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Two actinobacterial strains were isolated from samples collected from the University of Cape Town, South Africa. A third actinobacterial strain was isolated from soil collected in the town of Stellenbosch, South Africa, using a newly-developed Kribbella-selective medium. Analysis of the 16S rRNA genes showed that the three strains belonged to the genus Kribbella. A multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes showed that strains YM55 T and SK5 were most closely related to the type strains of Kribbella sindirgiensis and Kribbella soli, while strain YM53 T was most closely related to the type strain of Kribbella pittospori. Digital DNA-DNA hybridisation and Average Nucleotide Identity (ANI) analyses showed that strains YM55 T and SK5 belong to the same genomic species (OrthoANI value = 98.4%), but are distinct from the genomic species represented by the type strains of K. sindirgiensis (OrthoANI values < 95.6%) and K. soli (OrthoANI values < 91.4%). Strain YM53 T is distinct from the genomic species represented by the type strain of K. pittospori (OrthoANI value = 94.0%). Phenotypic comparisons showed that strains YM55 T and SK5 are distinct from the type strains of K. sindirgiensis and K. soli and that strain YM53 T is distinct from the type strain of K. pittospori. Strains YM53 T and YM55 T are thus presented as the type strains of novel species, for which the names Kribbella capetownensis sp. nov. (= DSM 29426 T  = NRRL B-65062 T ) and Kribbella speibonae sp. nov. (= DSM 29425 T  = NRRL B-59161 T ), respectively, are proposed.

Two novel members of the genus Amycolatopsis were isolated from soil samples collected in South Africa. Strains JS72(T) and M29(T) clustered in the same clade in the 16S-rRNA, gyrB-16S-rRNA and gyrB-recN gene trees. Both strains showed anti-mycobacterial activity. The oxyB P450 monooxygenase B gene required for the production of glycopeptide antibiotics was detected in both strains, while strain JS72(T) was also shown to contain the 3-amino-5-hydroxy-benzoic acid synthase gene, which is required for the production of the ansamycin class of antibiotics. Genetic distance values (based on the gyrB and recN genes) were calculated between strains JS72(T) and M29(T) and their closest phylogenetic relatives. The values for strain JS72(T) were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis-type strains. The gyrB-based values for strain M29(T) were above the threshold for all but one strain; the recN-based values were all above the threshold. These data, along with DNA-DNA hybridization data, showed that strains JS72(T) and M29(T) belong to distinct genomic species. The physiological, phylogenetic and genetic distance data support the description of strains JS72(T) and M29(T) as the type strains of novel species, for which the names Amycolatopsis speibonae sp. nov. (=DSM 46660(T)=NRRL B-24958(T)) and Amycolatopsis roodepoortensis sp. nov. (=DSM 46661(T)=NRRL B-24959(T)) are proposed, respectively.

A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16(T), grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16(T) and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridisation experiments confirmed that strain UM16(T) represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16(T) as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272(T) = NRRL B-24724(T)).

An actinomycete, strain BS2T, was isolated from a sand sample collected from an estuary in Plettenberg Bay, Western Cape Province, South Africa. Based on 16S rRNA gene sequence similarities and chemotaxonomy, strain BS2T was identified as a member of the genus Gordonia. It exhibited weak antibiosis against Mycobacterium aurum A+ and Mycobacterium smegmatis LR222. Phenotypic and phylogenetic results allowed for the differentiation of strain BS2T from other species within the genus Gordonia. DNA-DNA hybridization further differentiated strain BS2T from its nearest phylogenetic neighbour, Gordonia terrae NRRL B-16283T (57.5+/-4.4% DNA relatedness). Strain BS2T is therefore a novel species within the genus Gordonia, for which the name Gordonia lacunae is proposed, with the type strain being BS2T (=DSM 45085T=NRRL B-24551T).

A novel actinomycete, designated strain S1.4(T), was isolated from a soil sample collected from Kenilworth Racecourse in the Western Cape, South Africa. The strain was able to grow in the presence of 5 % NaCl. It contained ll-diaminopimelic acid and glycine in the cell-wall peptidoglycan with glucose present in the whole-cell sugar profile. Strain S1.4(T) was shown to be a member of either the genus Kribbella or the genus Nocardioides based on a rapid molecular identification method by using single-enzyme restriction endonuclease digestion of the PCR-amplified 16S rRNA gene with MboI, VspI, SphI, SnaBI, SalI and AgeI. Analysis of the 16S rRNA gene sequence indicated that strain S1.4(T) belonged to the genus Kribbella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain S1.4(T) was related most closely to Kribbella solani DSA1(T). Strain S1.4(T) was phenotypically distinct from K. solani DSA1(T) and was shown to be a separate genomic species based on DNA-DNA hybridization experiments (40.4+/-3.8 % DNA-DNA relatedness between the two). Strain S1.4(T) (=DSM 19227(T) =NRRL B-24553(T)) is thus presented as the type strain of a novel species, for which the name Kribbella hippodromi sp. nov. is proposed.

As part of an antibiotic-screening programme, the actinomycete strain HMC1(T) was isolated from soil collected from the banks of the Gamka River in the Swartberg Nature Reserve, Western Cape Province, South Africa. The isolate produced branching vegetative mycelia, which entwined to form rope-like structures. It exhibited antibiosis against Enterococcus faecium VanA (a vancomycin-resistant clinical strain) and Mycobacterium aurum A+. Organic solvent extracts of the culture filtrate and mycelial mass of strain HMC1(T) exhibited moderate antibiosis against Mycobacterium aurum A+, Mycobacterium bovis BCG (Tokyo) and Mycobacterium tuberculosis H37Rv(T). The chemotaxonomic characteristics of strain HMC1(T) corresponded with those of members of the genus Actinomadura. Furthermore, phylogenetic analysis based on the 16S rRNA gene showed that the strain was closely related to members of the genus Actinomadura. Phenotypic and 16S rRNA gene sequence analyses indicated that strain HMC1(T) represents a novel species of the genus Actinomadura, for which the name Actinomadura rudentiformis sp. nov. is proposed. The type strain is HMC1(T) (=DSM 44962(T)=NRRL B-24458(T)).

Two novel nocardioform actinomycetes, strains Q41T and HMC25T, were isolated from soil samples collected in the Western Cape province, South Africa. Rapid genus identification revealed that the isolates belonged to the genus Kribbella (based on single-digestion restriction analysis of the 16S rRNA gene sequences with MboI, VspI, SphI, SnaBI, SalI and AgeI). Both isolates had ll-diaminopimelic acid and glycine in their cell-wall peptidoglycan, and contained mannose and ribose as whole-cell sugars. Strain HMC25T is able to grow at 45 degrees C and in the presence of NaCl (3 %), cephaloridine (10 microg ml(-1)) and gentamicin sulphate (10 microg ml(-1)). Strain Q41T grows in the presence of NaCl (2 %). Neither strain was able to grow under anaerobic conditions, whereas Kribbella flavida KACC 20248T, Kribbella jejuensis HD9T, Kribbella koreensis KACC 20250T and Kribbella sandramycini KACC 20249T exhibited weak but distinct growth under anaerobic conditions. Physiological test results and 16S rRNA gene sequence analysis allowed Q41T and HMC25T to be distinguished from other members of the genus with validly published names. Strains HMC25T (=NRRL B-24426T=DSM 17345T) and Q41T (=NRRL B-24425T=DSM 17344T) therefore represent the type strains of novel species, for which the names Kribbella swartbergensis sp. nov. and Kribbella karoonensis sp. nov., respectively, are proposed.

An actinomycete, strain B60(T), was isolated from a soil sample in Napier, Western Cape province of South Africa. Based on 16S rRNA gene sequence analysis and chemotaxonomy, strain B60(T) was identified as a member of the genus Actinomadura. Strain B60(T) produced an antibiotic with activity against Escherichia coli, Enterococcus faecium and Mycobacterium aurum, but not against Mycobacterium tuberculosis. Significant differences in morphological and physiological characteristics indicate that strain B60(T) represents a novel species of the genus Actinomadura. The name Actinomadura napierensis sp. nov. is proposed. The type strain is B60(T) (=DSM 44846(T)=NRRL B-24319(T)).

Actinomycete strains isolated from lesions on equine placentas from two horses in Kentucky and one in South Africa were subjected to a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics indicated that the isolates are members of the genus AMYCOLATOPSIS: On the basis of phylogenetic analysis of 16S rDNA sequences, the isolates are related most closely to Amycolatopsis mediterranei. Physiological characteristics of these strains indicated that they do not belong to A. mediterranei and DNA relatedness determinations confirmed that these strains represent three novel species of the genus Amycolatopsis, for which the names Amycolatopsis kentuckyensis (type strain, NRRL B-24129(T)=LDDC 9447-99(T)=DSM 44652(T)), Amycolatopsis lexingtonensis (type strain, NRRL B-24131(T)=LDDC 12275-99(T)=DSM 44653(T)) and Amycolatopsis pretoriensis (type strain, NRRL B-24133(T)=ARC OV1 0181(T)=DSM 44654(T)) are proposed.

Since the late 1980s a distinct form of focally-extensive mucoid to mucopurulent uterine body chronic placentitis,caused by nocardioform organisms, hasbeen recognised in horses in the USA state of Kentucky and possibly in other areas. This disease has led to increasing numbers of foal losses from late abortions, still-births, prematurity, or early neonatal deaths. The foals are usually not infected, but may be small or emaciated. Modes of infection and transmission are as yet unknown. Nocardia spp. and related nocardioform bacteria as causes of equine infertility, endometritis and foal death are briefly reviewed. A case of near full-term abortion involving a Friesian mare in the Pretoria district of Gauteng Province in South Africa during February 2000, with the same placental lesion as described in the Kentucky cases, is presented. Nocardioform organisms were visualised on impression smears and histological sections of affected foetal membranes, and were also cultured. The organism has been identified at the Livestock Disease Diagnostic Center of the University of Kentucky as an Amycolatopsis sp. of the less-commonly diagnosed group of nocardioforms causing placentitis in the USA. The organism was cultured from the uterus of the mare 18 days post-foaling, but after a 2-week course of oral trimethoprim and sulphamethoxazole, based on antibiogram sensitivity testing, a uterine flush yielded no growth. A semen sample from the sire of the aborted foal did not yield any Gram-positive filamentous branching bacteria. The mare subsequently conceived to a single insemination.

This study investigated the prevalence of nim genes (proposed to encode a 5-nitroimidazole resistance product) in 64 anaerobic/facultative anaerobic bacteria. Employing universal nim gene primers, 458-bp amplified fragments were recorded as presumptive positives in 22/64 strains at an annealing temperature of 52 degrees C and 15/64 strains at 62 degrees C, of which seven were propionibacteria. DNA sequencing confirmed the presence of nimA genes in Propionibacterium spp. (five strains), Actinomyces odontolyticus (one strain), Prevotella bivia (one strain) and Clostridium bifermentans (one strain) and nimB genes from five strains of Bacteroides fragilis. nimA genes were predominant in propionibacteria indicating a potential nimA gene source in anaerobic environments.