Lillian V. Holdeman

Some current concepts in intestinal bacteriology

Quantitative studies of the fecal flora of populations at different risk of colon cancer indicate that the relative proportions of some particular species of bacteria rather than of different genera of bacteria may be correlated with colon cancer incidence. Since the metabolic activity of different species in each genus varies widely, a shift in proportions of species could cause a major change in total metabolic activity in the individual. In samples taken from various areas of the intestinal tract and in scrapings from the intestinal wall, the composition of the flora remained relatively constant from the ascending colon to the rectum. Therefore, the bacteria in feces do reflect the flora of the large colon. The composition of the flora was not significantly affected by drastic changes in diet, but statistically significant shifts in the proportions of some species were noted in individuals under conditions of anger or fear stress. Although diet may not change the flora the individual maintains, the bacteria present may convert the different substrates provided by a high-fat diet as opposed to a high-fiber diet into metabolites that are potentially carcinogenic. The conversion of dietary components to carcinogenic compounds, identification of the bacteria capable of effecting such conversions, and the conditions favoring the proliferation of such bacteria will be investigated in greater detail.

New genus, coprococcus, twelve new species, and emended descriptions of four previously described species of bacteria from human feces.

A new genus of anaerobic cocci, Coprococcus, and 12 new species of anaerobes, Coprococcus eutactus, C. catus, C. comes, Ruminococcus callidus, R. torques, Streptococcus hansenii, Bacteroides eggerthii, Eubacterium eligens, E. formicigenerans, E. hallii, Lactobacillus rogosae, and Clostridium nexile, are described. Emended descriptions and proposed neotype strains for Streptococcus constellatus (Prevot) comb. nov., S. morbillorum (Prevot) comb. nov., S. intermedius Prevot, and Eubacterium biforme (Eggerth) Prevot are presented.

Emendation of Bacteroidaceae and Butyrivibrio and Descriptions of Desulfomonas gen. nov. and Ten New Species in the Genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus

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.

Description of Bacteroides loescheii sp. nov. and Emendation of the Descriptions of Bacteroides melaninogenicus (Oliver and Wherry) Roy and Kelly 1939 and Bacteroides denticola Shah and Collins 1981

Bacteroides loescheii, a new species from periodontal pockets and superficially cleaned tooth surfaces coronal to gingival margins and from various types of human infections, is described. Strains of B. loescheii are obligately anaerobic, gram-negative, usually pigmenting, nonmotile, nonsporeforming rods that do not grow well in 10% bile and that ferment carbohydrates. These strains previously were identified as Bacteroides melaninogenicus or Bacteroides oralis, but they have no deoxyribonucleic acid homology with the type strain of either of these two species. The type strain of B. loescheii is ATCC 15930. The descriptions of B. melaninogenicus and Bacteroides denticola are emended.

Descriptions of Eubacterium timidum sp. nov., Eubacterium brachy sp. nov., and Eubacterium nodatum sp. nov. Isolated from Human Periodontitis

Three new species of Eubacterium, E. timidum, E. brachy, and E. nodatum, which were isolated principally from subgingival areas associated with periodontitis, are described. All are anaerobic, gram-positive, non-saccharolytic rods. They are differentiated from each other and from other non-saccharolytic species of eubacteria by acid and gas products in broth cultures and by morphological and growth characteristics. The type strains for the species are as follows: E. timidum ATCC 33093; E. brachy, ATCC 33089; and E. nodatum, ATCC 33099. These species were detected in 35 to 42% of the subgingival samples examined and, where present, constituted 3 to 57% of the cultivable flora. Strains of these species were isolated only occasionally from the adjacent supragingival areas sampled.

Taxonomy of the Genus Veillonella Prévot

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.

Bacteroides oris and Bacteroides buccae New Species from Human Periodontitis and Other Human Infections

Bacteroides oris and B. buccae, two new species isolated from periodontal pockets and the superficially cleaned tooth surface coronal to the gingival margin, from various types of human infections, and from chicken intestinal contents are described. They were obligately anaerobic, gram-negative, nonpigmenting, nonmotile, non-spore-forming rods that did not grow well in 10% bile and that fermented carbohydrates. Although we had previously identified many of these strains as members of B. ruminicola subsp. brevis biovar (biotype) 3 (Holdeman et al. [ed.], Anaerobe Laboratory Manual, 4th ed., 1977), in the present study, we found that the strains had no deoxyribonucleic acid homology with the type strains of B. ruminicola subsp. ruminicola or B. ruminicola subsp. brevis. The strains also had no deoxyribonucleic acid homology with the type strain of B. oralis. ATCC 27518, which we deposited as representative of human isolates of B. ruminicola subsp. brevis biovar 3, is now identified as a strain of B. oris. The type strains of B. oris and B. buccae are B. oris ATCC 33573 and B. buccae ATCC 33574, respectively.

Fermentation Patterns of some Clostridium Species.

SUMMARY The present study of the fermentation characteristics of 20 species of clostridia has shown that the relative proportions and concentrations of the acids and alcohols produced by these cultures may be very useful in their characterization and identification. The chromatographic methods described are rapid and the patterns are highly reproducible among strains of the same species.

Bacteroides disiens sp. nov. and Bacteroides bivius sp. nov. from Human Clinical Infections

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.

Metabolism of primary bile acids by Clostridium perfringens

Abstract C. perfringens degraded chenodeoxycholic acid (CDC) into two major products: 7α-hydroxy-3-oxo-5β-cholanoic acid and 3β,7α-dihydroxy-5β-cholanoic acid, the latter appearing very quickly and the former very slowly in whole cell cultures. Yields of about 60 and 16% were obtained for the respective products. Both products, as substrates in C. perfringens cultures, were quickly transformed back to CDC (about 84%) and 3β,7α-dihydroxy-5β-cholanoic acid (about 16%), whereas 7α-hydroxy-3-oxo-5β-cholanoic acid was formed slowly (4–5 days). In contrast to CDC, cholic acid was not epimerized at 3α-OH position; however, 7α, 12α-dihydroxy-3-oxo-cholanoic acid was formed slowly. When 7α,12α-dihydroxy-3-oxo cholanoic acid was substrate, rapid quantitative reduction, back to cholic acid then slow oxidation back to the 3-oxo product was observed. Thirty-six strains of C. perfringens (18 from a culture collection and 18 isolated from human feces) were screened for 3α-OH epimerization and oxidation of the primary bile acids. All but three strains epimerized CDC (yields 14–20%), while none epimerized cholic acid. Oxidation at the 3 position varied from 0–30% for CDC and 0–90% for cholic acid. Cell-free preparations of C. perfringens in the presence of NADP produced both 3-oxo and 3β-hydroxyl products with CDC, but only the 3-oxo product with cholic acid; these activities were non-inducible. The authors propose that 3α-OH isomerization takes place early in log phase via a 3α- and 3β-hydroxysteroid dehydrogenase (HSDH) system. Accumulation of 3-oxo product occurs late in stationary phase as the Redox (Eh) value rises above —100 mV.