 29098, 29175, 29149, 29176, 29174, 29143, 29173, 29099, 29066, and 29065, respectively.

Deoxyribonucleic acid similarity experiments in which the S1 nuclease methodology was used were performed on strains of Pseudomonas species, including some that had not been previously subjected to similarity measurements. The results obtained with this technique confirmed and expanded previous observations on the low levels of deoxyribonucleic acid similarity among species of the genus as determined by membrane competition experiments. A general discussion of the results and nomenclatural status of some of the species is included.

Results of deoxyribonucleic acid homology studies of 116 strains of Veillonella Prevot, representing the two species and seven subspecies currently recognized in this genus, showed seven deoxyribonucleic acid homology groups distinct at the species level. Because the type strains of V. parvula subsp. parvula and V. alcalescens subsp. alcalescens had high homology, we regard V. alcalescens Prevot 1933 as a later subjective synonym of V. parvula (Veillon and Zuber, 1896) Prevot 1933. The species V. parvula, V. dispar (Rogosa) comb. nov., V. atypica (Rogosa) comb. nov., V. rodentium (Rogosa) comb. nov., V. ratti (Rogosa) comb. nov., V. criceti (Rogosa) comb. nov., and V. caviae sp. nov. (type strain, ATCC 33540) are recognized. Because most strains of V. criceti produced acid in peptone-yeast extract-fructose media, the genus description is emended to include strains that ferment fructose.

The organisms currently recognized as subspecies of Bacteroides fragilis have been shown to be genetically distinct. Species rank is therefore restored to these organisms, and type or neotype strains have been selected for the five species described. ATCC 25285 (= NCTC 9343) is designated the neotype strain of Bacteroides fragilis (Veillon and Zuber) Castellani and Chalmers; ATCC 29184 (= strain Werner E50 = NCTC 10582) is designated the neotype strain of Bacteroides thetaiotaomicron (Distaso) Castellani and Chalmers; ATCC 8503 is designated the type strain of Bacteroides distasonis Eggerth and Gagnon; ATCC 8483 is designated the type strain of Bacteroides ovatus Eggerth and Gagnon; and ATCC 8482 is designated the type strain of Bacteroides vulgatus Eggerth and Gagnon. Characteristics of these strains are presented.

A new species, Treponema socranskii, and three new subspecies, T. socranskii subsp. socranskii, T. socranskii subsp. buccale, and T. socranskii subsp. paredis, which were isolated from supragingival and subgingival samples from patients with periodontitis and from patients with experimental gingivitis, are described. These organisms are treponemes that ferment carbohydrates and require rumen fluid or shortchain volatile fatty acids for growth. Fermentable carbohydrates are required as an energy source. The major products of fermentation are acetic, lactic, and succinic acids. Trace amounts of formic acid are also produced. The level of deoxyribonucleic acid-deoxyribonucleic acid homology within each subspecies is greater than 80%, whereas the level of homology between subspecies is about 60%. The average guanineplus-cytosine content of the deoxyribonucleic acid is 51 ± 1 mol%. The type strain of T. socranskii is strain ATCC 35536 (= VPI DR56BRIII6); the type strain of T. socranskii subsp. buccale is strain ATCC 35534 (= VPI D2B8); and the type strain T. socranskii subsp. paredis is strain ATCC 35535 (= VPI D46CPE1).

The soluble cellular proteins of strains of Peptococcus magnus and Peptostreptococcus micros were examined by polyacrylamide gel electrophoresis. The protein patterns were distinctive and repeatable, and the two species could be separated redily. The protein pattern of strain ATCC 23195, the type strain of Peptococcus glycinophilus (Cardon and Barker 1946) Douglas 1957, was identical to that of strain ATCC 33270 (= VPI 5464), the type strain of Peptostreptococcus micros (Prevot 1933) Smith 1957. Because these two strains were 84% homologous as determined by deoxyribonucleic acid-deoxyribonucleic acid homology experiments, the name Peptococcus glycinophilus is a later subjective synonym of Peptostreptococcus micros. Preliminary results indicated that ”Peptococcus variabilis“ (Foubert and Douglas 1948) Douglas 1957 may be a valid species, but reinstatement is not proposed at this time.

Deoxyribonucleic acid homology experiments among representatives of the clostridia and anaerobic corynebacteria generally correlate with the sugar composition and the isomeric form of diaminopimelic acid found in the cell walls and with the serological reactions. These correlations appear to be unique for a given group of bacteria and cannot be directly extended to others.

Nucleic acid homology studies are providing a common base for establishing bacterial groups. Few phenotypic characteristics have consistently correlated with homology data among the various groups of organisms that we have investigated. However, there are correlations that are specific for a given group of bacteria such that nucleic-acid homology data can be used to select those phenotypic properties that will be most useful for identification and taxonomic purposes.

Three new saccharolytic Bacteroides species that have DNAs with guanine-plus-cytosine contents of 40 to 46 mol%, produce major amounts of succinate, and were isolated principally from human feces are described: Bacteroides caccae, with ATCC 43185 as the type strain; B. merdae, with ATCC 43184 as the type strain; and B. stercoris, with ATCC 43183 as the type strain. These groups previously have been referred to as the “3452A,” “T4-1,” and “subsp. a” groups, respectively.

The type strain of Lactobacillus crispatus (VPI 3199, parent strain of strain ATCC 33820) and the deoxyribonucleic acid homology reference strain of “Lactobacillus acidophilus” group A2 (strain ATCC 33197) have 100% deoxyribonucleic acid homology. L. crispatus and strains in “L. acidophilus” group A2 also produce similar polyacrylamide gel electrophoresis patterns of soluble cellular proteins and are similar in other phenotypic characteristics. Therefore, the group A2 strains are members of the species L. crispatus (Brygoo and Aladame 1953) Moore and Holdeman 1970.

Comparisons of deoxyribonucleic acid base sequence homology and phenotypic properties of Capnocytophaga gingivalis and Cytophaga sp. DR2001 and DR2002 revealed that the three strains belonged to the same species but that the original species description was not accurate. An emended description of C. gingivalis is presented.

Campylobacter sputorum biovar sputorum ATCC 35980 is designated the neotype strain of the species.

The type strain of Bacteroides pentosaceus Shah and Collins and the type strain of Bacteroides buccae Holdeman et al. have more than 80% deoxyribonucleic acid homology with the type strain of Bacteroides capillus Kornman and Holt, and therefore the three names are subjective synonyms. Since B. buccae Holdeman et al. was the first validly published name applied to this taxon, B. capillus and B. pentosaceus are later synonyms of B. buccae.