A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources

Phenotypic data on 203 Gram-negative non-fermentative bacteria of the Flavobacterium-Cytophaga group isolated from milk and butter were analyzed by numerical taxonomic techniques. Twenty reference strains including species of Flavobacterium, Cytophaga and strains of Pseudomonas paucimobilis were included in the study. Using the matching coefficient of Sokal & Michener with antibiotic susceptibility data included, 139 isolates were recovered in nine clusters. Six of these clusters were linked at or above the 85% S level while three were linked at or above the 79% S level. The largest cluster, representing 46.3% of the isolates, could be equated with Flavobacterium sp. Group IIb. Other clusters could be equated with Flavobacterium sp. L 16/1 (22.7% of isolates), F. balustinum (10.8% of isolates), F. breve (4.4%), F. multivorum (3.5%) and Cytophaga johnsonae (1.5%). The cluster resembling Flavobacterium sp. L 16/1 and a smaller unclassified cluster, were exceptional in being susceptible to the antibiotics cephalothin and penicillin G.     

A numerical taxonomic study of Propionibacterium strains from dairy sources

T.J. BRITZ AND K-H.J. RIEDEL. 1991. Phenotypic results from 81 tests conducted on 73 propionibacteria, including five type strains, 22 reference strains, unidentified propionibacteria and strains isolated from dairy sources, were analysed by numerical taxonomy. Characters giving uniform results were excluded. With the simple matching coefficient and the single linkage cluster analysis, 61 cultures were recovered in five major clusters. Final linkage of all the Propionibacterium cultures examined was at the 77% S-level. The results clearly showed that it was possible to distinguish between the 'classical' and 'cutaneous' Propionibacterium spp., corresponding with the type habitat of each group. The major 'classical' clusters were equated with the P. freudenreichii, P. thoenii, P. jensenii and P. acidipropionici species, while the only major 'cutaneous' cluster was equated with the P. acnes species. The major clusters were identified by relating them to specific type strains and by comparing phenotypic characteristics. The differentiating characteristics of each cluster were determined. The largest cluster, representing 37% of the strains, was equated with P. jensenii but contained cultures that produced an atypical brown/red pigment. These strains, although positively identified as P. jensenii , could also be identified as the 'old' P. rubrum ' species. Thus if pigmentation is used as differential characteristic two distinct groups of propionibacteria could be identified within the P. jensenii species.     

A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources

Phenotypic data on 203 Gram-negative non-fermentative bacteria of the Flavobacterium-Cytophaga group isolated from milk and butter were analyzed by numerical taxonomic techniques. Twenty reference strains including species of Flavobacterium, Cytophaga and strains of Pseudomonas paucimobilis were included in the study. Using the matching coefficient of Sokal & Michener with antibiotic susceptibility data included, 189 isolates were recovered in nine clusters. Six of these clusters were linked at or above the 85% S level while three were linked at or above the 79% S level. The largest cluster, representing 46.3% of the isolates, could be equated with Flavobacterium sp. Group IIb. Other clusters could be equated with Flavobacterium sp. L 16/1 (22.7% of isolates), F. balustinum (10.8% of isolates), F. breve (4.4%), F. multivorum (3.5%) and Cytophaga johnsonae (1.5%). The cluster resembling Flavobacterium sp. L 16/1 and a smaller unclassified cluster, were exceptional in being susceptible to the antibiotics cephalothin and penicillin G.     

Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals

Members of most Chryseobacterium species occur in aquatic environments or food products, while strains of some other species are pathogenic to humans and animals. A collection of 52 Chryseobacterium sp. strains isolated from diseased fish, one frog isolate and 22 reference strains were included in a polyphasic taxonomy study. Fourteen clusters of strains were delineated following the comparison of whole-cell protein profiles. Most of these clusters were confirmed when the phenotypic and RAPD profiles and the 16S rRNA gene sequences were compared. Fatty acid composition helped differentiate the Chryseobacterium strains from members of related genera. None of the fish isolates could be allocated to the two species previously reported from fish but two isolates belonged to C. joostei, while the frog isolate was identified as Elizabethkingia meningoseptica, a human pathogen previously included in the genus Chryseobacterium. Three clusters grouping from 3 to 13 isolates will probably constitute the core of new Chryseobacterium species but all other isolates occupied separate or uncertain positions in the genus. This study further demonstrated the overall high similarity displayed by most Chryseobacterium strains whatever the technique used and the resulting difficulty in delineating new species in the genus. Members of this bacterial group should be considered potential emergent pathogens in various fish and frog species, farming conditions and geographical areas.     

A polyphasic taxonomic study of thermophilic bacilli from shallow, marine vents

Eighty-seven thermophilic, aerobic, spore-forming bacteria were isolated from shallow, marine, thermal vents of the Eolian Islands (Italy) and tested for a broad spectrum of phenotypic characteristics. A numerical taxonomy study was performed on these isolates and 8 thermophilic Bacillus and Geobacillus reference strains by 89 selected features. Results from cluster analysis showed the formation of nine clusters. Most of the isolates (83%) fell into several phenetically well distinguished clusters, loosely related to Geobacillus thermodenitrificans. The remaining isolates grouped together with different reference strains. Eighteen isolates, representative of the different clusters, were selected for subsequent genotypic characterisation, including partial 16S rDNA sequence analysis of 18 strains and almost complete 16S rDNA sequences of 9 strains. Subsequent DNA/DNA reassociation studies and determination of the base composition of DNA identified seven isolates as Geobacillus thermodenitrificans, two isolates as G. thermoleovorans and one isolate as Bacillus pallidus. Four isolates represented two novel species of Bacillus. The remaining four represented novel Geobacillus species, one of which has recently been described as Bacillus vulcani DSMZ 13174 T.     

A numerical taxonomic study of fluorescent Pseudomonas strains isolated from natural mineral waters

M. ELOMARI, L. COROLER, D. IZARD AND H. LECLERC. 1995. Forty-six strains of fluorescent pseudomonads, isolated from natural mineral waters, together with 12 strains from clinical material and 44 reference strains, were phenotypically classified by 281 characteristics. The data were processed by the Dice similarity coefficient and unweighted pair group algorithm with arithmetic averages. Eight clusters were defined at the 62% similarity level. Clusters I, II and IV were further divided into nine subclusters. Virtually all the mineral water strains fall into three groups: Ib (eight strains), Ha (14 strains) and V (16 strains). Subclusters Ib and IIa included natural mineral water strains only. Cluster V contained 13 mineral water strains and three culture collection strains of Pseudomonas fluorescens biovar III. DNA/DNA hybridization studies are needed to define the taxonomic status of these three groups within the genus Pseudomonas.     

A polyphasic approach for the characterization of endophytic Alternaria strains isolated from grapevines

A polyphasic approach was set up and applied to characterize 20 fungal endophytes belonging to the genus Alternaria, recovered from grapevine in different Italian regions.Morphological, microscopical, molecular and chemical investigations were performed and the obtained results were combined in a pooled cluster analysis. Following morphological analyses, all strains were grouped according to their three-dimensional sporulation pattern on PCA and to the colony characteristics on different substrates. After DNA extraction, all strains were analyzed by RAPD-PCR and the resulting profiles were subjected to cluster analysis. The metabolites extracted from the 20 Alternaria endophytes were analyzed by a HPLC and the resulting metabolite profiles were subjected to multivariate statistic analyses. In comparison with reference ‘small-spored’ Alternaria species, the 20 strains were segregated into two morphological groups: one belonging to the A. arborescens species-group and a second to the A. tenuissima species-group. RAPD analysis also showed that grapevine endophytes belonged to either the A. arborescens or the A. tenuissima species-group and that they were molecularly distinct from strains belonging to A. alternata. Chemotaxonomy gave the same grouping: the grapevine endophytic strains belong to A. arborescens or A. tenuissima species-groups producing known metabolites typical of these species-groups. Interestingly, the 20 grapevine endophytes were able to produce also a number of unknown metabolites, whose characterization could be useful for a more precise segregation of the two species-groups.The results show how complementary morphological, molecular and chemical data can clarify relationships among endophyte species-groups of low morphological divergence.     

A polyphasic study on the taxonomic position of industrial sour dough yeasts

The sour dough bread making process is extensively used to produce wholesome palatable rye bread. The process is traditionally done using a back-slopping procedure. Traditional sour doughs in Finland comprise of lactic acid bacteria and yeasts. The yeasts present in these doughs have been enriched in the doughs due to their metabolic activities, e.g. acid tolerance. We characterized the yeasts in five major sour bread bakeries in Finland. We found that most of the commercial sour doughs contained yeasts which were similar to Candida milleri on the basis of 18S rDNA and EF-3 PCR-RFLP patterns and metabolic activities. Some of the bakery yeasts exhibited extensive karyotype polymorphism. The minimum growth temperature was 8 degrees C for C. milleri and also for most of sour dough yeasts.     

A study ofPasteurella strains from animal sources

Fifty-twoPasteurella cultures isolated from mice, mostly from cases of pneumonia, are described. The strains are closely related toPasteurella pneumotropica, introduced by Jawetz, but differ from this species in some biochemical characteristics. It is suggested thatPasteurella pneumotropica can be considered as a group of related biotypes. For the cultures under discussion the name ofPasteurella pneumotropia var.xylophila is proposed.     

A taxonomic study on erysipelothrix by DNA-DNA hybridization experiments with numerous strains isolated from extensive origins

The purpose of this study was to clarify the taxonomic relationship between all the serovars and species of the genus Erysipelothrix by performing DNA-DNA hybridization experiments, the customary criterion for separation of bacterial genospecies. A total of 93 strains were isolated from a wide variety of sources, including pigs affected with acute or chronic erysipelas, other diseased animals, healthy animals, fish, retail meats, and environmental materials from throughout the world during the period 1958 to 1996. The present data on phenotypic characterization and DNA relatedness values demonstrate that 24 strains (96%) of E. tonsillarum are avirulent for swine, whereas 39 strains (66%) of genomic E. rhusiopathiae induced generalized or local urticarial lesion in swine after intradermal inoculation. This observation suggests that genomic E. tonsillarum has little etiological significance. Three minor groups contained several strains which exhibited minimal association with each type strain of E. rhusiopathiae and E. tonsillarum. In conclusion, it was confirmed that members of the E. rhusiopathiae and E. tonsillarum groups resemble each other in regard to many phenotypic characteristics, but differ in their ability to produce acid from saccharose and in their pathogenicity for swine. The genus Erysipelothrix certainly contains two main species: E. rhusiopathiae and E. tonsillarum.     

A numerical taxonomic study of Pseudomonas strains from spoiled meat

A numerical taxonomic study using 160 unit characters has been performed on 110 isolates of pseudomonads from aerobically spoiled beef and pork and on 13 named strains from the genus Pseudomonas. Four clusters of meat strains were detected at 87% S. Non-fluorescent strains were contained in two closely related clusters (1 and 2) which were identified with P. fragi. Clusters 3 and 4 contained fluorescent strains which were distinct from P. fluorescens, P. putida and the other named strains examined. An identification scheme based on 11 carbon source tests is presented for the recognition of cluster members.     

A numerical taxonomic study of Leuconostoc oenos strains from wine

Phenotypic data of 108 tests conducted on 70 malolactic bacteria, including 54 presumptive Leuconostoc oenos strains, five presumptive pediococci isolated from wine and 11 reference strains, were analysed by numerical taxonomic techniques. Using the simple matching coefficient, 58 strains were grouped in six clusters at the 87% S level. Cell wall analysis of the interpeptide bridges and morphology was also used to differentiate between the strains. No L. oenos reference strains were found to group in any cluster. The hypothetical median organism (HMO) of cluster A was related at only the 63% S level to the L. oenos type strain and it is proposed that these strains be regarded as 'L. gracile'. The majority of the L. oenos strains (35) grouped together at above the 91% S level in cluster B, with the HMO of this cluster related at the 75% S level to the L. oenos type strain. Results indicate that the majority of L. oenos strains included in this study are closely related, but more research is needed to justify the separation of these strains into more than one species.     

Relationships between Arctic and Antarctic Shewanella strains evaluated by a polyphasic taxonomic approach

As a result of the recent application of DNA-based technologies to investigate bacterial diversity in the polar marine environment, bacterial strains sharing significant 16S rRNA gene sequence similarities were isolated from both the Arctic and the Antarctic sea waters. Three selected marine bacterial isolates (BSw20248, BSw20661 and BSw10166) from two Arctic regions (the Greenland Sea and Canada Basin) and from Antarctica (Prydz Bay) were studied to determine their evolutionary relationships and phylogenetic position using a polyphasic taxonomic approach, including phenotypic characterization and genotypic analyses. These bacterial isolates proved to belong to the same species and were identified as Shewanella frigidimarina. Differences in phenotypic properties observed among them revealed a diversity of ecotypes for adaptation to the changing ecological or geographical conditions. It provided the evidence that Shewanella frigidimarina has a bipolar, or even global, distribution in the marine environment.     

Cytotoxic activity of lactobacilli isolated from plant and dairy sources

Forty four cultures of Lactobacilli isolated from their natural sources such as dahi, raw milk and fermenting rice-pulse doughs etc. along with four standard strains of Lactobacilli were assayed for their cytotoxic activity against three secondary tumour cell lines. Three cultures isolated from dahi samples and identified as Lactobacillus casei D-34, L. casei D-48a, L. plantarum D-70a along with one standard strain L. casei B 1922 exhibited significant cytotoxic activity in the range of 30 to 36%.     

Ribotyping ofLactobacillus casei group strains isolated from dairy products

A series of lactobacilli isolated from dairy products were characterized using biotyping and ribotyping with EcoRI and HindIII restriction enzymes. Biotyping assigned 14 strains as Lactobacillus casei, 6 strains as Lactobacillus paracasei subsp. paracasei and 12 as Lactobacillus rhamnosus. The obtained ribotype patterns separated all analyzed strains into two clearly distinguished groups corresponding to L. rhamnosus and L. casei/L. paracasei subsp. paracasei. The HindIII ribotypes of individual strains representing these two groups were visually very similar. In contrast, EcoRI ribotyping revealed high intraspecies variability. All ribotypes of L. casei and L. paracasei subsp. paracasei dairy strains were very close and some strains even shared identical ribotype profiles. The type strains L. casei CCM 7088T (= ATCC 393T) and Lactobacillus zeae CCM 7069T revealing similar ribopatterns formed a separate subcluster using both restriction enzymes. In contrast, the ribotype profile of L. casei CCM 7089 (= ATCC 334) was very close to ribopatterns obtained from the dairy strains. These results support synonymy of L. casei and L. paracasei species revealed by other studies as well as reclassification of the type strain L. casei CCM 7088T as L. zeae and designation of L. casei CCM 7089 as the neotype strain.     

A numerical taxonomic study of the Pseudomonas flora isolated from poultry meat

Pseudomonas strains were isolated from both fresh and cold-stored broiler skin. Phenotypically-based numerical taxonomic techniques were used to characterize the isolates and 36 reference strains. For this purpose, Biolog GN Microplates, API 20NE and a number of other biochemical tests were used. Jaccard clustering revealed the predominance of four major Pseudomonas groups: Ps. fragi, Ps. lundensis, strains belonging to Ps. fluorescens biovars and an unidentified group of strains displaying a high degree of similarity to Ps. fluorescens biovars. Within Ps. fluorescens, biovar A was best represented. The marked proteolytic character of members of Ps. fluorescens biovars A, B and C, as well as of members of the unidentified cluster, supports their possible role in the origin of organoleptic defects. In the Ps. lundensis cluster, a distinct group of Ps. lundensis-like species was found. Further genotypic studies should be carried out to clarify the taxonomic status of the Ps. lundensis-like strains and that of the unidentified group resembling Ps. fluorescens biovars A and B.     

A cooperative taxonomic study of mycobacteria isolated from armadillos infected with Mycobacterium leprae

Seventeen strains of mycobacteria, recovered from six armadillos experimentally infected with Mycobacterium leprae, were examined in ten different laboratories. This collaborative study included use of conventional bacteriological tests, lipid analyses, determination of mycobactins and peptidoglycans, characterization by Py-MS, and immunological, metabolic, pathological and DNA studies. These armadillo-derived mycobacteria (ADM) formed five homogeneous groups (numbered ADM 1 to 5) on the basis of phenetic analyses. However, DNA studies revealed only four homogeneous groups since group ADM 1 and one of the two strains in group ADM 3 showed a high level of DNA relatedness. The phenetic and DNA studies confirmed that the ADM strains differed from all other known mycobacteria. Cultural, biochemical, metabolic and pathogenic properties as well as DNA-DNA hybridizations clearly differentiated these ADM from M. leprae.     

A numerical taxonomic study of proteolytic and lipolytic psychrotrophs isolated from caprine milk

Lipolytic and proteolytic psychrotrophs were isolated from raw and pasteurized goats' milk, which had been stored at 5 degrees C for 7 d. The 241 strains isolated and 20 reference strains were examined by 149 biochemical, physiological, and morphological tests. The results yielded 195 characters suitable for taxonomic analysis. Computer-assisted complete linkage analysis, using the Jaccard coefficient, produced 22 phenons at 75% S. The results showed that Pseudomonas fluorescens was the predominant psychrotrophic bacterium, but that Pseudomonas fragi was dominant in some milk samples. Strains of Serratia liquefaciens and Flavobacterium balustinum were also identified.