Paul Segers

Cutting a gordian knot: Emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom nov (basonym, Cytophaga aquatilis Strohl and Tait 1978).

The phylogenetic positions and G+C contents of most species belonging to the genera Flavobacterium, Cytophaga, and Flexibacter and several related taxa were determined. Most of the strains included in this study belong to rRNA superfamily V, as shown by DNA-rRNA hybridization data, but the three main genera are highly polyphyletic. Several so-called Cytophaga and Flexibacter species isolated from soil and freshwater cluster with the type species of the genus Flavobacterium, Flavobacterium aquatile, and with Flavobacterium branchiophilum. The fatty acid and protein profiles of members of this group of organisms were determined. We provide an emended description of the genus Flavobacterium and propose new combinations for the following 7 of the 10 validly described species included in this genus: Flavobacterium columnare, Flavobacterium flevense, Flavobacterium johnsoniae (we also correct the specific epithet of this taxon), Flavobacterium pectinovarum, Flavobacterium psychrophilum, Flavobacterium saccharophilum, and Flavobacterium succinicans. A new name, Flavobacterium hydatis, is proposed for [Cytophaga] aquatilis Strohl and Tait 1978. The emended genus Flavobacterium contains bacteria that have the following main characteristics: gram-negative rods that are motile by gliding, produce yellow colonies on agar, are chemoorganotrophs and aerobes, decompose several polysaccharides but not cellulose, and are widely distributed in soil and freshwater habitats. Three Flavobacterium species are pathogenic for fish. The G+C contents of Flavobacterium DNAs range from 32 to 37 mol%. An emended description of the family Flavobacteriaceae is also provided.

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.

Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov.

Sixteen heparinase-producing isolates, related to Sphingobacterium heparinum, were grouped into three major clusters by SDS-PAGE and DNA-rRNA hybridizations. Based on a polyphasic approach, it was shown that isolates of two of these clusters and S. heparinum species belong to a new genus for which the name Pedobacter is proposed. The genus consists of Pedobacter heparinus comb. nov. (formerly Sphingobacterium heparinum), which is the type species, Pedobacter piscium comb. nov. (formerly Sphingobacterium piscium), Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. and four as-yet-unnamed DNA hybridization groups. All the previously named taxa can be discriminated by phenotypic features, but have strong overall similarities with representatives of the genus Sphingobacterium and the misclassified species [Flexibacter] canadensis. All these organisms constitute a separate rRNA branch in rRNA superfamily V for which the family Sphingobacteriaceae fam. nov. is proposed.

Bordetella avium sp. nov., Isolated from the Respiratory Tracts of Turkeys and Other Birds

Bordetella avium is proposed as the name of a new species containing 28 avian strains that cause coryza (rhinotracheitis) in turkey poults. The type strain is Hinz 591-77 (= ATCC 35086). The majority of the strains investigated were previously known as Bordetella-like or Bordetella bronchiseptica-like bacteria; one of the strains was previously referred to as Alcaligenes faecalis. The B. avium strains were compared with more than 50 culture collection strains belonging Bordetella bronchiseptica, Bordetella pertussis, Bordetella parapertussis, Alcaligenes faecalis, “Alcaligenes odorans,” Alcaligenes denitrificans, Achromobacter xylosoxidans, Pseudomonas pertucinogena, and unnamed groups IVc-2 and IVe. The properties of B. avium and its taxonomic position relative to the above-mentioned taxa were determined by morphological, physiological, nutritional, and serological studies and by a numerical analysis of protein electropherograms, deoxyribonucleic acid-ribosomal ribonucleic acid hybridizations, and pathogenicity tests for turkey poults. The 28 B. avium strains formed a tight cluster, sharing very similar phenotypic features and protein gel electropherograms. We observed no significant differences among strains isolated from turkeys in different geographical areas. The 28 strains were strictly aerobic, gram-negative, peritrichously flagellated, urease-negative rods; the deoxyribonucleic acid base composition ranged from 61.6 to 62.6 mol% guanine plus cytosine. The phenotypic and serological characteristics, together with the properties of the deoxyribonucleic acid-ribosomal ribonucleic acid hybrids, indicated that this new species is a member of the genus Bordetella. The Alcaligenes denitrificans-Achromobacter xylosoxidans cluster is the closest neighbor of Bordetella, which is clearly different from all of the other taxa examined. B. avium has been isolated from the respiratory tracts of turkeys and from some other birds, such as a chicken, a duck, and a goose. All of the B. avium strains investigated caused coryza in turkey poults. An extensive phenotypic description of B. avium is given, and this species is differentiated phenotypically from the following taxa: B. pertussis, B. parapertussis, B. bronchiseptica, Alcaligenes faecalis, Alcaligenes denitrificans, Achromobacter xylosoxidans, and groups IVc-2 and IVe.

Intra- and Intergeneric Similarities of Chromobacterium and Janthinobacterium Ribosomal Ribonucleic Acid Cistrons

We prepared hybrids between 14C-labeled ribosomal ribonucleic acid (rRNA) from either Chromobacterium violaceum NCTC 9757 or Chromobacterium lividum NCTC 9796 and deoxyribonucleic acid (DNA) from a great variety of named gram-negative bacteria, including many type and reference strains. Each hybrid was described by two parameters: (i) Tm(e) , the temperature at which 50% of the hybrid was denatured; (ii) the percent rRNA binding, the amount (micrograms) of [14C]rRNA duplexed in stringent conditions per 100 μg of filter-fixed homologous or heterologous DNA. Each taxon occupied a definite area on the rRNA similarity maps. All C. lividum and C. violaceum strains formed tight separate clusters around their neotype strains. The rRNA parameters of both taxa were about as different from each other as was the case for many genera. Both taxa are phenotypically and genotypically (by DNA-DNA hybridization) likewise very different. We proposed to elevate each cluster to genus rank as C. violaceum and Janthinobacterium lividum. The following strains were misnamed and belonged in neither genus: “C. lividum” = “C.” folium NCTC 10590 and 10591; “C. lividum” GA; “C.” marismortui ATCC 17056; “Pseudomonas” (“Chromobacterium”) iodinum ATCC 9897, 15728, and 15729; “C.” indicum-rubrum (now Serratia marcescens) NCTC 2847; and “C.” viscosum (now Corynebacterium sp.) NCTC 2416. The rRNA cistrons of Chromobacterium and Janthinobacterium resembled most closely those of Pseudomonas section II and III, the authentic Alcaligenes, Bordetella bronchiseptica, the H2-oxidizing Alcaligenes eutrophus and Alcaligenes paradoxus, and Comamonas percolans NCIB 8193. These taxa displayed a number of phenotypical similarities. We suggested that all these taxa are the closest taxonomic relatives of Chromobacterium and Janthinobacterium.

Genotypic relationships and taxonomic localization of unclassified Pseudomonas and Pseudomonas-like strains by deoxyribonucleic acid: ribosomal ribonucleic acid hybridizations

The deoxyribonucleic acid (DNA):ribosomal ribonucleic acid (rRNA) hybridization technique was used to reveal the relationships and taxonomic positions of an additional 83 strains belonging to 43 saprophytic or pathogenic Pseudomonas species and 29 named and unnamed Pseudomonas-like strains. The DNA:rRNA hybrids were characterized by the following two parameters: (i) the temperature at which one-half of the hybrid was eluted and (ii) the percentage of rRNA binding (the amount of rRNA bound per 100 g of filter-fixed DNA). We also used, for a limited number of strains, numerical analysis of carbon assimilation tests to delineate the finer taxonomic relationships of organisms. Of the 83 strains examined, 78 could be definitely assigned either to an rRNA branch or to an rRNA superfamily within the Proteobacteria. Only 25 of our strains belong in the genus Pseudomonas sensu stricto (our Pseudomonas fluorescens rRNA branch). In general, about two-thirds of the named Pseudomonas species have been misclassified and are distributed over at least seven genera all through the Proteobacteria. These organisms need to be reclassified and generically renamed according to their phylogenetic relationships. However, more detailed phenotypic and genotypic studies are necessary before definite nomenclatural proposals can be made. A comprehensive list of the phylogenetic affiliations of the Pseudomonas species is included.

Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family, Alcaligenaceae

Hybridization experiments were carried out between 3H-labeled ribosomal ribonucleic acid from Bordetella bronchiseptica NCTC 452T (T = type strain), 14C-labeled ribosomal ribonucleic acid from Alcaligenes faecalis NCIB 8156T, or 14C-labeled ribosomal ribonucleic acid from Alcaligenes xylosoxidans subsp. denitrificans ATCC 15173T and deoxyribonucleic acids from various strains of Bordetella, Alcaligenes and other taxa. A numerical analysis of phenotypic features was also done. The genera Bordetella and Alcaligenes are very closely related, which warrants the proposal of a new family, the Alcaligenaceae.

Ribosomal ribonucleic acid cistron similarities and taxonomic neighborhood of Brucella and CDC group Vd

Hybridizations were performed between labeled ribosomal ribonucleic acids from Brucella abortus ATCC 23448T(T = type strain) and from several other organisms on the one hand and deoxyribonucleic acids from type and representative Brucella strains and from many other gram-negative organisms on the other hand. Brucella forms a tight cluster, with deoxyribonucleic acid homologies close to 100%; its closest neighbors are CDC group Vd, followed by Phyllobacterium. This Brucella ribosomal ribonucleic acid branch links most closely at about 73.1°C Tm(e) with the Agrobacterium-Rhizobium cluster, which is itself a member of ribosomal ribonucleic acid superfamily IV. The deoxyribonucleic acid base compositions of Brucella strains range from 57.9 to 59.2 mol% guanine plus cytosine; the average genome molecular weights of the six species range from 2.37 × 109to 2.82 × 109.

Reclassification of Flavobacterium odoratum (Stutzer 1929) strains to a new genus, Myroides, as Myroides odoratus comb. nov. and Myroides odoratimimus sp. nov.

On the basis of genotypic, chemotaxonomic, and phenotypic data, Flavobacterium odoratum was excluded from the emended genus Flavobacterium. In the present study, the known heterogeneity within this species was examined by a polyphasic approach that included DNA-rRNA hybridizations, a determination of DNA base ratios, DNA-DNA hybridizations, a numerical analysis of whole-cell protein patterns, a determination of cellular fatty acid compositions, and a phenotypic analysis. All of the methods revealed the presence of two distinct species. We propose that F. odoratum strains should be placed in a new genus, the genus Myroides, which comprises two species, Myroides odoratus comb. nov. and Myroides odoratimimus sp. nov.

Oligella, a New Genus Including Oligella urethralis comb. nov. (Formerly Moraxella urethralis) and Oligella ureolytica sp. nov. (Formerly CDC Group IVe): Relationship to Taylorella equigenitalis and Related Taxa

The taxonomic relationships of Moraxella urethralis, the Centers for Disease Control (CDC) group IVe, Taylorella equigenitalis, and other gram-negative bacteria were studied by deoxyribonucleic acid (DNA)-DNA polyacrylamide gel electrophoresis of cellular proteins, and serological, biochemical, and auxanographic analyses. A high relationship was detected between M. urethralis and the CDC group IVe strains. However, no relationship of M. urethralis and CDC group IVe with genuine Moraxella species was observed. We describe a new genus, Oligella, containing two species: Oligella urethralis (to accommodate Moraxella urethralis) and Oligella ureolytica (to accommodate CDC group IVe strains). The type species is Oligella urethralis, with type strain ATCC 17960T. The type strain of Oligella ureolytica is CDC C379 (ATCC 43534, CCUG 1465, LMG 6519). Oligella is a member of rRNA superfamily III, containing, e.g., the Pseudomonas acidovorans and Pseudomonas solanacearum complexes and Chromobacterium, Janthinobacterium, and Neisseria species. The closest relatives of Oligella species are Taylorella equigenitalis and the Alcaligenaceae family.