Gordonia metallireducens sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream.

A polyphasic taxonomic study was carried out on strain TSed Te1T, isolated from sediment of a stream contaminated with acid drainage from a coal mine. The bacterium forms pink-pigmented colonies and has a rod-coccus growth cycle, which also includes some coryneform arrangements. This bacterium is capable of growing in the presence of up to 750 µg ml-1 tellurite and 5000 µg ml-1 selenite, reducing each to elemental form. Nearly complete 16S rRNA gene sequence analysis associated the strain with Gordonia, with 99.5 and 99.3 % similarity to Gordonia namibiensis and Gordonia rubripertincta, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization comparisons with the closest phylogenetic neighbour of TSed Te1T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids were C16 : 0, C18 : 1, C16 : 1 and tuberculostearic acid. The DNA G+C content was 67.6 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside, while MK-9(H2) was the only menaquinone found. Mycolic acids of C56-C60 were present. Whole-cell hydrolysates contained meso-diaminopimelic acid along with arabinose and galactose as the major cell-wall sugars. On the basis of the results obtained in this study, the bacterium was assigned to the genus Gordonia and represents a new species with the name Gordonia metallireducens sp. nov. The type strain is TSed Te1T (=NRRL B-65678T=DSM 114093T).

Native fungal community remains resilient during bioremediation of DBP pollution by exogenous Gordonia phthalatica QH-11T.

Microbial bioremediation is a highly effective method to degrade phthalates in the environment. However, the response of native microbial communities to the exogenously introduced microorganism remains unknown. In this study, the native fungal community was monitored by amplicon sequencing of the fungal ITS region during the restoration process of the di-n-butyl phthalate (DBP)-contaminated soils with Gordonia phthalatica QH-11T. Our results showed that the diversity, composition, and structure of the fungal community in the bioremediation treatment did not differ from the control, and no significant correlations were found between number of Gordonia and variation of fungal community. It was also observed that DBP pollution initially increased the relative abundance of plant pathogens and soil saprotrophs first, but their proportions returned to the initial level. Molecular ecological network analysis showed that DBP pollution increased the network complexity, while the network was not significantly altered by bioremediation. Overall, the introduction of Gordonia was shown to not have a long-term impact on the native soil fungal community. Therefore, this restoration method can be considered safe in terms of soil ecosystem stability. The present study provides a deeper insight into the effect of bioremediation on fungal communities and provides an extended basis to further explore the ecological risks of introducing exogenous microorganisms.

Evaluation of distinct molecular architectures and coordinated regulation of the catabolic pathways of oestrogenic dioctyl phthalate isomers in Gordonia sp.

Bacterial strain GONU, belonging to the genus Gordonia, was isolated from a municipal waste-contaminated soil sample and was capable of utilizing an array of endocrine-disrupting phthalate diesters, including di-n-octyl phthalate (DnOP) and its isomer di(2-ethylhexyl) phthalate (DEHP), as the sole carbon and energy sources. The biochemical pathways of the degradation of DnOP and DEHP were evaluated in strain GONU by using a combination of various chromatographic, spectrometric and enzymatic analyses. Further, the upregulation of three different esterases (estG2, estG3 and estG5), a phthalic acid (PA)-metabolizing pht operon and a protocatechuic acid (PCA)-metabolizing pca operon were revealed based on de novo whole genome sequence information and substrate-induced protein profiling by LC-ESI-MS/MS analysis followed by differential gene expression by real-time PCR. Subsequently, functional characterization of the differentially upregulated esterases on the inducible hydrolytic metabolism of DnOP and DEHP revealed that EstG5 is involved in the hydrolysis of DnOP to PA, whereas EstG2 and EstG3 are involved in the metabolism of DEHP to PA. Finally, gene knockout experiments further validated the role of EstG2 and EstG5, and the present study deciphered the inducible regulation of the specific genes and operons in the assimilation of DOP isomers.

Characteristics and Treatment of Gordonia spp. Bacteremia, France.

Systemic Gordonia spp. infections are rare and occur mostly among immunocompromised patients. We analyzed 10 cases of Gordonia bacteremia diagnosed in 3 tertiary care centers in France to assess risk factors, treatment, and clinical outcomes. Most patients were cured within 10 days by using ß-lactam antimicrobial therapy and removing central catheters.

Gordonia aquimaris sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand.

An actinobacterium strain, SW21T, was isolated from seawater collected in the upper Gulf of Thailand. Cells were Gram-stain-positive, aerobic and rod-shaped. Growth was observed from 15 to 37 °C and at pH 6-8. Maximum NaCl for growth was 14 % (w/v). meso-Diaminopimelic acid, arabinose, galactose, glucose, rhamnose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside were detected as the phospholipids in the cells. The major menaquinones were MK-9(H2) and MK-7(H2). The major cellular fatty acids were C16 : 0, C18 : 1 ω9c, C18 : 0 and C18 : 010-methyl (TBSA). The 16S rRNA gene sequence data supported the assignment of strain SW21T to the genus Gordonia and showed that Gordonia mangrovi KCTC 49383T (98.7 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA-DNA hybridization (30.7 %) values between strain SW21T and its closest neighbour were below the threshold values for delineation of a novel species. The combination of genotypic and phenotypic data indicated that strain SW21T is representative of novel species of the genus Gordonia. The name Gordonia aquimaris sp. nov. is proposed for strain SW21T. The type strain is SW21T (=TBRC 15691T=NBRC 115558T).

Whole genome sequencing and transcriptomics-based characterization of a novel ß-cypermethrin-degrading Gordonia alkanivorans GH-1 isolated from fermented foods.

Beta-cypermethrin (ß-CY) is an organic compound that is widely used as a synthetic pesticide in agriculture and family. Excessive accumulation of ß-CY inevitably causes environmental pollution, which has led to food safety and human health concerns. Identification of microorganisms from food sources that are capable of ß-CY biodegradation may help prevent pollution due to ß-CY accumulation. Here, Gordonia alkanivorans GH-1, which was isolated from the traditional Sichuan fermented food, Pixian Doubanjiang, could not only degrade 82.76% of 50 mg/L ß-CY at 96 h, but also degraded the intermediate degradation products including dibutyl phthalate (DBP), benzoic acid (BA) and phenol (Ph). This bacterial strain, thus, effectively improved the efficiency of removal of ß-CY and its related metabolites, without being limited by toxic intermediates. Whole genome sequencing and transcriptomics analyses have demonstrated that the bacteria affected the transcription of genes related to cell response and material transport under the stress induced by ß-CY, and thereby promoted degradation and transformation of ß-CY. Moreover, a complete pathway of ß-CY degradation is proposed based on the key genes involved in degradation. This study provides important theoretical significance and reference value for eliminating pesticide residues in agricultural products and food to ensure food safety.

Biotransformation of 3-cyanopyridine to nicotinic acid using whole-cell nitrilase of Gordonia terrae mutant MN12.

In the present study, the Gordonia terrae was subjected to chemical mutagenesis using ethyl methane sulfonate (EMS) and methyl methane sulfonate (MMS), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), 5-bromouracil (5-BU) and hydroxylamine with the aim of improving the catalytic efficiency of its nitrilase for conversion of 3-cyanopyridine to nicotinic acid. A mutant MN12 generated with MNNG exhibited increase in nitrilase activity from 0.5 U/mg dcw (dry cell weight) (in the wild G. terrae) to 1.33 U/mg dcw. Further optimizations of culture conditions using response surface methodology enhanced the enzyme production to 1.2-fold. Whole-cell catalysis was adopted for bench-scale synthesis of nicotinic acid, and 100% conversion of 100 mM 3-cyanopyridine was achieved in potassium phosphate buffer (0.1 M, pH 8.0) at 40 °C in 15 min. The whole-cell nitrilase of the mutant MN12 exhibited higher rate of product formation and volumetric productivity, i.e., 24.56 g/h/g dcw and 221 g/L as compared to 8.95 g/h/g dcw and 196.8 g/L of the wild G. terrae. The recovered product was confirmed by HPLC, FTIR and NMR analysis with high purity (> 99.9%). These results indicated that the mutant MN12 of G. terrae as whole-cell nitrilase is a very promising biocatalyst for the large-scale synthesis of nicotinic acid.

A cytotoxic triterpenoid from a Periplaneta americana-derived, Gordonia hongkongensis WA12-1-1.

The secondary metabolites produced by microorganisms are a source of novel compounds with antitumor activities. In this study, we isolated biologically active secondary metabolites produced by microorganisms in the intestinal tract of Periplaneta americana. Based on the 16S rRNA gene sequencing, Gordonia hongkongensis WA12-1-1 was identified as the main microorganisms in the intestinal tract of P. americana. The obtained sequence was deposited in the National Center for Biotechnology Information (NCBI) database under the accession number MZ348554. The isolated secondary metabolites were separated and purified by thin layer chromatography, silica gel column chromatography, Sephadex column chromatography, open octadecyl silane column chromatography, high-performance liquid chromatography (HPLC), and semipreparative HPLC. Next, the structure of individual compounds was determined by ultraviolet spectroscopy, nuclear magnetic resonance, and mass spectrometry. A total of 20 compounds were isolated from the secondary metabolites produced by G. hongkongensis WA12-1-1. A total of 12 compounds were obtained from the crude ethyl acetate extract of the culture supernatant and eight from the cellular fraction. Compound 1 was identified as a triterpenoid named gordonterpene and showed cytotoxicity against A549 and HepG2 cell lines. These findings form a basis for further studies on the bioactivity of gordonterpene to tumor cells.

Epidemiology and in vitro antimicrobial susceptibility of aerobic Actinomycetales in a clinical setting / Epidemiología y sensibilidad in vitro de especies de Actinomycetales aerobios en la rutina asistencial

Introduction: The incidence of infections caused by aerobic actinomycetes is increasing. Recent changes in taxonomy and the variability in susceptibility patterns among species make necessary a proper identification and antibiotic susceptibility testing. Material and methods: Fifty-three strains of aerobic actinomycetes were identified by MALDI-TOF MS using the VITEK MS Mycobacterium/Nocardia kit (bioMérieux, France) in a tertiary hospital in Spain during a six-year period. Antimicrobial susceptibility testing of the isolates was performed using the Sensititre Rapmycoi microdilution panel (Thermo Fisher Scientific, Massachusetts, USA). Results: Forty strains of Nocardia spp. were identified in the study, being N. farcinica and N. cyriacigeorgica the most prevalent ones. All isolates were susceptible to linezolid and the resistance to amikacin was only observed in one isolate of Gordonia sputi. Resistance to cotrimoxazole was only found in five isolates. Conclusions: Routine identification and antimicrobial susceptibility testing of aerobic actinomycetes is advisable for an efficient identification of species and effective treatment.(AU)

Introducción: La incidencia de infecciones por actinomicetos aerobios está aumentando. Los recientes cambios en la taxonomía y la variabilidad en la sensibilidad entre especies hacen necesaria una identificación y estudio de sensibilidad adecuados. Material y métodos: Se identificaron 53 cepas de actinomicetos aerobios mediante MALDI-TOF utilizando el kit VITEK-MS Mycobacterium/Nocardia (bioMérieux, Francia) en un hospital terciario español durante seis años. Los estudios de sensibilidad de los aislados se realizaron utilizando el panel de microdilución Sensititre Rapmycoi (Thermo Fisher Scientific, Massachusetts, EE. UU.). Resultados: Se identificaron 40 cepas de Nocardia spp., siendo Nocardia farcinica y Nocardia cyriacigeorgica las más prevalentes. Todos los aislados fueron sensibles a linezolid, y solo se detectó resistencia a amikacina en un aislado de Gordonia sputi. Solo se encontró resistencia al cotrimoxazol en cinco aislados. Conclusiones: Es aconsejable realizar la identificación de rutina y las pruebas de sensibilidad antimicrobiana de los actinomicetos aerobios para conseguir una identificación eficiente de las especies y un tratamiento eficaz.(AU)

Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta.

Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large "pores" in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1-4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.

Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants.

The taxonomic status of two Gordonia strains, designated BEN371 and CON9T, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of Gordonia species and three authenticated Gordonia amarae strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the G. amarae strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the G. amarae strains and Gordonia type strains confirmed the assignment of the isolates and the G. amarae strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA-DNA hybridisation (dDDH) similarities showed that BEN371 and CON9T belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus Gordonia. The isolates and the G. amarae strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9T represent a novel species of the genus Gordonia. The name proposed for members of this taxon is Gordonia pseudamarae sp. nov. with isolate CON9T (=DSM 43602T=JCM 35249T) as the type strain.

Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages.

Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera-from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.

Pacemaker-induced endocarditis by Gordonia bronchialis.

PURPOSE: Gordonia species are known to be opportunistic human pathogens causing secondary infections. We present the second case in the world of endocarditis caused by Gordonia bronchialis and a review of all the cases of endocarditis caused by Gordonia spp. METHODS: The identification was performed by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing were performed to confirm the identification. Antimicrobial susceptibility was performed by MIC test Strip on Mueller-Hinton agar supplemented with 5% defibrinated sheep blood according to Clinical and Laboratory Standards Institute. RESULTS: Pacemaker-induced endocarditis due to Gordonia bronchialis infection was determined in an 88-year old woman. The patient was treated with ceftriaxone and ciprofloxacin until completing 6 weeks from the pacemaker explant with a good evolution. CONCLUSION: The case presented supports the pathogenic role of Gordonia bronchialis as an opportunistic pathogen and highlights the high risk of suffering infections caused by environmental bacteria.

Pacemaker-induced endocarditis by Gordonia bronchialis / Endocarditis del marcapasos debido a infección por Gordonia bronchialis

PurposeGordonia species are known to be opportunistic human pathogens causing secondary infections. We present the second case in the world of endocarditis caused by Gordonia bronchialis and a review of all the cases of endocarditis caused by Gordonia spp.MethodsThe identification was performed by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing were performed to confirm the identification. Antimicrobial susceptibility was performed by MIC test Strip on Mueller-Hinton agar supplemented with 5% defibrinated sheep blood according to Clinical and Laboratory Standards Institute.ResultsPacemaker-induced endocarditis due to Gordonia bronchialis infection was determined in an 88-year old woman. The patient was treated with ceftriaxone and ciprofloxacin until completing 6 weeks from the pacemaker explant with a good evolution.ConclusionThe case presented supports the pathogenic role of Gordonia bronchialis as an opportunistic pathogen and highlights the high risk of suffering infections caused by environmental bacteria.

ObjetivoLas especies de Gordonia son patógenos humanos oportunistas que causan infecciones secundarias. Presentamos el segundo caso en el mundo de endocarditis causada por Gordonia bronchialis, así como una revisión de todos los casos de endocarditis causados por Gordonia spp.MétodosLa identificación fue realizada mediante espectrometría de masas MALDI-TOF MS, y se confirmó mediante secuenciación del gen 16S rRNA. La susceptibilidad antimicrobiana se realizó mediante tiras reactivas MIC en agar Müller-Hinton suplementado con un 5% de sangre ovina desfibrinada, conforme al Clinical and Laboratory Standards Institute (CLSI).ResultadosLa endocarditis del marcapasos debido a infección por Gordonia bronchialis se encontró en una mujer de 88 años. La paciente fue tratada con ceftriaxona y ciprofloxacina hasta completar el periodo de 6 semanas desde el explante del marcapasos, con buena evolución.ConclusiónEste caso respalda el rol patogénico de Gordonia bronchialis como patógeno oportunista, subrayando el alto riesgo de padecer infecciones causadas por bacterias ambientales.

Mastitis granulomatosa idiopática complicada con absceso de mama producido por Gordonia sputi, caso clínico / Idiopathic granulomatous mastitis complicated with a breast abscess caused by Gornodia sputi, a case report

La mastitis granulomatosa idiopática es una entidad rara, benigna y crónica de causa desconocida que afecta a la mama. Es un diagnóstico de exclusión. Se deben descartar, entre otras etiologías, la tuberculosis, las infecciones, la sarcoidosis y otras enfermedades autoinmunes, como la arteritis de células gigantes. Los principales retos que plantea esta entidad son su diagnóstico diferencial con enfermedad maligna y su tratamiento. La afectación mamaria es anecdótica y ha sido solo reportada en relación con prótesis mamarias. Presentamos el caso de una paciente diagnosticada de mastitis granulomatosa idiopática complicada con un absceso de mama por Gordonia sputi.

Idiopathic granulomatous mastitis is a rare, benign, chronic entity of unknown cause affecting the breast. It is a diagnosis of exclusion. Among other aetiologies, tuberculosis, infections, sarcoidosis, and other autoimmune diseases such as giant cell arteritis must be ruled out. The main challenges posed by this entity are its differential diagnosis with malignant pathology and its treatment.Gordonia spp. are a group of emerging pathogens that are mainly associated with infections associated with medical devices, mainly catheters. Breast involvement is anecdotal and has only been reported in relation to breast prostheses.We present the case of a patient diagnosed with idiopathic granulomatous mastitis complicated with a breast abscess due to Gordonia sputi.

Mechanistic Understanding of Gordonia sp. in Biodesulfurization of Organosulfur Compounds.

Although conventional oil refining process like hydrodesulfurization (HDS) is capable of removing sulfur compounds present in crude oil, it cannot desulfurize recalcitrant organosulfur compounds such as dibenzothiophenes (DBTs), benzothiophenes (BTs), etc. Biodesulfurization (BDS) is a process of selective removal of sulfur moieties from DBT or BT by desulfurizing microbes. Therefore, BDS can be used as a complementary and economically feasible technology to achieve deep desulfurization of crude oil without affecting the calorific value. In the recent past, members of biodesulfurizing actinomycete genus Gordonia, isolated from versatile environments like soil, activated sludge, human beings etc. have been greatly exploited in the field of petroleum refining technology. The bacterium Gordonia sp. is slightly acid-fast and has been used for unconventional but potential oil refining processes like BDS in petroleum refineries. Gordonia sp. is unique in a way, that it can desulfurize both aliphatic and aromatic organosulfurs without affecting the calorific value of hydrocarbon molecules. Till date, approximately six different species and nineteen strains of the genus Gordonia have been recognized for BDS activity. Various factors such as enzyme specificity, availability of essential cofactors, feedback inhibition, toxicity of organic pollutants and the oil-water separations limit the desulfurization rate of microbial biocatalyst and influence its commercial applications. The current review selectively highlights the role of this versatile genus in removing sulfur from fossil fuels, mechanisms and future prospects on sustainable environment friendly technologies for crude oil refining.