Barry Holmes

Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family

In this paper minimal standards for the description of new genera and cultivable species in the family Flavobacteriaceae are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision). In addition to specified phenotypic characteristics, the description of new species should be based on DNA-DNA hybridization data, and the placement of new taxa should be consistent with phylogenetic data derived from 16S rRNA sequencing. An emended description of the family is also proposed as several new taxa have been described since 1996. These proposals have been endorsed by the members of the Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes.

Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov.

We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.

New perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen-nov, and Empedobacter nom-rev.

Our present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members of the genus Flavobacterium and some related genera, including the genus Weeksella, was used to revise the classification of these organisms. The generically misclassified organisms Flavobacterium balustinum, Flavobacterium gleum, Flavobacterium indologenes, Flavobacterium indoltheticum, Flavobacterium meningosepticum, and Flavobacterium scophthalmum are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as the type species. The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Empedobacter brevis, whereas the generically misclassified organism Weeksella zoohelcum is included in the new genus Bergeyella as Bergeyella zoohelcum.

Burkholderia cenocepacia sp. nov.--a new twist to an old story.

DNA-DNA hybridisation experiments between isolates representing Burkholderia cepacia genomovar III recA lineages IIIA and IIIB reinforced the classification of both phylogenetic subgroups as a single genospecies, distinct from B. cepacia (genomovar I). A formal classification of B. cepacia genomovar III encompassing the recA lineages IIIA and IIIB, and the new recA lineages IIIC and IIID, as B. cenocepacia sp. nov., with LMG 16656 as the type strain, is proposed.

Pseudomonas paucimobilis, a New Species Isolated from Human Clinical Specimens, the Hospital Environment, and Other Sources

Forty-seven strains of yellow-pigmented, non-fermentative, gram-negative, rod-shaped bacteria isolated from clinical specimens (14 strains), the hospital environment (20 strains), and miscellaneous sources (13 strains) were characterized with respect to 68 phenotypic tests. The results, along with those of the same 68 tests carried out on 51 reference strains that represented species of Pseudomonas and six other genera of gram-negative bacteria, were analyzed by numerical taxonomic methods. Twenty-nine of the 47 yellow-pigmented strains, including two strains of Weaver group IIk, biotype 1, formed a homogeneous phenetic group (within-group similarity: 93.4% SG). The group consisted of strictly aerobic, heterotrophic rod-shaped bacteria. Cells were motile by means of a single polar flagellum. Only a few of the cells were actively motile in nutrient broth cultures, so this characteristic was often difficult to demonstrate. The strains were homogeneous in their susceptibilities to antimicrobial agents, and the mean guanine-plus-cytosine. content of the deoxyribonucleic acids from 13 of the isolates was 64.9 ± 1.4 mol%. The 29 strains conformed to the general characteristics of the genus Pseudomonas. The reasons for excluding the strains from Xanthomonas are discussed. We consider these strains to represent a new species, for which we propose the name Pseudomonas paucimobilis. The type strain of the new species is CL1/70 (=NCTC 11030). The remaining 18 yellow-pigmented isolates were unclassified except for two strains which corresponded to a Flavobacterium sp. (King group IIb).

A review of numerical methods in bacterial identification

Part A of this review describes the particular computer-assisted identification service operated by the NCTC. In Part B, the use of probability matrices is examined, discussing various methods of calculating likelihoods and the problems that arise when calculating these from probability matrices. Part C describes the alternative numerical methods of constructing identification keys and the supplementary methods of selecting “best sets” of characters to aid identification. Finally, in Part D, the prospects and limitations of numerical methods in bacterial identification are assessed, first with regard to methodology used and then in terms of performance and practical limitations.

Flavobacterium gleum, a New Species Found in Human Clinical Specimens

We propose a new species, Flavobacterium gleum. Each of the 12 strains placed in this new species was examined for 129 characteristics, including reactions in 58 enzyme tests (API ZYM System). These bacteria are rod shaped, aerobic, gram negative, and nonmotile and attack carbohydrates oxidatively. The mean guanine-plus-cytosine content of the deoxyribonucleic acids of six representative strains is 37.6 ± 1.0 mol%. Most strains of the new species were isolated from human clinical specimens; vaginal specimens were a common source. One of the strains included in the new species (strain NCTC 10795) is a reference strain of the unnamed taxon Flavobacterium species group IIb. The type strain is strain F93 (= NCTC 11432).

Classification of Proteus vulgaris biogroup 3 with recognition of Proteus hauseri sp. nov., nom. rev. and unnamed Proteus genomospecies 4, 5 and 6

Strains traditionally identified as Proteus vulgaris formed three biogroups. Biogroup 1, characterized by negative reactions for indole production, salicin fermentation and aesculin hydrolysis, is now known as Proteus penneri. Biogroup 2, characterized by positive reactions for indole, salicin and aesculin, was shown by DNA hybridization (hydroxyapatite method) to be a genetic species separate from biogroup 1 and from biogroup 3 which is positive for indole production and negative for salicin and aesculin. In this study, 52 strains were examined, of which 36 strains were Proteus vulgaris biogroup 3, which included the current type strain of the species P. vulgaris (ATCC 29905T), and compared to seven strains of Proteus vulgaris biogroup 2 and nine type strains of other species in the genera Proteus, Providencia and Morganella. By DNA hybridization, these 36 strains were separated into four distinct groups, designated as Proteus genomospecies 3, 4, 5 and 6. DNAs within each separate Proteus genomospecies were 74-99% related to each other in 60 degrees C hybridization reactions with < or = 4.5% divergence between related sequences. Proteus genomospecies 3 contained the former P. vulgaris type strain and one other strain and was negative in reactions for salicin fermentation, aesculin hydrolysis and deoxyribonuclease, unlike the reactions associated with strains considered as typical P. vulgaris which are positive in reactions for salicin, aesculin and DNase. Genomospecies 3 can be distinguished from Proteus genomospecies 4, 5 and 6 because it is negative for Jordans tartrate. Proteus genomospecies 4, containing five strains, was differentiated from Proteus penneri, genomospecies 3 and 6 and most, but not all, strains of genomospecies 5, by its ability to ferment L-rhamnose. Proteus genomospecies 5 and 6, containing 18 and 11 strains, respectively, could not be separated from each other by traditional biochemical tests, by carbon source utilization tests or SDS-PAGE of whole-cell proteins. In an earlier publication, a request was made to the Judicial Commission that the former type strain of P. vulgaris (ATCC 13315) be replaced by P. vulgaris biogroup 2 strain ATCC 29905T, a strain considered more biochemically typical of P. vulgaris strains. This would have the effect of assigning the name P. vulgaris to P. vulgaris biogroup 2. Since this request has been acceded to, the name Proteus hauseri is herein proposed for Proteus vulgaris genomospecies 3. Its type strain is ATCC 700826T. Proteus genomospecies 4, 5 and 6 will remain unnamed until better phenotypic differentiation can be accomplished. All Proteus genomospecies were similar in their antimicrobial susceptibility patterns. Nineteen strains were isolated from urine, four from faeces, two from wounds, nine from other human sources and two from animals.

Chryseomonas luteola comb. nov. and Flavimonas oryzihabitans gen. nov., comb. nov., Pseudomonas-Like Species from Human Clinical Specimens and Formerly Known, Respectively, as Groups Ve-1 and Ve-2

Pseudomonas luteola Kodama et al. 1985 is a senior subjective synonym of Chryseomonas polytricha Holmes et al. 1986 (formerly group Ve-1). The type strain of P. luteola (JCM 3352) was 78% related to the type strain of C. polytricha (NCTC 11843). We propose the new combination Chryseomonas luteola for this organism. For Pseudomonas oryzihabitans Kodama et al. 1985 (formerly group Ve-2) we propose the new genus and new combination Flavimonas oryzihabitans. We were in the process of proposing a scientific name for group Ve-2 on the basis of an examination of 19 strains when the description of P. oryzihabitans was published. We have included the type strain of P. oryzihabitans for comparison and here present our results for all 20 strains. Each of the 20 strains was examined for 129 characteristics, including reactions in 58 enzyme tests (API ZYM system). These bacteria are rod shaped, aerobic, gram negative, yellow pigmented, motile by a single polar flagellum, and saccharolytic, but they do not produce cytochrome oxidase. The mean guanine-plus-cytosine content of the deoxyribonucleic acid of three representative strains was 63.6 ± 1.6 mol%. The deoxyribonucleic acid relatedness of 11 strains of group Ve-2 to the strain we would have proposed as the type strain, CL162/81 (= NCTC 11850), averaged 93% (hydroxyapatite method, 70°C). The type strain of P. oryzihabitans (JCM 2952) was 93% related to CL162/81. The relatedness of CL162/81 to the respective type strains of the five major ribosomal ribonucleic acid hybridization groups of the genus Pseudomonas and to the type strain of C. polytricha (formerly group Ve-1) was 5% or less. All strains, except the type strain, of F. oryzihabitans were isolated from human clinical specimens.

Classification and Identification of Campylobacters, Helicobacters and Allied Taxa by Numerical Analysis of Phenotypic Characters

Summary The value of numerical analysis of phenotypic characters for the classification and identification of campylobacteria was investigated. Sixty-seven phenotypic characters were determined for 347 strains representing forty-three species, subspecies, biovars or unnamed groups assigned or affiliated to the genera Crmpylobacter, Arcobacter, Helicobacter , and Anaerobiospirillum . The data were subjected to numerical analysis using a computer program, MVSP. The results indicated that, (i) there was considerable agreement between the groupings obtained and previously determined genomic relationships, (ii) most strains could be identified accurately to the specific or subspecific level, and (iii) two novel groups could be delineated. Although highly atypical strains proved difficult to classify, the method has considerable potential for accurately differentiating members of this taxonomically complex and economically important group of bacteria.