Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.

Antifungal metabolites, their novel sources, and targets to combat drug resistance

Excessive antibiotic prescriptions as well as their misuse in agriculture are the main causes of antimicrobial resistance which poses a growing threat to public health. It necessitates the search for novel chemicals to combat drug resistance. Since ancient times, naturally occurring medicines have been employed and the enormous variety of bioactive chemicals found in nature has long served as an inspiration for researchers looking for possible therapeutics. Secondary metabolites from microorganisms, particularly those from actinomycetes, have made it incredibly easy to find new molecules. Different actinomycetes species account for more than 70% of naturally generated antibiotics currently used in medicine, and they also produce a variety of secondary metabolites, including pigments, enzymes, and anti-inflammatory compounds. They continue to be a crucial source of fresh chemical diversity and a crucial component of drug discovery. This review summarizes some uncommon sources of antifungal metabolites and highlights the importance of further research on these unusual habitats as a source of novel antimicrobial molecules.

Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use

Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.

Lentzea tibetensis sp. nov., a novel Actinobacterium with antimicrobial activity isolated from soil of the Qinghai-Tibet Plateau

A novel filamentous Actinobacterium, designated strain FXJ1.1311^T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311^T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013^T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea. The genome-wide average nucleotide identity between strain FXJ1.1311^T and L. guizhouensis DHS C013^T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311^T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis. Based on the evidence presented here, strain FXJ1.1311^T represents a novel species of the genus Lentzea, for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311^T (=CGMCC 4.7383^T=DSM 104975^T).

Lentzea alba sp. nov., a novel actinobacterium isolated from soil

A novel actinobacterium, designated strain NEAU-D13^T, was isolated from soil collected from Aohan Banner, Chifeng, Inner Mongolia Autonomous Region, China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-D13^T belonged to the genus Lentzea and shared the highest sequence similarity with Lentzea kentuckyensisJCM 14913^T (99.17 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were ribose and mannose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and phosphatidylinositol. The menaquinone was only MK-9(H₄). The major fatty acids were iso-C_16:0, C_16:0, anteiso-C_17:0, iso-C_15:0 and anteiso-C_15:0. DNA G+C content was 68.71 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with L. kentuckyensisJCM 14913^T in the genus Lentzea. Meanwhile, a combination of digital DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-D13^T could be distinguished from its closely related strain. Therefore, it is concluded that strain NEAU-D13^T represents a novel species of the genus Lentzea, for which the name Lentzea alba sp. nov. is proposed, with NEAU-D13^T (=CCTCC AA 2019089^T=JCM 33970^T) as the type strain.

Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis

The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95-96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.

Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil

A novel actinobacterium, strain PSKA42^T was isolated from a soil sample of Kashmir Himalaya, India (latitude: 34°-01' N; longitude: 74°-47' E; altitude: 5328 ft). The morphological, biochemical and molecular characteristics predicted that PSKA42^T belongs to the genera Lentzea. Using the Ezbiocloud server it has also been manifested that the 16S rRNA gene sequence of PSKA42 was 98.4% similar with Lentzea guizhouensis DHSC013^T, Lentzea albidocapillata subsp. violacea IMSNU50388^T; 98.26% similar with Lentzea aerocolonigenes NRRLB-3298^T, Lentzea albidocapillata subsp. albidocapillata NRRLB-24057^T and 98.19% similar with Lentzea californiensis DSM43393^T. Whole-genome average nucleotide identity values between PSKA42^T and L. guizhouensis DHSC013^T, L. albidocapillata subsp. violaera IMSNU50388^T, L. aerocolonigenes NRRLB-3298^T, L. albidocapillata subsp. albidocapillata NRRLB-24057^T, L. californiensis DSM43393^T, L. flaviverucosa As40578^T were 84.94%, 85.8%, 87.15%, 87.71%, 79.29, and 87.22%, respectively, suggesting that PSKA42^T represented a new species. In-silco genome-to-genome distances analysis and MLSA with selected housekeeping genes also indicated that the isolate should be assigned to a new species under the genus Lentzea. Analysis of the whole-cell hydrolysate found mannose and ribose as major sugar while cell wall amino acid was identified as meso-diaminopimelic acid. Major fatty acids (> 5%) were observed as 15:0 iso (23.81%), and 16:0 iso (26.11%). PSKA42 contains polyketide synthase type-I genes but unable to show antimicrobial activity in laboratory conditions. The average GC content in its genome is 68.3%. Further, based on physicochemical, chemotaxonomic markers and molecular analysis, PSKA42^T can be assigned as novel species of Lentzea, we proposed Lentzea indica sp nov. The type strain is PSKA42^T (JCM 33729^T, MTCC 12936^T, MCC 4127^T).

Cave Actinobacteria as Producers of Bioactive Metabolites

Recently, there is an urgent need for new drugs due to the emergence of drug resistant pathogenic microorganisms and new infectious diseases. Members of phylum Actinobacteria are promising source of bioactive compounds notably antibiotics. The search for such new compounds has shifted to extreme or underexplored environments to increase the possibility of discovery. Cave ecosystems have attracted interest of the research community because of their unique characteristics and the microbiome residing inside including actinobacteria. At the time of writing, 47 species in 30 genera of actinobacteria were reported from cave and cave related habitats. Novel and promising bioactive compounds have been isolated and characterized. This mini-review focuses on the diversity of cultivable actinobacteria in cave and cave-related environments, and their bioactive metabolites from 1999 to 2018.

Lentzea isolaginshaensis sp. nov., an actinomycete isolated from desert soil

A novel actinomycete, designated strain NX62^T, was isolated from desert soil obtained from Isolaginsha, Ningxia Hui Autonomous Region, China. Its taxonomic position was determined using a polyphasic approach. The strain shows the typical morphological and chemotaxonomic features of members of the genus Lentzea: slight to dark yellow substrate mycelia and white to greyish white aerial hyphae fragmenting into rod-shaped elements; meso-diaminopimelic acid in the cell wall peptidoglycan; MK-9(H₄) and MK-9(H₂) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine and phosphatidylinositol as main polar lipids; iso-C_16:0 and iso-C_17:0 as major cellular fatty acids; and DNA G+C content of 70.1 mol%. 16S rRNA gene sequence analysis indicated that strain NX62^T shows high similarity to Lentzea cavernae SYSU K10001^T (99.3%) and Lentzea albida IFO 16102^T (98.9%), and formed a monophyletic clade with L. cavernae SYSU K10001^T in the phylogenetic tree. Based on a comparison of the phenotypic properties and the low level of DNA-DNA relatedness, strain NX62^T can be distinguished from phylogenetically related Lentzea species. Therefore, it is concluded that strain NX62^T represents a novel species of the genus Lentzea, for which the name Lentzea isolaginshaensis sp. nov. is proposed. The type strain is NX62^T (= CGMCC 4.7522^T = KCTC 49179^T).

Lentzea terrae sp. nov., isolated from soil and an emended description of Lentzea soli

A novel actinobacterium, designated strain NEAU-LZS 42^T, was isolated from soil collected from Mount Song, Henan Province, China, and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism should be assigned to the genus Lentzea and had the closest relationship with Lentzea soli NEAU-LZC 7^T (99.1 % similarity) and Lentzea cavernae SYSU K10001^T (98.2 %). The major menaquinones were identified as MK-9(H4) and MK-9(H2). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, glycophospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0, C16 : 1ω7c and C16 : 0. DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-LZS 42^T could be clearly differentiated from L. soli NEAU-LZC 7^T and L. cavernae SYSU K10001^T. Therefore, it is concluded that strain NEAU-LZS 42^T represents a novel species of the genus Lentzea, for which the name Lentzea terrae sp. nov. is proposed. The type stain is NEAU-LZS 42^T (=CGMCC 4.7428^T=DSM 105696^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Lentzea soli sp. nov., an actinomycete isolated from soil

A novel actinobacterium, designated strain NEAU-LZC 7^T, was isolated from soil collected from Mount Song and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LZC 7^T belonged to the genus Lentzea, with highest sequence similarity to Lentzea violacea JCM 10975^T (98.1 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. However, DNA-DNA relatedness, physiological and biochemical data showed that strain NEAU-LZC 7^T could be distinguished from its closest relative. Therefore, strain NEAU-LZC 7^T represents a novel species of the genus Lentzea, for which the name Lentzea soli sp. nov. is proposed, with NEAU-LZC 7^T (=CCTCC AA 2017027^T=JCM 32384^T) as the type strain.

Lentzea pudingi sp. nov., isolated from a weathered limestone sample in a karst area

A novel Gram-stain-positive, aerobic bacterium, designated strain DHS C021^T, was isolated from a limestone sample collected from the Puding Karst Ecosystem Research Station of Guizhou Province, southwest China. This strain developed branched vegetative mycelia, and its aerial mycelia fragmented into rod-shaped spores. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the whole-cell sugars comprised galactose, ribose and mannose. The respiratory quinone was identified as menaquinone MK-9(H4). The major cellular fatty acids were iso-C14 : 0 and iso-C16 : 0. The phospholipids detected were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidyethanolamine, phosphatidylinositol, phosphotidylinositolmannosides and one unidentified phospholipid. The genomic DNA G+C content was 69.8 mol% and 16S rRNA gene sequence analysis showed that the strain belonged to the genus Lentzea and shared highest sequence similarity with Lentzeaalbida CGMCC 4.1727^T (98.8 %) and Lentzea waywayandensis CGMCC 4.1646^T (98.5 %). However, it could be distinguished from these reference strains based on the low levels of DNA-DNA relatedness (54.5±2.7 and 41.7±3.2 %, respectively). On the basis of morphological, chemotaxonomic and phylogenetic characteristics, and DNA-DNA hybridization data, strain DHS C021^T represents a novel species of the genus Lentzea, for which the name Lentzeapudingi sp. nov. is proposed. The type strain is DHS C021^T (=CGMCC 4.7319^T=KCTC 39694^T).

Lentzea cavernae sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Lentzea

A novel actinobacterial strain, designated SYSU K10001T, was isolated from a limestone sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10001T was most closely related to the type strains of the genus Lentzea, Lentzea albida NBRC 16102T (98.8 % similarity) and Lentzea waywayandensis NRRL B-16159T (98.6 %), and is therefore considered to represent a member of the genus Lentzea. DNA-DNA hybridization values between strain SYSU K10001T and related type strains of the genus Lentzea were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, fructose, mannose and xylose. The major isoprenoid quinone was MK-9(H4), while the major fatty acids (>10 %) were iso-C16 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10001T was 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10001T represents a novel species of the genus Lentzea, for which the name Lentzea cavernae sp. nov. is proposed. The type strain is SYSU K10001T (=KCTC 39804T=CGMCC 4.7367T=NBRC 112394T).

The cave microbiome as a source for drug discovery: Reality or pipe dream?

This review highlights cave habitats, cave microbiomes and their potential for drug discovery. Such studies face many challenges, including access to remote and pristine caves, and sample collection and transport. Inappropriate physical and chemical growth conditions in the laboratory for the isolation and cultivation of cave microorganisms pose many complications including length of cultivation; some cave microorganisms can take weeks and even months to grow. Additionally, DNA extraction from cave environmental samples may be difficult due to the high concentration of various minerals that are natural DNA blocking agents. Once cave microorganisms are grown in the lab, other problems often arise, such as maintenance of pure culture, consistency of antimicrobial activity and fermentation conditions for antimicrobial production. In this review, we suggest that, although based on what has been done in the field, there is potential in using cave microorganisms to produce antimicrobial agents, one needs to be highly committed and prepared.

Lentzea guizhouensis sp. nov., a novel lithophilous actinobacterium isolated from limestone from the Karst area, Guizhou, China

A novel filamentous actinobacterium, designated strain DHS C013(T), was isolated from limestone collected in Guizhou Province, South-west China. Morphological and chemotaxonomic characteristics of the strain support its assignment to the genus Lentzea. Phylogenetic analyses showed that strain DHS C013(T) is closely related to Lentzea jiangxiensis FXJ1.034(T) (98.7 % 16S rRNA gene similarity) and Lentzea flaviverrucosa 4.0578(T) (98.0 % 16S rRNA gene similarity), but it can be distinguished from these strains based on low levels of DNA:DNA relatedness (~44 and ~37 %, respectively). Physiological and biochemical tests also allowed phenotypic differentiation of the novel strain from these closely related species. On the basis of the evidence presented here, strain DHS C013(T) is concluded to represent a novel species of the genus Lentzea, for which the name Lentzea guizhouensis sp. nov. is proposed. The type strain is DHS C013(T) (=KCTC 29677(T) = CGMCC 4.7203(T)).

Saccharothrix lopnurensis sp. nov., a filamentous actinomycete isolated from sediment of Lop Nur

A novel actinomycete strain, designated YIM LPA2h(T), was isolated from a sediment sample collected from Lop Nur, Xinjiang Uygur Autonomous Region, North-West China. The taxonomic position of strain YIM LPA2h(T) was investigated by a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were in accordance with the members of the genus Saccharothrix. The 16S rRNA gene sequence of the strain showed highest similarities to Saccharothrix yanglingensis (98.6 %), Saccharothrix longispora (98.4 %) and Saccharothrix hoggarensis (98.3 %). However, the DNA-DNA hybridization values between the new isolate YIM LPA2h(T) and S. yanglingensis, S. longispora and S. hoggarensis were significantly below 70 %. Strain YIM LPA2h(T) was found to contain meso-diaminopimelic acid as diagnostic diamino acid. The major sugars in whole-cell hydrolysates were rhamnose, galactose, mannose, glucose and fructose. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylhydroxylethanolamine, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant respiratory menaquinones were MK-9 (H4) and MK-10 (H4). The major fatty acids were C17:1 ω8c (15 %), iso-C15:0 (12 %), anteiso-C15:0 (12 %) and summed feature 3 (C16:1 ω6c/C16:1 ω7c, 10 %). The genomic DNA G+C content of strain YIM LPA2h(T) was determined to be 75 mol %. The genotypic and phenotypic results suggest that strain YIM LPA2h(T) represents a novel species of the genus Saccharothrix, for which the name Saccharothrix lopnurensis sp. nov. is proposed. The type strain is YIM LPA2h(T) (=CGMCC 4.7246(T)=KCTC 39545(T)).

Diversity and isolation of rare actinomycetes: an overview

A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.

Lentzea jiangxiensis sp. nov., isolated from acidic soil

A novel actinomycete, designated strain FXJ1.034(T), was isolated from acidic soil collected in Jiangxi Province, South-east China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.034(T) belonged to the genus Lentzea and showed high sequence similarities to Lentzea kentuckyensis NRRL B-24416(T) (98.5%) and Lentzea albida NBRC 16102(T) (98.3%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of the novel strain from closely related species. Based on the evidence presented here, strain FXJ1.034(T) represents a novel species of the genus Lentzea, for which the name Lentzea jiangxiensis sp. nov. is proposed. The type strain is FXJ1.034(T) ( = CGMCC 4.6609(T)  = NBRC 106680(T)).

Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm

A novel actinomycete, strain OFN S31(T), was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31(T) formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31(T) (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31(T) is characterized by the absence of mycelium and mycolic acids. Strain OFN S31(T) had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31(T) is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31(T) (=CIP 109864(T) =DSM 45258(T)).

Lentzea kentuckyensis sp. nov., of equine origin

A novel actinomycete, designated strain LDDC 2876-05T, was isolated from an equine placenta during the course of routine diagnostic tests for nocardioform placentitis. In a preliminary study, the strain was observed to be phylogenetically distinct from the generaCrossiellaandAmycolatopsisand probably a member of the genusLentzea.A polyphasic study of strain LDDC 2876-05Tconfirmed its identification as a member ofLentzeaon the basis of its chemotaxonomic and morphological similarity to all of the known species of the genus. Moreover, the strain could be distinguished from other species with validly published names on the basis of its phylogenetic and physiological characteristics and its fatty acid profile. Therefore strain LDDC 2876-05Trepresents a novel species of the genusLentzea, for which the nameLentzea kentuckyensissp. nov. is proposed. The type strain is LDDC 2876-05T(=NRRL B-24416T=DSM 44909T).

Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

Nocardia harenae sp. nov., an actinomycete isolated from beach sand

A novel actinomycete, strain WS-26T, was isolated from beach sand on the coast of Jeju Island, Republic of Korea, and subjected to a polyphasic taxonomic characterization. The organism produced reddish orange-coloured substrate mycelium and white aerial mycelium, both of which fragmented into rod-shaped elements. A neighbour-joining tree, based on 16S rRNA gene sequence studies, revealed that the isolate formed a distinct branch at the base of a cluster that included Nocardia carnea, N. flavorosea, N. pigrifrangens, N. sienata and N. testacea. This branching pattern was also found in a tree constructed using the maximum-likelihood method, but was not supported by the maximum-parsimony method. Levels of 16S rRNA gene sequence similarity between the isolate and its phylogenetic neighbours ranged from 96.5 to 97.8 %. Chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported its assignment to the genus Nocardia. On the basis of phenotypic and phylogenetic data, the organism was different from Nocardia species with validly published names. The name Nocardia harenae sp. nov. is proposed, with WS-26T (=KCCM 42317T=NRRL B-24459T) as the type strain.

Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment

A novel actinomycete, strain SST-8T, was isolated from sand sediment of Samyang Beach in Jeju, Korea, and subjected to a polyphasic taxonomic study. The organism, which produced opaque, circular, yellow colonies, with a coryneform morphology, showed the following chemotaxonomic characteristics:meso-diaminopimelic acid as the diamino acid in the peptidoglycan, MK-8(H2) as the major menaquinone, phosphatidylglycerol as the only polar lipid, anteiso-C15 : 0and anteiso-C17 : 0as major fatty acids and a DNA G+C content of 70.7 mol%. The combination of morphological and chemotaxonomic features supported its classification in the genusBrevibacterium. Phylogenetic analyses, based on 16S rRNA gene sequence studies, showed that strain SST-8Tformed an intermediate branch between theBrevibacterium luteolum/Brevibacterium otitidisandBrevibacterium mcbrellneri/Brevibacterium paucivoransclusters. Sequence similarity calculations based on a neighbour-joining analysis revealed that the closest relatives of strain SST-8Twere the type strains ofB. paucivorans(96.6 %),B. luteolum(96.5 %),B. mcbrellneri(96.3 %),Brevibacterium avium(96.0 %) andB. otitidis(95.9 %). Based on a broad set of phenotypic and genetic data, it was evident that the strain represents a novel species of the genusBrevibacterium. The nameBrevibacterium samyangensesp. nov. is proposed, with SST-8T(=NRRL B-41420T=KCCM 42316T) as the type strain.

Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea

A novel actinomycete, strain N3-2T, was isolated from a natural cave on Jeju Island, Republic of Korea, using a dilution method and was subjected to polyphasic taxonomy. The almost complete 16S rRNA gene sequence was determined by direct sequencing of the purified PCR product and was compared with those of representatives of the genus Nocardia. It was revealed from the phylogenetic analysis that the organism forms a distinct clade between the Nocardia salmonicida cluster and the Nocardia alba branch within the evolutionary radius occupied by the genus Nocardia of the family Nocardiaceae. The organism showed 16S rRNA gene sequence similarity of 97·4 % with its nearest phylogenetic neighbours, namely N. salmonicida and N. alba. The chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported the classification in the genus Nocardia. The organism was readily differentiated from Nocardia species with validly published names by a broad set of phenotypic properties and its unique phylogenetic position; the name Nocardia jejuensis sp. nov. is proposed, with N3-2T (=JCM 13281T=NRRL B-24430T) as the type strain.

Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave

Two actinomycete strains, designated N7-3T and N4-6T, were isolated from a natural cave on Jeju Island, Republic of Korea, by using a dilution method, and were subjected to physiological, chemical and molecular characterization. The nearly complete sequences of the 16S rRNA gene were aligned and compared with those of representatives of the genus Amycolatopsis. Phylogenetic analysis showed that the organisms belong to the family Pseudonocardiaceae and formed two distinct lineages within the evolutionary radius of the genus Amycolatopsis. The chemotaxonomic and morphological properties support their classification in the genus Amycolatopsis. The 16S rRNA gene sequence data revealed that the closest relatives of strains N7-3T and N4-6T were Amycolatopsis sulphurea (97·9 % similarity) and Amycolatopsis albidoflavus (98·7 % similarity), respectively. The combination of physiological and genetic data supported the observation that the organisms could be distinguished from each other and from established species of the genus Amycolatopsis. The names Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov. are proposed for the two novel species, with N7-3T (=NRRL B-24427T=JCM 13280T) and N4-6T (=NRRL B-24428T=JCM 13279T) as the respective type strains.

A lipomannan variant with strong TLR-2-dependent pro-inflammatory activity in Saccharothrix aerocolonigenes

Lipomannans (LMs) are powerful pro-inflammatory lipoglycans found in mycobacteria and related genera, however the molecular bases of their activity are not fully understood. We report here the isolation and the structural and functional characterization of a new lipomannan variant present in the Pseudonocardineae, Saccharothrix aerocolonigenes, designated SaeLM. Using a range of chemical degradations, NMR experiments, and mass spectrometry analyses, SaeLM revealed a mannosylphosphatidyl-myo-inositol (MPI) anchor glycosylated by an original carbohydrate structure whereby an (alpha1-->6)-Manp backbone is substituted at >80% of the O-2 position by side chains composed of Manp-(alpha1-->2)-Manp-(alpha1-->. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis indicated a distribution of SaeLM glyco-forms ranging from 19 to 61 Manp units, which centered on species containing 37 or 40 Manp units. SaeLM induced a Toll-like receptor 2 (TLR-2)-dependent production of tumor necrosis factor-alpha (TNF-alpha) by human THP-1 monocyte/macrophage cell lines and interestingly was found to be the strongest inducer of this pro-inflammatory cytokine when compared with other LAM/LM-like molecules. We previously established that a linear (alpha1-->6)-Manp chain, linked to the MPI anchor, is sufficient in providing pro-inflammatory activity. We demonstrate here that by adding side chains and increasing their size, one may potentiate this activity. These findings should enable a better understanding of the structure/function relationships of TLR-2-dependent lipoglycan signaling.

Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake, Xinjiang, China

A pyrene-degrading isolate, strain PYX-6(T), was obtained from Tianchi Lake, Xinjiang Uygur Autonomous Region, China, and was identified by means of polyphasic taxonomy. On the basis of 16S rRNA gene sequence similarity, strain PYX-6(T) was closely related to members of the genus Saccharothrix. Its 16S rRNA gene sequence similarity to each of Saccharothrix syringae, Saccharothrix australiensis, Saccharothrix algeriensis and Saccharothrix coeruleofusca was 98 %. Chemotaxonomic and physiological properties of strain PYX-6(T) further supported its affiliation to the genus Saccharothrix. DNA-DNA hybridization results and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PYX-6(T) from recognized Saccharothrix species. Therefore, strain PYX-6(T) represents a novel species, for which the name Saccharothrix xinjiangensis sp. nov. is proposed, with type strain PYX-6(T) (=AS 4.1731(T)=JCM 12329(T)).

Oxalotrophic bacteria

Oxalic acid and its salts are widespread in nature, as they are produced by many species of plants, algae and fungi. The bacteria, which are capable of using oxalate as a sole carbon and energy source, are described as being "oxalotrophic". Oxalotrophic bacteria do not constitute a homogeneous taxonomic group, but they do constitute a well-defined physiological group. A limited number of aerobic bacteria which are able to utilize oxalate as sole carbon and energy source have been completely described. Most of them are facultative methylotrophs and/or facultative hydrogen-oxidizing chemolithoautotrophs. In this review, the current status of the taxonomy and biodiversity of oxalotrophic bacteria in various environments, and aspects of their biotechnological potential, are briefly summarized.