Streptomyces bullii sp. nov., isolated from a hyper-arid Atacama Desert soil

A Streptomyces strain isolated from a hyper-arid Atacama Desert soil was characterised using a polyphasic taxonomic approach. The strain, designated C2^T, had chemical and morphological properties typical of the genus Streptomyces. The isolate formed a branch in the Streptomyces 16S rRNA gene tree together with the type strain of Streptomyces chromofuscus and was also loosely related to Streptomyces fragilis NRRL 2424^T. DNA:DNA relatedness values between the isolate and its two phylogenetic neighbours showed that it formed a distinct genomic species. The strain was readily distinguished from these organisms using a combination of morphological and phenotypic data. Based on the genotypic and phenotypic results, isolate C2^T represents a novel species in the genus Streptomyces, for which the name Streptomyces bullii sp. nov. is proposed. The type strain is C2^T (=CGMCC 4.7019^T = KACC 15426^T).     

Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov

Aims: To describe three new Amycolatopsis strains and assess the antibiotic biosynthetic potential of the genus. Methods and Results: Three strains, designated S1·3^T, S3·6^T and SE(8)3^T, belonging to the genus Amycolatopsis were isolated and found to cluster together by 16S rRNA and gyrB gene‐based phylogenetic analysis. Genetic distance values, based on the gyrB gene, were calculated between the strains and their closest relatives and were all above the threshold value of 0·02 that has been proposed to distinguish Amycolatopsis type strains. DNA–DNA hybridization experiments against related type strains confirmed that strain S3·6^T represents a unique genomic species. Strain S3·6^T was also found to be distinct from strains S1·3^T and SE(8)3^T, the latter two of which were also shown to be distinct from each other. Antibiotic biosynthetic genes were identified from multiple Amycolatopsis strains, and their presence was found to be phylogenetically associated. Conclusions: The data presented in this study indicate that strains S1·3^T, SE(8)3^T and S3·6^T belong to three novel species, for which the names Amycolatopsis circi sp. nov. (= DSM 45561^T = NRRL B‐24841^T), Amycolatopsis equina sp. nov. (= DSM 45563^T = NRRL B‐24842^T) and Amycolatopsis hippodromi sp. nov. (= DSM 45562^T = NRRL B‐24843^T) are proposed. Significance and Impact of the Study: Three new species of Amycolatopsis are described, and the knowledge of the antibiotic biosynthetic potential of the genus has been extended.     

Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus

An actinobacterial strain A23^T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23^T was most closely related to Amycolatopsis pretoriensis DSM 44654^T. Average nucleotide identity and digital DNA–DNA hybridization values between the genome sequences of isolate A23^T and its closest relative, Amycolatopsis pretoriensis DSM 44654^T, were 39.5% and 88.6%, which were below the 70% and 95–96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23^T was 10,560,374 bp with a DNA G?+?C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C_16:0, iso-C_15:0, anteiso-C_17:0 and C_16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23^T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23^T (=?DSM 111725^T?=?VKM Ac-2882^T).

     

Saccharopolyspora pathumthaniensis sp. nov., a novel actinomycetes isolated from termite guts (Speculitermes sp.)

Morphological and chemotaxonomic characterization of actinomycete strain S582 isolated from the gut of a termite (Speculitermes sp.) in Pathum Thani Province, Thailand, clearly demonstrated that this strain is a member of the genus Saccharopolyspora. 16S rDNA sequence analysis for the strain supported the assignment of the strain to the genus Saccharopolyspora. The similarity value of sequences between this strain and the closely related species Saccharopolyspora endophytica was 99.5%. The DNA G+C content was 70.2 mol%. DNA-DNA hybridization results (53.3%) and some physiological and biochemical properties indicated that strain S582(T) was distinguished from the phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain S582(T) should be a new species in the genus Saccharopolyspora and the name Saccharopolyspora pathumthaniensis sp. nov. is proposed for the strain. The type strain is S582(T) (=NBRC 104112(T) =BCC 28624(T)).     

Mycoplasma simbae sp. nov., Mycoplasma leopharyngis sp. nov., and Mycoplasma leocaptivus sp. nov., isolated from lions.

Mycoplasmas isolated from the throats of lions were shown to belong to three serotypes, all of which were serologically distinct from the previously recognized Mycoplasma and Acholeplasma spp. Eight mycoplasma colonies were cloned, including one from a leopard (strain LP), and were examined in detail for morphology, growth, and biochemical characteristics. The strains had the following properties: guanine-plus-cytosine contents of 37 mol% (strain LXT [T = type strain]), 28 mol% (strain LL2T), and 27 mol% (strain 3L2T) and a requirement for sterol. Strain 3L2T metabolized glucose, which was not metabolized by strains LXT and LL2T. Arginine and urea were not hydrolyzed. Strain LX (= NCTC 11724) is the type strain of a new species, Mycoplasma simbae; strain LL2 (= NCTC 11725) is the type strain of a second new species, Mycoplasma leopharyngis; and strain 3L2 (= NCTC 11726) is the type strain of a third new species, Mycoplasma leocaptivus.     

Legionella impletisoli sp. nov. and Legionella yabuuchiae sp. nov., isolated from soils contaminated with industrial wastes in Japan

In this study, we tried to isolate legionellae from nine Legionella DNA-positive soil samples collected from four different sites contaminated with industrial wastes in Japan. Using culture methods with or without Acanthamoeba culbertsoni, a total of 22 isolates of legionellae were obtained from five of the nine samples. Identification of species and/or serogroups (SGs), performed by DNA-DNA hybridization and agglutination tests, revealed that the 22 isolates consisted of ten isolates of Legionella pneumophila including five SGs, five Legionella feeleii, and one each of Legionella dumoffii, Legionella longbeachae, and Legionella jamestownensis. The species of the remaining four isolates (strains OA1-1, -2, -3, and -4) could not be determined, suggesting that these isolates may belong to new species. The 16S rDNA sequences (1476-1488bp) of the isolates had similarities of less than 95.0% compared to other Legionella species. A phylogenetic tree created by analysis of the 16S rRNA (1270bp) genes demonstrated that the isolates formed distinct clusters within the genus Legionella. Quantitative DNA-DNA hybridization tests on the OA1 strains indicated that OA1-1 should be categorized as a new taxon, whereas OA1-2, -3, and -4 were also genetically independent in another taxon. Based on the evaluated phenotypic and phylogenetic characteristics, it is proposed that one of these isolates from the soils, OA1-1, be classified as a novel species, Legionella impletisoli sp. nov.; the type strain is strain OA1-1(T) (=JCM 13919(T)=DSMZ 18493(T)). The remaining three isolates belong to another novel Legionella species, Legionella yabuuchiae sp. nov.; the type strain is strain OA1-2(T) (=JCM 14148(T)=DSMZ 18492(T)). This is the first report on the isolation of legionellae from soils contaminated with industrial wastes.     

Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidarum sp. nov., isolated from green lacewings and beetles

Fourteen yeast isolates belonging to the Metschnikowia clade were isolated from the digestive tracts of lacewings (Neuroptera: Chrysopidae), soldier beetles and leaf beetles (Coleoptera: Cantharidae and Chrysomelidae), and a caddisfly (Trichoptera: Hydropsychidae). The insect hosts were associated with sugary substances of plants, a typical habitat for yeasts in this clade. Based on DNA sequence comparisons and phenetic characters, the yeasts were identified as Candida picachoensis, Candida pimensis, and four undescribed taxa. Among the undescribed taxa, three yeasts were distinguished from one another and from other described taxa by nucleotide differences in the ribosomal DNA repeat, which were sufficient to consider them as new species. Two of the novel yeast species are described as Metschnikowia noctiluminum (NRRL Y-27753^T) and M. corniflorae spp. nov. (NRRL Y-27750^T) based in part on production of needle-shaped ascospores, which are found in most Metschnikowia species. Sexual reproduction was not observed in the third new yeast, Candida chrysomelidarum sp. nov. (NRRL Y-27749^T). A fourth isolate, NRRL Y-27752, was not significantly distinct from Metschnikowia viticola and Candida kofuensis to be described as a new species. Phylogenetic analysis of the D1/D2 loop sequences placed M. noctiluminum within the M. viticola clade, while C. chrysomelidarum was a sister taxon of Candida rancensis. Metschnikowia corniflorae was phylogenetically distinct from other new species and fell outside of the large-spored Metschnikowia group.     

Weizmannia acidilactici sp. nov., a lactic acid producing bacterium isolated from soils

The strains designed PP-18^T, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced l-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18^T, JC-4 and JC-7 were closely related to Weizmannia coagulans LMG 6326^T (97.27–97.64%) and W. acidiproducens KCTC 13078^T (96.46–96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained meso-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18^T were iso-C_15:0, anteiso-C_17:0, iso-C_16:0 and anteiso-C_15:0. The ANIb and ANIm values among the genomes of strains PP-18^T, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and W. coagulans LMG 6326^T and W. acidiproducens KCTC 13078^T were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7–23.6% when compared with W. coagulans LMG 6326^T and W. acidiproducens DSM 23148^T. The DNA G + C contents of strains PP-18^T, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18^T, JC-4 and JC-7 should be represented as a novel species within the genus Weizmannia for which the name Weizmannia acidilactici sp. nov. is proposed. The type strain is PP-18^T (=KCTC 33974^T = NBRC 113028^T = TISTR 2515^T).     

Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries

Three Gram-positive, anaerobic, pleomorphic strains (PG10(T), PG18 and PG22), were selected among five strains isolated from pig slurries while searching for host specific bifidobacteria to track the source of fecal pollution in water. Analysis of the 16S rRNA gene sequence showed a maximum identity of 94% to various species of the family Bifidobacteriaceae. However, phylogenetic analyses of 16S rRNA and HSP60 gene sequences revealed a closer relationship of these strains to members of the recently described Aeriscardovia, Parascardovia and Scardovia genera, than to other Bifidobacterium species. The names Neoscardovia gen. nov. and Neoscardovia arbecensis sp. nov. are proposed for a new genus and for the first species belonging to this genus, respectively, and for which PG10(T) (CECT 8111(T), DSM 25737(T)) was designated as the type strain. This new species should be placed in the Bifidobacteriaceae family within the class Actinobacteria, with Aeriscardovia aeriphila being the closest relative. The prevailing cellular fatty acids were C(16:0) and C(18:1)ω9c, and the major polar lipids consisted of a variety of glycolipids, diphosphatidyl glycerol, two unidentified phospholipids, and phosphatidyl glycerol. The peptidoglycan structure was A1γmeso-Dpm-direct. The GenBank accession numbers for the 16S rRNA gene and HSP60 gene sequences of strains PG10(T), PG18 and PG22 are JF519691, JF519693, JQ767128 and JQ767130, JQ767131, JQ767133, respectively.     

Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces

Morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from dog feces. The unknown bacterium was tentatively identified as a Eubacterium species, based on cellular morphological and biochemical tests. 16S rRNA gene sequencing studies, however, revealed that it was phylogenetically distant from Eubacterium limosum, the type species of the genus Eubacterium. Phylogenetically, the unknown species forms a hitherto unknown sub-line proximal to the base of a cluster of organisms (designated rRNA cluster XVI), which includes Clostridium innocuum, Streptococcus pleomorphus, and some Eubacterium species. Based on both phenotypic and phylogenetic criteria, it is proposed that the unknown bacterium be classified as a new genus and species, Allobaculum stercoricanis. Using a specific rRNA-targeted probe designed to identify Allobaculum stercoricanis, in situ hybridisation showed this novel species represents a significant organism in canine feces comprising between 0.1% and 3.7% of total cells stained with DAPI (21 dog fecal samples). The type strain of Allobaculum stercoricanis is DSM 13633(T)=CCUG 45212(T).