Biomedical subjects

M D Collins

Publications and source records attributed to M D Collins.

At least 163 records · Page 9Linked to original sources

PubMed1996

Phylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences.

A molecular systematic investigation of members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces was performed by using 18S rRNA gene sequence analysis. Our comparative sequence analysis revealed that Brettanomyces anomalus and Brettanomyces bruxellensis were closely related to one another and also to their teleomorphs, Dekkera anomala and Dekkera bruxellensis, respectively. Together with Dekkera custersiana and Dekkera naardenensis, these four species formed a stable and distinct phylogenetic group. The three representative species of the genus Debaryomyces examined (viz., Debaryomyces castellii, Debaryomyces hansenii, and Debaryomyces udenii) were found to be genealogically highly related to each other and exhibited a specific phylogenetic affinity (level of sequence similarity, approximately 99.2%) with Candida guilliermondii (teleomorph, Pichia guilliermondii). Debaryomyces species and C. guilliermondii formed a distinct phylogenetic group, which displayed a significant association with a phylogenetically coherent cluster encompassing Lodderomyces elongisporus, Candida albicans, and four other Candida species. In contrast to the situation with the genera Brettanomyces and Debaryomyces, the genus Kluyveromyces displayed very marked phylogenetic heterogeneity. Kluyveromyces polysporus, the type species of the genus Kluyveromyces, and six other Kluyveromyces species (viz., Kluyveromyces africanus, Kluyveromyces delphensis, Kluyveromyces lodderae, Kluyveromyces thermotolerans, Kluyveromyces waltii, and Kluyveromyces yarrowii) were phylogenetically intermixed with species of the genera Zygosaccharomyces, Saccharomyces, and Torulaspora. In contrast, Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, Kluyveromyces wickerhamii, and three Kluyveromyces marxianus varieties, along with their anamorph, Candida kefyr, formed a highly stable monophyletic group worthy of separate generic status. Kluyveromyces blattae and Kluyveromyces phaffii formed two distinct phylogenetic lines that did not exhibit particularly close affinity with each other or other ascomycetous yeast genera. Our phylogenetic findings are discussed in the context of the results of other genotypic and phenotypic studies.

Ascomycota↗

PubMed1996

Actinobacillus delphinicola sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from sea mammals.

We performed phenotypic and phylogenetic studies of a gram-negative, rod-shaped bacterium isolated from cetaceans. The results of a 16S rRNA gene sequence analysis demonstrated that this bacterium represents a previously unknown line of descent in the family Pasteurellaceae. On the basis of the results of our phylogenetic analysis and phenotypic criteria, we propose that this organism should be classified as a new species, Actinobacillus delphinicola sp. nov. The type strain of A. delphinicola sp. nov. is strain NCTC 12870.

Actinobacillus↗

PubMed1996

Sanguibacter inulinus sp. nov.

Six strains of coryneform bacteria were isolated from blood samples obtained from healthy cows. Phenotypic and molecular genetic studies showed that these isolates represent a new species of the genus Sanguibacter, for which the name Sanguibacter inulinus is proposed. The type strain of S. inulinus is strain ST-50 (= NCFB 3024).

Actinomycetales↗

PubMed1996

Analysis of the beta' subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium.

rRNA sequencing has shown that leuconostocs comprise three distinct phylogenetic lineages which have been designated separate genera (viz., the genera Leuconostoc sensu stricto, Oenococcus, and Weissella). In addition, the 16S rRNA line formed by Oenococcus oeni (formerly Leuconostoc oenos) is exceptionally long; this fact, together with variations in the compositions of conserved positions in the 16S rRNA, has led to the hypothesis (D. Yang and C. R. Woese, Syst. Appl. Microbiol. 12:145-149, 1989) that this organism is a fast-evolving bacterium. Previous evidence that the leuconostocs should be divided into three genera and that O. oeni is an example of tachytelic evolution has come solely from rRNA analyses. In this study we seqenced the rpoC gene encoding the beta' subunit of DNA-dependent RNA polymerase of leuconostocs and performed a comparative phylogenetic analysis. The subdivision of the leuconostocs into three distinct lineages was confirmed by the rpoC gene data, but no evidence that indicated that O. oeni is evolving at an extraordinary rate was found. If O. oeni is truly tachytelic, then fast-evolving phenomena would be expected to occur throughout the whole genome, including this independent molecular chronometer.

Amino Acid Sequence↗

PubMed1996

Phylogenetic relationships of the genera Acetobacterium and Eubacterium sensu stricto and reclassification of Eubacterium alactolyticum as Pseudoramibacter alactolyticus gen. nov., comb. nov.

16S rRNA gene sequences of the type strains of the seven previously described Acetobacterium species were determined. The Acetobacterium species were found to form a tight phylogenetic cluster within the Clostridium subphylum of the gram-positive bacteria. Within this subphylum these organisms belong to cluster XV as defined by Collins et al. (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) together with Eubacterium alactolyticum barkeri, Eubacterium callanderi, and Eubacterium limosum. Our data indicate that Clostridium cluster XV consists of at least the following three genera: the genus Acetobacterium, the genus Eubacterium sensu stricto (comprising E. limosum, E. barkeri, and E. callanderi), and the genus Pseudoramibacter gen. nov., which is created for E. alactolyticum, which we reclassify as Pseudoramibacter alactolyticus comb. nov.

Base Sequence↗

PubMed1996

Organization and phylogenetic interrelationships of genes encoding components of the botulinum toxin complex in proteolytic Clostridium botulinum types A, B, and F: evidence of chimeric sequences in the gene encoding the nontoxic nonhemagglutinin component.

The cluster of genes encoding components of the botulinum neurotoxin (BoNT) complex was mapped in proteolytic (group I) Clostridium botulinum strains encoding BoNT types A, B, and F. Two different arrangements of genes were found: type A strain 62A and type B strain NCTC 7273 have similar organizations of genes encoding BoNT, the nontoxic nonhemagglutinin component (NTNH), hemagglutinin components, and P-21; type F strain Langeland has genes encoding BoNT, NTNH, and P-21, and a previously unidentified open reading frame encoding a protein of 416 amino acids. A group of type A strains typified by infant strain Kyoto-F, which is unlike type A strain 62A, lacks genes for hemagglutinin components and exhibits an organization similar to that of type F. Sequencing and pairwise analysis revealed the presence of possible chimeric sequences in some NTNH genes of proteolytic C. botulinum. Discordance in genealogical trees derived from different regions of the NTNH genes was observed which could be symptomatic of recombination and which may indicate that the NTNH gene represents a hot spot for such events within the cluster of genes encoding the BoNT complex. It is also evident that the phylogenetics of the NTNH gene, which is linked to the gene encoding BoNT, does not mirror the evolutionary history of the BoNT, upon which the C. botulinum species complex is defined and subdivided.

Amino Acid Sequence↗

PubMed1996

Phylogenetic characterization of a novel salt-tolerant Bacillus species: description of Bacillus dipsosauri sp. nov.

The taxonomic position of a novel halophilic endospore-forming bacterium previously isolated from a desert iguana was investigated by 16S rRNA gene sequencing. Comparative sequence analyses showed the unidentified bacterium to be phylogenetically loosely associated with some other spore-forming (Bacillus pantothenticus, Sporosarcina halophila) and non-spore-forming (Marinococcus albus) halotolerant bacteria. Based on the phenotypic and phylogenetic distinctiveness of the unidentified bacterium, it is proposed that it is classified in the genus Bacillus as a new species, Bacillus dipsosauri.

Animals↗

PubMed1996

Isolation of Arthrobacter spp. from clinical specimens and description of Arthrobacter cumminsii sp. nov. and Arthrobacter woluwensis sp. nov.

Arthrobacter spp. are very widely distributed in the environment (e.g., soil) but have not been described as causing disease in humans. Over a 6-year period, two reference laboratories isolated or received 11 strains which were eventually identified as belonging to the genus Arthrobacter. These strains had been initially identified as Centers for Disease Control and Prevention coryneform group B-1 and B-3 bacteria (whitishgrayish colonies of 2 mm or greater in diameter after 24 h of incubation, respiratory metabolism, absent or weak acid production from sugars, and hydrolysis of gelatin). However, chemotaxonomic investigations revealed lysine as the diamino acid of the cell wall and the presence of branched cellular fatty acids (with anteiso-pentadecanoic acid predominating) which was compatible with an assignment of the 11 isolates to the genus Arthrobacter only. Peptidoglycan and 16S rRNA gene sequence analyses demonstrated that three of the strains studied were representatives of a new Arthrobacter species for which the name Arthrobacter cumminsii sp. nov. is proposed and that one other strain represented a second new Arthrobacter species for which the name Arthrobacter woluwensis sp. nov. is proposed. This report is the first on the isolation of Arthrobacter spp. from clinical specimens.

Arthrobacter↗

PubMed1996

Most Corynebacterium xerosis strains identified in the routine clinical laboratory correspond to Corynebacterium amycolatum.

A comprehensive study was performed on 25 bacterial clinical isolates originally identified as Corynebacterium xerosis. Three reference strains of C. xerosis were also included in the study. On the basis of a variety of phenotypic characteristics tested, all strains could be divided into two separate clusters: reference strains ATCC 373 (the type strain of C. xerosis) and ATCC 7711 showed yellow-pigmented, dry, rough colonies, fermented 5-keto-gluconate, exhibited strong leucine arylamidase and alpha-glucosidase activities, produced lactate as the major end product of glucose metabolism, were susceptible to most of the 19 antimicrobial agents tested, and showed an inhibition zone around disks containing the vibriocidal compound O/129. In contrast, the remaining 26 strains including reference strain NCTC 7243 as well as all clinical isolates formed white-grayish, dry, slightly rough colonies, did not ferment 5-keto-gluconate, exhibited only weak leucine arylamidase and no alpha-glucosidase activity, produced large amounts of propionic acid as the end product of glucose metabolism, and were resistant to most antimicrobial agents tested, including O/129. Chemotaxonomic (cellular fatty acids, mycolic acids, and G+C content) and molecular genetic (16S rRNA gene sequence) investigations revealed that the strains of the second cluster unambiguously belonged to the species C. amycolatum. Our data suggest that most strains reported in the literature as C. xerosis are probably misidentified and correspond to C. amycolatum.

Bacterial Typing Techniques↗

PubMed1995

Estimating intracellular pH in developing rodent embryos using a computer imaging technique: changes in embryonic pH and proliferation rates following maternal treatment with acetazolamide.

Using the transplacental distribution of the weak acid 5,5-dimethyloxazolidine-2,4-dione (DMO), a computer assisted imaging technique has been developed to permit the estimation of intracellular pH (pHi) in very specific areas of the developing rodent embryo. The study reported here demonstrates the heterogeneity of radiolabeled DMO distribution in the developing mouse forelimb. The pattern of pHi distribution shifts from one of high pHi values in the proximal core of the mesoderm on day 10 of gestation to one of higher pHi values in the mesoderm just underlying the ectoderm on day 11. Studies [Scott et al. (1990) Toxicol. Appl. Pharmacol. 103:238-254] in which DMO concentration was monitored following treatment with acetazolamide or acetazolamide plus amiloride were done in whole embryo homogenates or pooled limb samples which allow for the calculation of an average pHi but may not reflect the pHi in very specific locations of the limb. Two hours after acetazolamide administration, the pHi pattern was not significantly changed from control. Intracellular pH was raised above control levels but was not significant statistically except in the peripheral mesoderm in the ventral third of the forelimb. Fifteen hours after acetazolamide treatment, there was a significant decrease in pHi values with no change in pattern. However, treatment with acetazolamide plus amiloride for 15 hr produced a marked reduction of pHi values throughout the forelimb bud. Changes in bromodeoxyuridine labeling index (an indication of proliferative activity) following treatment with acetazolamide or acetazolamide plus amiloride are reported. The combination treatment reduced the labeling index by approximately 15% below that of control embryos in the limb region where absence of digit(s) will occur. However, we found no overall correlation of proliferative rate and pHi of limb bud mesoderm in treated embryos. Consequently, we were unable to causally associate reduced pHi with decreased proliferative rate.

Abnormalities, Drug-Induced↗

PubMed1995

Single versus multiple dose administration of all-trans-retinoic acid during organogenesis: differential metabolism and transplacental kinetics in rat and rabbit.

Standard teratogenicity testing is usually performed by administration of a test compound daily throughout an extended period of organogenesis (e.g., between Days 6 and 15 in rat and 6 and 18 in rabbit). On the other hand, single dose experiments during a specific period were often demonstrated to be more effective in unveiling a particular teratogenic effect. We have assessed here if toxicokinetics is an important factor for the interpretation of the differences between two administration regimens of all-trans-retinoic acid (all-trans-RA) in two species. The transplacental pharmacokinetics of a low teratogenic dose of all-trans-RA administered orally were compared in a single versus multiple dose regimen in both the Wistar rat and the Swiss hare rabbit. In both species, the single dose animals were treated on Gestational Day 12, while the multiple dose animals received daily doses from Gestational Days 7 through 12. Pharmacokinetic profiles were determined for maternal plasma and embryo after dosing on Gestational Day 12 (for both the single and multiple dose regimens) and analyzed by reverse-phase HPLC. The dose used for both species was 6 mg/kg body wt/day which has recently been reported to be a marginal to low teratogenic dose when administered daily throughout organogenesis. In both rat and rabbit, the AUC of all-trans-retinoic acid in maternal plasma was much reduced (factor of 9 in the rat, factor of 2 in the rabbit) after multiple application as compared to the single administration, presumably due to enzyme induction. A similar, but not as pronounced effect was also observed in the embryo of both species. This diminished effect in the embryo indicates a relative increase of placental transfer at the lower maternal plasma concentration observed after multiple dosing, which may possibly be due to an increased availability of binding sites such as cytosolic retinoic acid binding protein and nuclear receptors in the embryo. In the rat, also the metabolite levels were reduced, while in the rabbit, the metabolites of the 13-cis-configuration were concomitantly increased. Our results suggest that multiple administration of a drug such as retinoic acid, which induces its own elimination pathways, results in substantially lowered drug levels in maternal plasma and embryo.(ABSTRACT TRUNCATED AT 400 WORDS)

Administration, Oral↗

PubMed1995

Developmental stage-associated differences in the transplacental distribution of 13-cis- and all-trans-retinoic acid as well as their glucuronides in rats and mice.

In mice and rats, 13-cis-retinoic acid (13-cis-RA) has a much lower teratogenic potency than all-trans-retinoic acid (all-trans-RA). Previous studies on Gestational Day (GD) 11 or 12 (in mice or rats, respectively) showed a limited transfer of 13-cis-RA to the embryo, in contrast to the efficient transplacental passage of all-trans-RA. In the present study we examined if the distribution between maternal circulation and embryo of 13-cis- and all-trans-RA as well as their metabolites is different at gestational times when the placenta is developing from a choriovitelline to a chorioallantoic type. In the first experiment, 13-cis-RA was administered orally to pregnant rats (75 mg/kg/day) daily, from either GD 7 to 12 or 11 to 16. In the second experiment, 13-cis-RA or all-trans-RA was given orally to pregnant mice once on either GD 11 or 14, at two dose levels (10 and 100 mg/kg). HPLC analysis of plasma and embryo samples collected at various time points post-treatment showed that 13-cis-RA was predominantly metabolized to its beta-glucuronide (13-cis-RAG) while all-trans-RA was primarily biotransformed to all-trans-4-oxo-RA and to a lesser extent to all-trans-RAG. 13-cis-RA showed a more efficient transplacental passage to the rat embryo on GD 16 than on GD 12, as indicated by higher ratios of embryonic to maternal plasma concentrations (E/M concentration ratio) on GD 16 vs. GD 12 and its E/M ratio of area-under-the-concentration-time-curve values (E/M AUC ratio; twofold higher on GD 16 vs. GD 12). In the mouse, the E/M concentration ratio of 13-cis-RA was significantly higher on GD 14 than on GD 11 only at the low dose. On the other hand, all-trans-RA and all-trans-4-oxo-RA showed an efficient transfer to the mouse embryo at both gestational times. In both species, 13-cis- and all-trans-RAG embryonic concentrations on the later gestational days exceeded significantly the corresponding ones on the earlier gestational days which resulted in far higher E/M concentration and AUC ratios for each of these metabolites on the later vs earlier gestational days. This may result from a more efficient placental transfer of the RAGs during later gestational stages and/or higher capacity of the late embryo or other conceptal tissues to biotransform RAs in situ to their glucuronides.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1995

Description of human-derived Centers for Disease Control coryneform group 2 bacteria as Actinomyces bernardiae sp. nov.

Biochemical, chemotaxonomic, and molecular methods were used to establish the precise taxonomic position of the Centers for Disease Control (CDC) coryneform group 2 bacteria. The results of a comparative 16S rRNA sequence analysis demonstrated that the CDC coryneform group 2 bacteria constitute a distinct species within the genus Actinomyces. Actinomyces pyogenes was found to be the closest genealogical relative of the CDC coryneform group 2 bacteria, although these taxa were readily distinguished from each other and other Actinomyces spp. by using phenotypic criteria. On the basis of our findings we propose the name Actinomyces bernardiae sp. nov. for the CDC coryneform group 2 bacteria. The type strain is DSM 9152 (CCUG 33419).

Actinomyces↗

PubMed1995

"Streptococcus milleri" strains displaying a gliding type of motility.

Isolates belonging to the "Streptococcus milleri" species group that appear to exhibit a gliding type of motility, which is expressed as spreading growth on certain types of agar media, are described. These strains resembled a biotype of "S. milleri" that is usually isolated from genitourinary sources and is notable for its ability to ferment a wide array of carbohydrates. This biotype, which is currently included in the species Streptococcus anginosus, has been implicated in cases of neonatal infection. The "S. milleri" isolates which we studied lacked any observable organelles of motility and gave negative results when they were tested in conventional motility test medium stab cultures. Colonies growing on certain agar media, however, spread over the surfaces of plates and increased in area with increasing time of incubation. Chocolate agar supported maximum spreading, while this characteristic was barely discernible on blood agar. Electron microscopy studies revealed that there was more production of extracellular glycocalyx by motile strains than by a nonmotile isolate having a similar biotype. The results of an analysis of 16S rRNA gene sequences suggested that the motile strains are closely related to S. anginosus and represent a distinct rRNA population within the "S. milleri" species complex.

Base Sequence↗

PubMed1995

Proposal to reclassify Leuconostoc oenos as Oenococcus oeni [corrig.] gen. nov., comb. nov..

Wine strains belonging to the genus Leuconostoc were classified as Leuconostoc oenos by Garvie in 1967, and this name was confirmed on the Approved Lists of Bacterial Names in 1980. L. oenos is distinguished from other Leuconostoc spp. by its growth in acidic media, by its requirement for a growth factor in tomato juice, and by a number of carbohydrate fermentation characteristics. In addition, the results of a total soluble cell protein analysis, an electrophoretic analysis of NAD-dependent D-(-)-lactate dehydrogenase, 6-phosphogluconate dehydrogenase, and alcohol dehydrogenase, and an analysis of cross-reactivity with anti-glucose-6-phosphate dehydrogenase and anti-NAD-dependent D-(-)-lactate dehydrogenase performed with other Leuconostoc spp. clearly indicated that L. oenos should be distinguished from the other Leuconostoc species. Phylogenetic studies, in particular 16S and 23S rRNA sequencing studies, have revealed that L. oenos represents a distinct subline that is separate from other Leuconostoc spp. and lactic acid bacteria. In view of the phenotypic and phylogenetic distinctiveness of L. oenos, we propose that this species should be assigned to a new genus as Oenococcus oeni [corrig.] gen. nov., comb. nov. The type strain of O. oeni is NCDO 1674 (= ATCC 23179).

DNA, Bacterial↗

PubMed1995

Phylogenetic placement of Dialister pneumosintes (formerly Bacteroides pneumosintes) within the Sporomusa subbranch of the Clostridium subphylum of the gram-positive bacteria.

The nucleotide sequence of the 16S rRNA gene of the type strain of Dialister pneumosintes was determined. Phylogenetic analysis revealed that this species belongs to the Sporomusa branch of the Clostridium subphylum of the gram-positive bacteria and should therefore be excluded from the family Bacteroidaceae. Within this branch, which encompasses several other gram-negative taxa, such as Acidaminococcus, Pectinatus, Phascolarcobacterium, Quinella, Selenomonas, and Zymophilus, Dialister showed a specific, albeit distant, affinity with the genera Megasphaera and Veillonella.

Bacteroidaceae↗

PubMed1995

Phylogenetic evidence that the gram-negative nonsporulating bacterium Tissierella (Bacteroides) praeacuta is a member of the Clostridium subphylum of the gram-positive bacteria and description of Tissierella creatinini sp. nov.

The 16S rRNA gene sequence of the type strain of Tissierella praeacuta (formerly Bacteroides praeacutus) was determined by PCR direct sequencing. A comparative sequence analysis showed that T. praeacuta is a member of the Clostridium subphylum of the gram-positive bacteria and has a close phylogenetic affinity with the species that form Clostridium cluster XII (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). Although T. praeacuta is gram negative and does not produce endospores, 16S rRNA sequence data showed that it is closely related genealogically (level of sequence similarity, 99.9%) to Clostridium hastiforme. On the basis of our results and the results of previous studies, a second species of Tissierella, Tissierella creatinini sp. nov., is described.

Amino Acids↗

PubMed1995

Phylogenetic analysis of Ruminococcus flavefaciens, the type species of the genus Ruminococcus, does not support the reclassification of Streptococcus hansenii and Peptostreptococcus productus as ruminococci.

The 16S rRNA gene sequence of the type strain of Ruminococcus flavefaciens, the type species of the genus Ruminococcus, was determined by PCR direct sequencing. A comparative sequence analysis showed that R. flavefaciens is phylogenetically related to a small cluster (cluster IV of Collins et al. [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]) of organisms which includes several Clostridium and Eubacterium species. R. flavefaciens was found to be phylogenetically only remotely related to Ruminococcus gnavus, Ruminococcus torques, Peptostreptococcus productus, and Streptococcus hansenii. These findings demonstrate that the genus Ruminococcus is not a monophyletic group, and the proposed transfer of P. productus and S. hansenii to this genus (T. Ezaki, N. Li, Y. Hashimoto, H. Miura, and H. Yamamoto, Int. J. Syst. Bacteriol. 44:130-136, 1994) is not supported.

Base Sequence↗