Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae A Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6 T , was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbour was the type strain of Georgenia muralis (94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6 T were as follows: the major menaquinone was MK-8(H 4 ); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C 15 : 0 , anteiso-C 17 : 0 and iso-C 16 : 0 ; mycolic acids were absent. A new murein type, L-Lys-Gly-L-Glu-L-Glu (A4a), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6 T represents a novel species of a new genus within the suborder Micrococcineae, for which the name Ruania albidiflava gen. nov., sp. nov. is proposed. The type strain of Ruania albidiflava is 3-6 T (=CGMCC 4.3142 T =DSM 18029 T =JCM 13910 T =PCM 2644 T ).According to the estimation performed by Hammond (1995), the number of bacteria that have been successfully isolated and identified comprises only a small portion of the total that exist in nature. In the past decade, the Micrococcineae (Stackebrandt et al., 1997) has been one of the most studied suborders in the class Actinobacteria; numerous novel taxa in this suborder have been cultured and described (Martin et al., 1997; Groth et al., 1999a Groth et al., , b, 2001Groth et al., , 2002von Wintzingerode et al., 2001; Altenburger et al., 2002;Takahashi et al., 2006). In the current study, we describe a bacterium isolated from farmland soil collected in Shandong Province, China, and propose a novel species of a new genus in the suborder Micrococcineae.Farmland soil samples were collected from a cotton field in Shandong Province. A 1 g soil sample was suspended in 10 ml sterile distilled water and mixed thoroughly by shaking overnight at room temperature. The suspension was serially diluted and spread onto yeast extract-starch agar (JCM medium no. 42) plates, followed by incubation for 1 week under humid conditions at 28 uC. The organism thus isolated, designated strain 3-6 T , was picked and transferred to fresh nutrient agar for purification. The pure culture was tested for growth in various media and was maintained on nutrient agar slants at 4 u C.For observation of colony and cell morphology, strain 3-6 T was grown on nutrient agar, R agar (Groth et al., 1999b) and trypticase soy agar (TSA; BBL) for up to 5 days at 28 uC. Light and scanning electron micrographs were taken according to methods described previously (Huang et al., 2004). The presence of flagella was examined via transmission electron micros...

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Propionibacterium propionicum belongs to the "acnes group" of propionibacteria, which is currently considered as clinically important because of its growing potential in infections, in particular with those connected with immune system dysfunctions. Propionibacteria are thought to be actinomycete-like microorganisms and may still cause diagnostic difficulties. The chloroformmethanol extracts of the cell mass of P. propionicum (type strain) gave in TLC analysis the characteristic glycolipid profile containing four major glycolipids, labeled G 1 through G 4 . These polar lipids were found to be useful chemotaxonomic markers to differentiate P. propionicum from other cutaneous propionibacteria, in particular from strains of the acnes group. Glycolipids G 1 -G 4 were isolated and purified using gel-permeation chromatography, TLC, and high performance liquid chromatography, and their structures were elucidated by compositional and methylation analyses, specific chemical degradations, MALDI-TOF mass spectrometry, and 1 H NMR and 13 C NMR spectroscopy, including HMBC, TOCSY, HMQC, and NOESY experiments. Glycolipids G 2 and G 3 possess as backbone ␣-D-Glcp-(1 3 3)-␣-D-Glcp-(1 3 1)-Gro (Gro, glycerol), in which position O-2 of the glycerol residue is acylated by a fatty acid (mainly C 15 :0) while O-3 is substituted by an alkyl ether chain. In glycolipid G 3 , an additional fatty acyl chain was linked to O-6 of the terminal glucose residue. Glycolipid G 4 was structurally related to G 2 but devoid of one glucose residue. Glycolipid G 1 was isolated in small amounts, and its structure was therefore deduced from MALDI-TOF-MS experiments alone, which revealed that it possessed the structure of G 2 but was lacking one fatty acid residue. In studies on the biological properties of P. propionicum glycolipids, the anti-P. propionicum rabbit antisera reacted in dot enzyme-immunoblotting test with G 2 and G 3 . Glycolipid G 3 was able to induce the delayed type of hypersensitivity. The results indicated that these novel ether linkage-containing polar glycolipids are immunogenic and possibly active in hypersensitivity, and thus, in pathogenesis.

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The taxonomic position of an actinomycete, strain 1BDZ T , isolated from a clinical human source was determined using a polyphasic approach. Phylogenetic analysis based on almost complete 16S rDNA sequences showed that this organism consistently formed a distinct line with the Amycolatopsis methanolica subclade within the genus Amycolatopsis, and shared moderately low 16S rDNA similarity (<96?5 %) with other species. The organism was also found to have chemical and morphological properties typical of members of the genus Amycolatopsis. A range of phenotypic characteristics readily distinguished this strain from representatives of all species of Amycolatopsis with validly published names. On the basis of these data, a novel species, Amycolatopsis palatopharyngis sp. nov., is proposed to accommodate strain 1BDZ T

Background Elizabethkingia miricola is a rare Gram-negative bacterium found in water and clinical specimens. Typical culturing methods often misidentify Elizabethkingia spp. as Flavobacterium or Chryseobacterium. Although diagnosis is based on culturing samples taken from sterile sites, such as blood, a proper identification of this bacterium requires an expertise that goes beyond the capabilities of a typical clinical laboratory.Case presentationA 35-year-old woman diagnosed with common variable immunodeficiency was admitted to our center. Previous treatment with antibiotics (amoxicillin plus clavulanate, first and third generation of cephalosporins, macrolides) and systemic corticosteroids (up to 120 mg/day of prednisolone) failed to arrest the spread of inflammation. Gingival recession was observed in her oral cavity, resulting in an apparent lengthening of her teeth. In addition to typical commensal bacteria, including streptococci and neisseriae, strains of Rothia mucilaginosa and Elizabethkingia miricola were identified upon a detailed microbiological examination using a MALDI-TOF MS Biotyper system. The presence of the latter strain correlated with severe periodontitis, lack of IgA in her saliva and serum, a very low IgG concentration (< 50 mg/dl), IgM-paraproteinemia, decreases in C3a and C5a and microvascular abnormality. High-dose immunoglobulin (to maintain IgG > 500 mg/dl) and targeted levofloxacin treatment resulted in immune system reconstitution, oral healing, and eradication of the Elizabethkingia infection.Conclusions E. miricola rarely causes disease in healthy individuals. However, the overgrowth of commensal bacteria, lack of IgG/IgA, microvasculopathy and complement cascade activation in patients with humoral immunodeficiency may facilitate Elizabethkingia invasion. Overuse of antibiotics, particularly beta-lactams, may cause mucosal colonization by E. miricola, followed by its multiplication combined with periodontitis that prompts bacterial translocation. MALDI-TOF Biotyper analysis may become a method of choice for identification of Elizabethkingia infections.Electronic supplementary materialThe online version of this article (10.1186/s12879-017-2886-7) contains supplementary material, which is available to authorized users.

e Nocardiosis is a rare disease that is caused by Gram-positive actinobacteria of the Nocardia genus and affects predominantly immunocompromised patients. In its disseminated form, it has a predilection for the central nervous system and is associated with high mortality rates. Therefore, prompt identification of the pathogen is critical. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a relatively novel technique used for identification of microorganisms. In this work, an upgraded MALDI-TOF Biotyper database containing Corynebacterineae representatives of strains deposited in the Polish Collection of Microorganisms was created and used for identification of the strain isolated from a nocardial brain abscess, mimicking a brain tumor, in an immunocompetent patient. Testing with the API Coryne system initially incorrectly identified Rhodococcus sp., while chemotaxonomic tests, especially mycolic acid analysis, enabled correct Nocardia identification only at the genus level. Subsequent sequence analysis of 16S rRNA and secA1 genes confirmed the identification. To improve the accuracy of the results, an in-house database was constructed using optimized parameters; with the use of the database, the strain was eventually identified as Nocardia farcinica. Clinical laboratories processing various clinical strains can upgrade a commercial database to improve and to accelerate the results obtained. This is especially important in the case of Nocardia, for which valid microbial diagnosis remains challenging; reference laboratories are often required to identify and to survey these rare actinobacteria.N ocardia represents Gram-positive actinobacteria that are etiological agents of the rare disease nocardiosis, which affects predominantly immunocompromised patients. Nocardiosis usually presents itself as a solitary lesion located in lung, skin, or brain (primary nocardiosis), but sometimes disseminated nocardiosis with multiple sites is observed. Nocardia spp. show a marked predilection for the central nervous system (CNS) (1).Nocardiosis of the CNS constitutes about 40% of all cases of disseminated nocardioses and is associated with high mortality rates. The true incidence of Nocardia infections is difficult to assess, because of problems with the identification of these bacteria. Many different phenotypic, chemotaxonomic, or genotyping methods are available, but each method possesses drawbacks; for this reason, fast reliable identification of Nocardia isolates is very important. Because Nocardia spp. differ in antibiotic susceptibility, correct identification of clinical strains is critical for adequate treatment.Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has been introduced for microbial identification in the past few years. Its reliability, accuracy, and cost-effectiveness have been well described in the literature (2-4). This method can be used to identify microorganisms from all domains of life, i.e., Archaea, Bacteria, and E...

We investigated the association between dietary intake of n-3 and n-6 polyunsaturated fatty acids (PUFAs), serum profiles, and immune and inflammatory markers in juvenile idiopathic arthritis (JIA) in relation to onset, activity, and duration. A total of 66 JIA patients and 42 controls were included. Serum PUFA levels were assessed by gas-liquid chromatography-mass spectrometry, a dietary intake by 7-day dietary record method, and IL-6, IL-10, and IL-17A levels using ELISA. Dietary PUFA intake did not differ between the JIA group and controls. Intakes of n-6 and n-3 PUFA and serum levels were not associated. Levels of total n-6 PUFA and linoleic acid (LA) were higher in inactive JIA than in active JIA. Patients with active and short-lasting disease (less than 3 months from diagnosis) had significantly lower levels of arachidonic acid (AA) and docosahexaenoic acid (DHA) than the control. Serum α-linolenic acid (ALA) levels were significantly higher in poly-JIA than in oligo-JIA and in controls. We found significantly higher serum IL-10 levels in JIA than in controls. Serum n-6 and n-3 levels were significantly negatively correlated with active joint count, erythrocyte sedimentation rate, and C-reactive protein and positively with platelet count. Our study presents the low levels of AA and DHA in the active phase of short-lasting JIA, particularly poly-JIA, and the relationship between n-6 and n-3 PUFA and classic markers of inflammation. PUFAs may contribute to the pathogenesis of JIA and support a necessity to identify new targets suitable for successful interventional studies in JIA patients.