Fermentation of non-digestible oligosaccharides by human colonic bacteria.
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Animals↗
Biomedical subjects
A Willems
Publications and source records attributed to A Willems.
Phylogenetic analysis of Butyrivibrio strains reveals three distinct groups of species within the Clostridium subphylum of the gram-positive bacteria.
The phylogenetic positions of 40 Butyrivibrio strains were determined by performing a comparative sequence analysis of the 16S rRNA genes of these organisms. We found that all of the strains which we studied belong to cluster XIVa (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 the Clostridium subphylum of the gram-positive bacteria, which also includes several Clostridium, Coprococcus, Eubacterium, and Ruminococcus species. We also found that the Butyrivibrio strains which we examined were genotypically heterogeneous and exhibited 12 distinct rRNA sequence types. The 12 rRNA sequence types formed three distinct lineages in cluster XIVa, which were separate from each other and from all other species belonging to this cluster. One lineage consisted of strains which exhibited a single rRNA type and corresponded to the species Butyrivibrio crossotus. The second lineage consisted of 12 strains designated Butyrivibrio fibrisolvens which exhibited seven distinct rRNA sequence types. The type strain of B. fibrisolvens was a member of this lineage, but its position was peripheral. The third lineage comprised 26 B. fibrisolvens strains which exhibited four distinct rRNA sequence types. Tree topology and sequence divergence considerations indicated that the three lineages correspond to three separate genera and that the genus Butyrivibrio should be restricted to the group that contains the type strain of B. fibrisolvens.
Base Sequence↗
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↗
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↗
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↗
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↗
Reclassification of Oribaculum catoniae (Moore and Moore 1994) as Porphyromonas catoniae comb. nov. and emendation of the genus Porphyromonas.
A partial 16S rRNA gene sequence of the type strain of Oribaculum catoniae was determined by using PCR direct sequencing. A comparative sequence analysis demonstrated that this species, although saccharolytic, is phylogenetically a member of the genus Porphyromonas. On the basis of the phylogenetic and phenotypic distinctiveness of O. catoniae, we formally propose that this species should be reclassified in the genus Porphyromonas catoniae comb. nov. An emended description of the genus Porphyromonas is presented.
Bacteroidaceae↗
16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapsalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. nov.
Because of similarities in the cellular fatty acid compositions of Hallella seregens and Mitsuokella dentalis, we determined the 16S rRNA gene sequences of the type strains of these species to assess their relationship. A very high level of sequence relatedness (approximately 99.8%) was found between H. seregens and M. dentalis, indicating that these species are genealogically closely related. A comparative sequence analysis revealed that these two species are members of the genus Prevotella and are phylogenetically remote from Mitsuokella multiacidus (the type species of the genus Mitsuokella), which was found to be a member of the Sporomusa subbranch of the Clostridium subphylum of the gram-positive bacteria. On the basis of our phylogenetic findings, we propose that M. dentalis should be reclassified as Prevotella dentalis comb. nov.
Base Sequence↗
Evidence for the placement of the gram-negative Catonella morbi (Moore and Moore) and Johnsonella ignava (Moore and Moore) within the Clostridium subphylum of the gram-positive bacteria on the basis of 16S rRNA sequences.
Comparative 16S rRNA analysis was used to determine the phylogenetic positions of Catonella morbi and Johnsonella ignava, which are members of two monospecific genera of gram-negative anaerobic bacilli isolated from human gingival crevices. Both of these genera were found to belong to cluster XIVa (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 the Clostridium subphylum of gram-positive bacteria. Within this cluster, which contains several Clostridium, Coprococcus, Eubacterium, and Ruminococcus species, C. morbi and J. ignava formed two distinct lines that were separate from all other taxa. Our findings support the separate generic status of the genera Catonella and Johnsonella and show that these genera do not belong to the family Bacteroidaceae but instead belong to the gram-positive Clostridium subphylum.
Base Sequence↗
Phenotypic and genotypic characterization of bradyrhizobia nodulating the leguminous tree Acacia albida.
Rhizobial isolates that were obtained from both surface and deep soil samples in the Sahelian and Sudano-Guinean areas of Senegal (West Africa) under Acacia albida trees were compared with representative strains of known rhizobial species and genera. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of proteins was used to determine the taxonomic positions of these organisms and the relationships between isolates obtained from the surface and isolates obtained from deep soil. Most of the isolates belonged to eight electrophoretic clusters containing representative strains of Bradyrhizobium japonicum, Bradyrhizobium elkanii, and Bradyrhizobium sp. Isolates were also characterized by the Biolog system, and the results were compared with the results obtained by SDS-PAGE of total proteins; the level of correlation was very low. DNA-rRNA hybridizations with 16S or 23S rRNA from Bradyrhizobium japonicum LMG 6138T (T = type strain) confirmed that most of the protein electrophoretic clusters belong in the Bradyrhizobium-Rhodopseudomonas rRNA complex. Sequencing of 16S rRNA genes showed that some of the A. albida-nodulating isolates belong to a separate lineage together with representatives of other protein electrophoretic clusters. Other isolates that belong to the same electrophoretic cluster as the type strain of Bradyrhizobium japonicum are considered members of the lineage represented by this type strain. The first lineage is as far removed from Bradyrhizobium japonicum as it is from the genus Afipia, Blastobacter denitrificans, and the genus Rhodopseudomonas. The possible relationship among electrophoretic group, geographic origin, and depth of isolation at a particular site is discussed.
Acacia↗
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.
The 16S rRNA gene sequences of Sarcina ventriculi DSM 286T (T = type strain) and Sarcina maxima DSM 316T 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 Clostridium are discussed.
Clostridium↗
Phylogenetic analysis of members of the genus Porphyromonas and description of Porphyromonas cangingivalis sp. nov. and Porphyromonas cansulci sp. nov.
The partial 16S rRNA gene sequences of representative strains of two groups of anaerobic, gram-negative, pigmented, asaccharolytic, rod-shaped bacteria isolated from subgingival plaque of dogs with naturally occurring periodontal disease were determined. A comparative analysis of the rRNA sequence data revealed that the two groups of organisms represent previously unknown lines of descent within the genus Porphyromonas. On the basis of our phylogenetic findings and the phenotypic distinctiveness of the organisms, two new species, Porphyromonas cangingivalis and Porphyromonas cansulci, are proposed.
Base Composition↗
The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations.
The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G + C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other spore-forming and non-spore-forming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.
Base Sequence↗
Sequence of the gene coding for the neurotoxin of Clostridium botulinum type A associated with infant botulism: comparison with other clostridial neurotoxins.
The neurotoxin gene from a strain of Clostridium botulinum type A causing infant botulism was cloned as a series of overlapping polymerase chain reaction (PCR) fragments generated using primers designed to conserved regions of published botulinal toxin (BoNT) sequences. Translation of the nucleotide sequence derived from cloned PCR fragments demonstrated that the toxin gene encodes a protein of 1,296 amino acid residues. Comparative alignment of the derived infant BoNT/A sequence with those of other published neurotoxins revealed highest sequence relatedness with BoNT/A of classical food-borne botulism. The sequence identity between infant and classical BoNT/A was 94.9% for the light chain (corresponding to 23 amino acid changes) and 87.1% for the heavy chain (corresponding to 109 amino acid changes).
Bacterial Proteins↗
Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences.
The phylogenetic relationships of members of the genera Rhizobium, Agrobacterium, Bradyrhizobium, and Azorhizobium were studied by direct sequencing of their amplified 16S rRNA genes. Comparative analysis of the sequence data confirmed that the genera Bradyrhizobium and Azorhizobium belong to distinct phylogenetic lineages. The genera Rhizobium and Agrobacterium were found to be phylogenetically heterogeneous, and several subgroupings in which Rhizobium and Agrobacterium species were intermixed were evident. The present findings show that the genus and species definitions of these organisms are in need of revision. Different possibilities for this are discussed in the light of sequencing data.
Base Sequence↗
Evidence for a close genealogical relationship between Afipia (the causal organism of cat scratch disease), Bradyrhizobium japonicum and Blastobacter denitrificans.
The primary structures of the small subunit rRNA of Bradyrhizobium japonicum and Blastobacter denitrificans were determined by direct sequencing of enzymatically amplified DNA. Comparative sequence analysis revealed that Bradyrhizobium japonicum and Blastobacter denitrificans are members of the alpha-2 subgroup of the Proteobacteria and show a very close phylogenetic relationship with the genus Afipia.
Animals↗
Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci.
DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenae, Pseudomonas rubrilineans, "Pseudomonas setariae," Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudomonas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenae. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenae and Acidovorax konjaci. Within Acidovorax avenae we distinguished the following three subspecies: Acidovorax avenae subsp. avenae, Acidovorax avenae subsp. cattleyae, and Acidovorax avenae subsp. citrulli. Emended descriptions of the new taxa are presented.
DNA, Bacterial↗
Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov.
Pseudomonas facilis and Pseudomonas delafieldii are inappropriately assigned to the genus Pseudomonas. They belong to the acidovorans rRNA complex in rRNA superfamily III (i.e., the beta subclass of the Proteobacteria). The taxonomic relationships of both of these species, two groups of clinical isolates (E. Falsen [EF] group 13 and EF group 16), and several unidentified or presently misnamed strains were examined by using DNA:rRNA hybridization, numerical analyses of biochemical and auxanographic features and of fatty acid patterns, polyacrylamide gel electrophoresis of cellular proteins, and DNA:DNA hybridization. These organisms form a separate group within the acidovorans rRNA complex, and we propose to transfer them to a new genus, Acidovorax. We describe the following three species in this genus: the type species, Acidovorax facilis (formerly Pseudomonas facilis), with type strain LMG 2193 (= CCUG 2113 = ATCC 11228); Acidovorax delafieldii (for the former Pseudomonas delafieldii and most of the EF group 13 strains), with type strain LMG 5943 (= CCUG 1779 = ATCC 17505); and Acidovorax temperans (for several former Pseudomonas and Alcaligenes strains and most of the EF group 16 strains), with type strain CCUG 11779 (= LMG 7169).
Base Composition↗