Streptococcus equi subsp ruminatorum subsp nov., isolated from mastitis in small ruminants

Six isolates of an unknown Gram-positive, catalase-negative, chain-forming, coccus-shaped organism isolated from ovine and caprine mastitis were characterized by phenotypic and molecular taxonomic methods. On the basis of cellular morphology and the results of biochemical tests, the organism was tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organism is a member of the genus Streptococcus, with Streptococcus equi as its closest phylogenetic relative (98(.)8% similarity). DNA-DNA pairing studies showed that the unidentified organism displayed more than 70% relatedness to the type strains of S. equi subsp. equi and subsp. zooepidemicus. Despite the relatively high DNA-DNA reassociation values, biotyping and ribotyping allowed clear differentiation of the unknown bacterium from the two recognized subspecies of S. equi. On the basis of phenotypic and molecular genetic evidence, it is proposed that the unknown Streptococcus isolates from ovine and caprine mastitis be classified as a novel subspecies, Streptococcus equi subsp. ruminatorum subsp. nov. The type strain is CECT 5772(T) (=CCUG 47520(T) = Mt 167(T)).

Fastidiosipila sanguinis gen. nov., sp nov., a new Gram-positive, coccus-shaped organism from human blood

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6% O-2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al, Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15% or more were observed between the unidentified bacterium and all other recognized species within this and related rRINIA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp, nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (= CIP 108292(T)).

The influence of ribosome modulation factor on the survival of stationary-phase Escherichia coli during acid stress

Ribosome modulation factor (RMF) was shown to have an influence on the survival of Escherichia coli under acid stress during stationary phase, since the viability of cultures of a mutant strain lacking functional RMF decreased more rapidly than that of the parent strain at pH 3. Loss of ribosomes was observed in both strains when exposed to low pH, although this occurred at a higher rate in the RMF-deficient mutant strain, which also suffered from higher levels of rRNA degradation. It was concluded that the action of RMF in limiting the damage to rRNA contributed to the protection of E coli under acid stress. Expression of the rmf gene was lower during stationary phase after growth in acidified media compared to media containing no added acid, and the increased rmf expression associated with transition from exponential phase to stationary phase was much reduced in acidified media. It was demonstrated that RMF was not involved in the stationary-phase acid-tolerance response in E coli by which growth under acidic conditions confers protection against subsequent acid shock. This response was sufficient to overcome the increased vulnerability of the RMF-deficient mutant strain to acid stress at pH values between 6.5 and 5.5.

Corrosion by sulfate reducing bacteria that utilize nitrate

16S rRNA gene sequencing was used to identify a sulfate-reducing bacterium (SRB) from a Danish North Sea oilfield water injection system. This species was cultivated, purified and subsequently identified as being >97% similar to Desulfovibrio gracilis. Like some other Desulfovibrio species this SRB, strain OP102, could reduce nitrate as an electron acceptor and produce ammonia in the absence of sulfate. In addition, in the presence of sulfate, when nitrate was dosed at 100 mg/l it was again reduced by the bacterium, with some ammonium production. Therefore, this mechanism could be important in oilfield systems where nitrate is applied to prevent sulfide generation by SRB which leads to reservoir souring. In static tests the influence of this Desulfovibrio on corrosion was assessed using carbon steel coupons, in the presence of sulfate and in the presence of sulfate with 100 mg/l nitrate. Corrosion rates were less than 1.5 mpy when coupons were incubated in the same water, with sulfate and with nitrate. Furthermore, the occurrence of pitting corrosion was fairly low under all circumstances.

Description of Enterococcus canis sp nov from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al. 2001

Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges-Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA-DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316(T) (= CCUG 46666(T)) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G + C Gram-positive bacteria. Sequence divergence values of > 8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T) = NRRL 23919(T) = DSM 15692(T). Crown Copyright (C) 2004 Published by Elsevier Ltd. All rights reserved.

Atopococcus tabaci gen. nov., sp nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4 alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega 9, C-16:0 and C(18:1)omega 9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allolustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (= CIP 108502(T)).

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on LL-diaminopimelic acid (type LL-Dpm-glycine(1)), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H-4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306(T) = DSM 15745(T)).

Streptococcus devriesei sp nov., from equine teeth

Phenotypic and phylogenetic studies were performed on four unidentified Gram-positive staining, catalase-negative, cc-hemolytic Streptococcus-like organisms recovered from the teeth of horses. SDS PAGE analysis of whole-cell proteins and comparative 16S rRNA gene sequencing demonstrated the four strains were highly related to each other but that they did not correspond to any recognised species of the genus Streptococcus. Phylogenetic analysis based on 16S rRNA gene sequences showed the unidentified organisms form a hitherto unknown sub-line within the Streptococcus genus, displaying a close affinity with Streptococcus mutans, Streptococcus ferus and related organisms. Sequence divergence values of > 5% with thew and other reference streptococcal species however demonstrated the organisms from equine sources represent a novel species. Based on the phenotypic distinctiveness of the new bacterium and molecular chemical and molecular genetic evidence, it is proposed that the unknown species be classified as Streptococcus devriesei sp. nov. The type strain of Streptococcus devriesei is CCUG 47155(T) (= CIP 107809T).

Luteococcus sanguinis sp. nov., isolated from human blood

An unusual catalase-positive, Gram-positive, coccus-shaped bacterium that originated from a human blood specimen was subjected to a polyphasic taxonomic study. Cell-wall murein and lipid composition analyses indicated that the unknown isolate was a member of the genus Luteococcus. The results of comparative 16S rRNA gene sequence analysis were consistent with chemotaxonomic findings and showed that the unidentified bacterium represents a hitherto unknown sublineage, within the genus Luteococcus that is closely related to, but distinct from, Luteococcus japonicus. On the basis of both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium from human blood should be classified as Luteococcus sanguinis sp. nov., with the type strain CCUG 33897(T) (=CIP 107216(T)).

Corynebacterium caspium sp nov., from a Caspian seal (Phoca caspica)

A previously unknown Gram-positive, non-spore-forming, non-lipophilic, catalase-positive, irregular rod-shaped bacterium (M/106/00/5(T)) was isolated, in mixed culture, from the penis of a Caspian seal (Phoca caspica). The strain was a facultative anaerobe that was able to grow at 22 and 42 degreesC. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of more than 5 % from other described Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium isolated from a Caspian seal (strain M/106/00/5(T) = CCUG 44566(T)=CIP 107965(T)) be classified as the type strain of a novel species of the genus Corynebacterium, Corynebacterium caspium sp. nov.

Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen

An unknown Gram-positive, catalase-negative, facultatively anaerobic, non-spore-forming, rod-shaped bacterium originating from semen of a pig was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a directly cross-linked cell wall murein based on L-lysine and a DNA G + C content of 39 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified rod-shaped organism formed a hitherto unknown subline related, albeit loosely, to Alkalibacterium olivapovliticus, Alloiococcus otitis, Dolosigranulum pigrum and related organisms, in the low-G + C-content Gram-positive bacteria. However, sequence divergence values of > 11 % from these recognized taxa. clearly indicated that the novel bacterium represents a separate genus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig semen be classified as a new genus and species, Allofustis seminis gen. nov., sp. nov. The type strain is strain 01-570-1(T) (=CCUG 45438(T)=CIP 107425(T)).

Helcococcus sueciensis sp nov., isolated from a human wound

A previously undescribed, Gram-positive, catalase-negative, coccus-shaped organism that originated from a human wound was subjected to taxonomic study. On the basis of its cellular morphology and the results of biochemical testing, the unknown organism was identified tentatively as a member of the genus Helcococcus, but it did not correspond to either of the two recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium was associated phylogenetically with the genus Helcococcus, with the unidentified organism forming a hitherto unknown subline within the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism that was recovered from a human wound should be classified as a novel species of the genus Helcococcus, namely Helcococcus sueciensis sp. nov. The type strain is CCUG 47334(T) ( = CIP 108183(T)).

Cloacibacterium normanense gen. nov., sp nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G + C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T)=CIP 108613(T) =ATCC BAA-825(T) = DSM 15886(T)).

Phenotypic and phylogenetic characterization of a new Corynebacterium species from dogs: description of Corynebacterium auriscanis sp. nov.

Six strains of a previously undescribed catalase-positive coryneform bacterium isolated from clinical specimens from dogs were characterized by phenotypic and molecular genetic methods. Biochemical and chemotaxonomic studies revealed that the unknown bacterium belonged to the genus Corynebacterium sensu stricto. Comparative 16S rRNA gene sequencing showed that the six strains were genealogically highly related and constitute a new subline within the genus Corynebacterium; this subline is close to but distinct from C. falsenii, C. jeikeium, and C. urealyticum. The unknown bacterium from dogs was distinguished from all currently validated Corynebacterium species by phenotypic tests including electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as a new species, Corynebacterium auriscanis. The type strain of C. auriscanis is CCUG 39938T.