Strains Of Other Species Research Articles

Comparative genomic analyses of the genus Robertmurraya and proposal of the novel species Robertmurraya mangrovi sp. nov., isolated from mangrove soil.

A Gram-positive, aerobic, motile, rod-shaped bacterial strain, designated 31A1RT, was isolated from the mangrove soil of Xilian village, Zhanjiang, China. Strain 31A1RT thrives at temperatures ranging from 15 to 45°C (optimum at 30°C), pH 6.5-10 (optimum at 8.5), and in the presence of 0-5% (w/v) NaCl (optimum at 1.5%). The strain shares the highest 16S rRNA gene sequence similarity with Robertmurraya crescens (97.24%) and Robertmurraya dakarensis (97.18%). The complete genome of strain 31A1RT spans 4.71 Mbp with a genomic DNA G + C content of 35.9 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain 31A1RT and type strains of other species of the genus Robertmurraya were 71.24-72.11% and 19.90-21.40%, respectively. The amino acid identity values and percentage of conserved proteins ranged from 66.94 to 68.10% and from 58.34 to 61.62%, respectively, aligning with intrageneric cutoff values. The major fatty acids (≥ 5.0%) were iso-C14:0 (5.0%), iso-C15:0 (41.4%), iso-C16:0 (12.6%), C16:1ω7c alcohol (12.2%), and iso-C17:1 ω10c (6.5%). The polar lipids profile was mainly composed of diphosphatidyl glycerol, phosphatidyl glycerol, and phosphatidyl ethanolamine. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Robertmurraya, which indicated functional capacities and metabolic similarities. Consequently, we propose that strain 31A1RT represents a new species in the genus Robertmurraya, for which the name Robertmurraya mangrovi sp. nov. is proposed, with the type strain being 31A1RT (= GDMCC 1.4378T = JCM 36937T).

Development and verification of crossing priming amplification on rapid detection of virulent and viable L. monocytogenes: In-depth analysis on the target and further application on food screening

Virulent Listeria monocytogenes is responsible for listeriosis, a highly fatal foodborne illness that impairs human health. One of the major causes of its pathogenicity is the carriage of virulence factor, listeriolysin O, encoded by hylA gene. Herein, the specificity and conservativity of hylA gene sequences were analyzed, with most conservative region selected. Then, a crossing priming amplification (CPA) assay targeting hylA conservative region was established under an isothermal condition (63 °C) to identify virulent L. monocytogenes within 60 min. Forty-four reference strains including two standard L. monocytogenes strains and forty-two strains of other species were selected to assess sensitivity and specificity. The CPA assay showed strong specificity and sensitivity (genomic DNA at 5.66 pg/μL). The practicality of the CPA assay was further confirmed in four artificially contaminated rice-flour products with limit of detection at 104 CFU/mL. In addition, a PMA-CPA assay was developed to direct detect L. monocytogenes viable cells with rice-flour products as a model system. In conclusion, the developed CPA method has advantages of high sensitivity, specificity and quick measurement in the detection of virulent L. monocytogenes, showing considerably feasible promise for future food safety.

Microsatellite markers for genotyping of Kodamaea ohmeri: Demonstrating outbreaks based on a multicenter surveillance study in China

Kodamaea ohmeri, an emerging human pathogen, caused both sporadic and nosocomial infections among immunocompromised people with high mortality. However, there is limited research on the molecular epidemiology of K. ohmeri. A total of fifty microsatellite loci were designed based on K. ohmeri type strain NRRL Y-1932 and three loci were finally selected for microsatellite analysis. Non-duplicated K. ohmeri isolates and strains of other species were collected across China as a part of CHIF-NET program for sensitivity and specificity verification. Antifungal susceptibility was determined using Sensititre YeastOne TM YO10. The three loci (P10, P11 and P26), with a cumulative discriminatory power of 0.98, exhibited a prospective specificity and reproducibility in the PCR of 92 K. ohmeri strains from different hospitals. A total of 54 microsatellite types (MT) were identified and most of them distributed sporadically. However, six strains of MT12 clustered in HZ hospital and were isolated in the same department within two months, indicating a potential outbreak. Of seven isolates exhibited MIC values of >8 mg/L for fluconazole, three isolates from LR hospital shared the same genotype of MT44. Herein, we established a set of microsatellite loci for K. ohmeri, as a rapid and specific tool for genotyping K. ohmeri, and identified several potential clusters. This study will help us better understand the molecular epidemiology of the emerging pathogen K. ohmeri.

Cytobacillus spongiae sp. nov. isolated from sponge Diacarnus spinipoculum.

A novel Gram-stain-positive, aerobic and motile bacterium, designated strain CY-GT, was isolated from a sponge (Diacarnus spinipoculum) collected from the Red Sea. The strain grew at 13-43 °C (optimum 30 °C), pH 5.5-10.0 (optimum pH 9.0) and with 0-8.0 % (w/v) (0-1.37 M) NaCl (optimum 0 %). The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that CY-GT represents a member of the genus Cytobacillus, with the highest sequence identity to Cytobacillus oceanisediminis H2T (97.05 %), followed by Cytobacillus firmus IAM 12464T (96.76 %). The major cellular fatty acids (>5 % of the total) of CY-GT were C15 : 0iso, C16 : 0iso, C16 : 1ω7c alcohol, C16 : 0, C17 : 1iso ω10c and C17 : 0iso. The major polar lipids were glycolipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major respiratory quinone is menaquinone-7 (MK-7). The cell-wall peptidoglycan contains meso-diaminopimelic acid. The total genome size of CY-GT is 4 789 051 bp. The DNA G+C content is 38.83 mol%. The average nucleotide identity and DNA-DNA hybridization among CY-GT and type strains of other species of the genus Cytobacillus were 76.79-78.97 % and 20.10-24.90 %, respectively. On the basis of the results of phylogenetic analysis, physiological and biochemical characterization, strain CY-GT represents a novel species of the genus Cytobacillus, for which the name Cytobacillus spongiae sp. nov. is proposed. The type strain is CY-GT (=MCCC 1K06383T=KCTC 43348T).

Brenneria bubanii sp. nov., isolated from decaying plant tissues.

Gram-negative, motile, rod-shaped bacterial strains (designated 4F2T and Kf) were isolated from decaying tissues of various deciduous tree species. Phylogenetic analyses based on their 16S rRNA gene sequences showed that the novel isolates belong to the genus Brenneria and showed highest (98.3 %) sequence similarity to Brenneria goodwinii. Isolate 4F2T formed a separate branch on the phylogenetic tree based on concatenated sequences of four housekeeping genes or whole genome sequences, clearly separate from Brenneria goodwinii, suggesting that novel isolates should belong to a novel species. Orthologous average nucleotide identity scores and in silico DNA-DNA hybridization values between isolate 4F2T and type strains of other species in the genus Brenneria were less than 85 and 30 %, respectively, significantly lower than the species boundary cut-off values (95 and 70 %). A negative reaction for β-galactosidase, the ability to use dextrin and maltose as carbon sources, and an inability to use lactose are the main phenotypic characteristics that can be used to differentiate the novel isolates from B. goodwinii. Based on phenotypic and genotypic characteristics, isolates 4F2T and Kf belong to a novel species of the genus Brenneria, for which the name Brenneria bubanii sp. nov. is proposed. The type strain is 4F2T (=NCAIM B 02661T=LMG 32183T).

Sphingobium nicotianae sp. nov., isolated from tobacco soil.

Bacterial strain H33T was isolated from tobacco plant soil and was characterized using a polyphasic taxonomy approach. Strain H33T was a Gram-stain-negative, rod-shaped, non-motile and strictly aerobic bacterium. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of the up-to-date bacterial core gene set (92 protein clusters) indicated that H33T belongs to the genus Sphingobium. Strain H33T showed the highest 16S rRNA gene sequence similarity to Sphingobium xanthum NL9T (97.2%) and showed 72.3-80.6 % average nucleotide identity and 19.7-29.2 % digital DNA-DNA hybridization identity with the strains of other species of the genus Sphingobium. Strain H33T grew optimally at 30°C, pH 7 and could tolerate 0.5 % (w/v) NaCl. The isoprenoid quinones were ubiquinone-9 (64.1%) and ubiquinone-10 (35.9%). Spermidine was the major polyamine. The major fatty acids of H33T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile consisted of a mixture of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, sphingoglycolipid, two unidentified lipids, two unidentified glycolipids, two unidentified aminoglycolipids and an unidentified phospholipid. The genomic DNA G+C content of H33T was 64.9 mol%. Based on the phylogenetic and phenotypic data, H33T was considered a representative of a novel species in the genus Sphingobium. We propose the name Sphingobium nicotianae sp. nov., with H33T (=CCTCC AB 2022073T=LMG 32569T) as the type strain.

Influence of Probiotics on Antibiotic Therapy

Antibiotics are the most prominent advances in medicine and have provided great benefits in the treatment and control of infectious diseases. Antibiotics do not differentiate good and bad germs, disrupting normal microflora and causing vitamin deficiency in the human body. They also kill healthy bacteria in the gut on a large scale, weakening the host's defence mechanism. AAD is a common side effect of antibiotic usage, which affects up to 30% of patients. Probiotics are live microorganisms, belonging to the genera Lactobacillus and Bifidobacterium, although strains of other species are commercialized, that have a beneficial effect on the host. From the perspective of antibiotic use, probiotics have been observed to reduce the risk of certain infectious disease such as antibiotic associated diarrhea, respiratory tract infection and also prevent secondary infections. This may be accompanied with a reduced need of antibiotics for secondary infections with protective and therapeutic effects against diseases and infectious agents. Probiotics have generally been considered safe; however, there have been rare reports of sepsis and fungemia associated with probiotic use, especially in critically ill and immunosuppressed patients. Keywords: Antibiotics, probiotics, lactobacillus, bifidobacterium.

Chryseolinea lacunae sp. nov. and Piscinibacter lacus sp. nov. Isolated from Artificial Pond Water.

Two Gram stain-negative bacterial strains designated Jin1T and Jin2T were isolated from artificial pond water in the Republic of Korea and investigated in the present study using a polyphasic taxonomic approach. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these two strains belonged to the genera Chryseolinea and Piscinibacter due to their highest similarities with the 16S rRNA gene sequences of Chryseolinea serpens RYGT (98.7%) and Piscinibacter aquaticus IMCC1728T (97.1%), respectively. The dDDH and ANI values were 18.1-20.5% and 68.9-76.8% between whole-genome sequences of strain Jin1T and type trains of the selected taxa, Chryseolinea species, and 20.1-20.2% and 75.5-76.1% between those of strain Jin2T and the type strains of the selected taxa, Piscinibacter species, respectively. A threshold AAI value of 44.7-64.8% for the species boundary (95-96%) was established for strains Jin1T, Jin2T, and type strains of other species involved in the system incidence, which confirms that strains Jin1T and Jin2T represent two new species of the genera Chryseolinea and Piscinibacter, respectively. Based on the phylogenetic, chemotaxonomic, and phenotypic analyses, strains Jin1T and Jin2T represent novel species of the genera Chryseolinea and Piscinibacter, respectively, for which the names Chryseolinea lacunae sp. nov. (type strain Jin1T = KCTC 82562T = NBRC 114837T) and Piscinibacter lacus sp. nov. (type strain Jin2T = KCTC 82556T = NBRC 114838T) have been proposed.

Sutcliffiella rhizosphaerae sp. nov. isolated from roots.

An aerobic, Gram-staining-positive, endospore-forming bacterium, isolated from the rhizosphere of roots of maize (Zea mays), was taxonomically studied. On the basis of 16S rRNA gene sequence similarity comparisons, strain JJ-125T clustered together with species of the genus Sutcliffiella and showed the highest similarities with Sutcliffiella zhanjiangensis (98.7 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other species of the genus Sutcliffiella were <98.4 %. The genome sequence of JJ-125T was 4 516 360 bp long and had a DNA G+C content of 37.3 %. A DNA-DNA hybridization with the type strain of S. zhanjiangensis DSM 23010T resulted in values of 42.3 and 43.9 % (reciprocal). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the JJ-125T genome assembly and those of the other type strains of species of the genus Sutcliffiella were <75%, <80 % and <21 %, respectively. Chemotaxonomic features supported the grouping of the strain with the genus Sutcliffiella, e.g. the major fatty acids included iso-C15 : 0, iso-C17 : 1 ω10c and iso-C17 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, the only quinone was menaquinone MK-7 and the characteristic diamino acid was meso-diaminopimelic acid. Physiological and biochemical test results were also different from those of the most closely related species. As a consequence, JJ-125T represents a novel species of the genus Sutcliffiella, for which we propose the name Sutcliffiella rhizosphaerae sp. nov., with JJ-125T (= CIP 111883T = LMG 32156T = CCM 9046T) as the type strain.

Algoriphagus algorifonticola sp. nov., a marine bacterium isolated from cold spring area of South China Sea.

A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated strain hg1T, was isolated from marine sediment within the cold spring area of South China Sea and subjected to a polyphasic taxonomic investigation. Colonies were circular and 1.0-2.0 mm in diameter, coral in colour, convex and smooth after growth on marine agar at 28 °C for 3 days. Strain hg1T was found to grow at 4-40 °C (optimum, 35-37 °C), at pH 6.5-9.0 (optimum, pH 7.5) and with 0-8 % (w/v) NaCl (optimum, 1.5-2 %). Chemotaxonomic analysis showed the sole respiratory quinone was MK-7, and the principal fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and iso-C16 : 0. The major polar lipids are phosphatidylethanolamine, an unidentified phospholipid and five unidentified glycolipids. The DNA G+C content of strain hg1T was 39.6 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that hg1T was closely related to Algoriphagus ornithinivorans DSM 15282T (98.6 % sequence similarity), Algoriphagus zhangzhouensis MCCC 1F01099T (97.9 %) and Algoriphagus vanfongensis DSM 17529T (97.2 %); it exhibited 97.0 % or less sequence similarity to the type strains of other species of the genus Algoriphagus with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain hg1T constituted a separate branch with A. ornithinivorans, A. zhangzhouensis, A. vanfongensis in a clade of the genus Algoriphagus. OrthoANI values between strain hg1T and A. ornithinivorans, A. zhangzhouensis and A. vanfongensis were 94.3, 74.1, 73.2 %, respectively, and in silico DNA-DNA hybridization values were 56.2, 18.5 and 18.3 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain hg1T is clearly distinct from recognized species of genus Algoriphagus. On the basis of these features, we propose that strain hg1T (=MCCC 1K03570T=KCTC 72111T) represents a novel species of the genus Algoriphagus with the name Algoriphagus algorifonticola sp. nov.

Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709.

Over the past decade, Apiotrichum mycotoxinivorans has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of A. mycotoxinivorans infections. Therefore, to investigate the genetic basis for the pathogenicity of A. mycotoxinivorans, we performed whole-genome sequencing and comparative genomic analysis of A. mycotoxinivorans GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that A. mycotoxinivorans exhibited the closest evolutionary affinity to A. veenhuisii, and both the A. mycotoxinivorans strains and the formerly Trichosporon cutaneum ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to A. mycotoxinivorans. Comparisons of three A. mycotoxinivorans strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the Trichosporonaceae family, we identified potential key genetic factors associated with A. mycotoxinivorans infection or pathogenicity. In addition, we also deduced that A. mycotoxinivorans had great potential to inactivate some antibiotics (e.g., tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the Trichosporonaceae family, uncover the underlying genetic basis of A. mycotoxinivorans infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.

Antibiotic susceptibility of four Enterobacteriaceae strains (Enterobacter cloacae, Citrobacter freundii, Salmonella typhi and Shigella sonnei) isolated from wastewater, surface water and groundwater in the equatorial zone of Cameroon (Central Africa)

The health problems caused waterborne pathogens bacteria belonging to the Enterobacteriaceae family are aggravated by the rise of antimicrobial resistant bacteria phenomenon. This has been identified as one of the biggest global health challenges. The present study aims to make a comparative approach of the sensitivity/resistance to antibiotics of 4 Enterobacteriaceae Enterobacter cloacae, Citrobacter freundii, Salmonella typhi and Shigella sonnei isolated from wastewater, streams and groundwater in Yaounde town (Cameroon, Central Africa). Bacteria were isolated using standard methods their identification using the API 20E systems. The antibiogram tests were carried out using the Müller-Hinton antibiotic disc diffusion method. Results showed that inhibition diameters of antibiotic varied (P&lt;0.05) with respect to the bacterial species on one hand, and with respect to the type of water harbored cells on the other hand. The proportion of bacterial strains of each isolated species, and which were sensitive or resistant varied from one antibiotic to another within the same antibiotics family. For β-lactams tested, no E. cloacae strain has been sensitive. The proportion of sensitive strains of other species varied between 5.88% and 23.53%. For the 2 aminoglycosides tested, 5.88% of the strains of each isolated species were resistant to gentamycin. Of the 3 quinolones tested, all strains of E. cloacae and C. freundii isolated were fully resistant to Norfloxacin and of Ofloxacin. For the 3 Sulfonamides+trimethoprim, all strains of C. freundii and S. typhi isolated were resistant to Nurofurantoin and Fosfomycin. Most of bacteria strains isolated in wastewater and surface water were resistant to all the antibiotics tested. Many bacterial strains tested were multi-resistant. This multidrug resistance was more marked in E. cloacae and C. freundii species isolated from wastewater and surface water. This represents a health risk for humans and the aquatic environment.

Effect of Cocultivation on Lactobacillus plantarum Strains Growth and Antagonistic Activity

The use of bacterial starters for the production of fermented foods has several advantages over traditional spontaneous fermentation, as it provides a rapid and controlled decrease of pH, improves the microbiological quality of the product, and prolongs the shelf-life. Fermented foods are typically produced using mixed cultures of lactic acid bacteria (LAB) due to the synergism between their constituent bacterial cultures. So, the compatibility of the LAB strains decides the efficacy of a multi-strain starter. The purpose of this study was to investigate the effect of the cocultivation of Lactobacillus plantarum strains on the growth, acidification, and antagonistic activity to determine suitable strain combinations for fermented vegetable production. Methods. The effect of cocultivation on growth characteristics of four L. plantarum strains was determined in MRS medium and cabbage-based medium with 2.5% NaCl. After 8 h of cultivation at 30°C and 37°C, the number of viable cells (CFU/ml) and the pH of the medium were determined. The antagonistic activity of monocultures of L. plantarum and their six compositions against opportunistic pathogenic microorganisms was determined by the method of delayed antagonism. Results. During growth in MRS broth at 30°C cocultivation of L. plantarum 47SM with L. plantarum 691T or L. plantarum 1047K strains led to enhanced rates of growth compared to the monocultures, suggesting some degree of symbiosis between these strains. Viable cell counts of L. plantarum 47SM, 1047K and 691T strains and ΔpH values of L. plantarum 952K, 1047K, and 691T strains were higher after 8 h growth in the cabbage-based medium at 30°C compared to MRS broth. Despite the intensive growth of L. plantarum monocultures in cabbage-based medium, a significant decrease of viable cell counts and ΔpH values during cocultivation at 30°C were found. Cocultivation did not affect the average size of the growth inhibition zones of most of the indicator strains used. However, growth inhibition zones of Shigella flexneri, Escherichia coli, and Proteus vulgaris decreased in some L. plantarum mixed cultures compared to monocultures. Thus, the growth inhibition zones of E. coli and S. flexneri by mixed culture L. plantarum 47 SM+1047K were significantly smaller compared to the growth inhibition zones of L. plantarum monocultures. Conclusions. Thus, based on the data obtained in present work, we can assume that some of these L. plantarum strains used in the work may be bactericinogenic. Although the four L. plantarum strains studied are compatible when cocultivated in a standard rich MRS medium, the results of cocultivation in a cabbage-based medium with 2.5% NaCl does not allow to recommend the use of these L. plantarum strains simultaneously in the starter for vegetable fermentation. Further investigation of bacteriocinogenic properties and mechanisms of growth inhibition under cocultivation in vegetable-like conditions are needed, which will allow combining of some of these L. plantarum strains with LAB strains of other species or genera to create multi-starters for vegetable fermentation.

Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex

A Gram-stain-negative, strictly aerobic bacterium, designated strain PeD5T, was isolated from a green alga Pediastrum duplex from the Nakdong river of the Republic of Korea. Cells were non-motile cocci, catalase-negative and oxidase-positive. Growth of PeD5T was observed at 25-40 °C (optimum, 35 °C) and pH 5.0-10.0 (optimum, pH 7-8), and in the presence of 0-0.25% (w/v) NaCl (optimum, 0%). PeD5T contained C16:0, C18:1ω7c 11-methyl, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) as major cellular fatty acids (>5%) and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified aminolipid were detected as major polar lipids. The genomic DNA G+C content of PeD5T was 71.0 mol%. PeD5T was most closely related to Roseomonas stagni HS-69T with a 97.6% 16S rRNA sequence similarity and shared less than 96.3% 16S rRNA sequence similarities with type strains of other species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that PeD5T formed a phyletic lineage with Roseomonas stagni HS-69T within the genus Roseomonas. On the basis of results of phenotypic, chemotaxonomic and molecular analysis, strain PeD5T clearly represents a novel species of the genus Roseomonas, for which the name Roseomonas algicola sp. nov. is proposed. The type strain is PeD5T (=KACC 19925T=JCM 33309T).

Development of a PCR-denaturing gradient gel electrophoresis method targeting the tuf gene to differentiate and identify Staphylococcus species

Staphylococcal intoxications are often associated with staphylococcal enterotoxins produced by Staphylococcus aureus. However, several studies revealed that other Staphylococcus species, such as S. intermedius and S. warneri, could produce enterotoxins as well. To facilitate the identification of a mixed culture while tracing the causative staphylococci of food poison, a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method was developed to differentiate Staphylococcus species using Staphylococcus-specific primers targeting the elongation factor Tu gene (tuf gene). Eleven tested species were differentiated to 10 separated patterns. Variance of the patterns between strains within a species was analyzed using 9 strains of S. aureus and several strains of other species. It was shown that strains within a species migrated the same distance in the DGGE assay. When mixed cultures of different Staphylococcus species in milk were subjected to DNA extraction and PCR-DGGE, the resulted patterns faithfully corresponded to the species of the mixed cultures, including those of potential to secret enterotoxins.

Amycolatopsis anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis elatior.

A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15-40 °C, pH 6.0-8.0 and in the presence of 0-6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus Amycolatopsis and shared the highest sequence similarities with Amycolatopsis nigrescens JCM 14717T (97.1 %) and Amycolatopsis sacchari DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus Amycolatopsis were less than 97.0 %. The average nucleotide identity and DNA-DNA hybridization values between strain EGI 650086T and the reference strains were 78.1-79.8 % and 22.1-23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).

Aquirufa rosea sp. nov., isolated from a freshwater lake.

A bacterial strain designated CAR-16T was isolated from a freshwater lake in Taiwan and characterized using the polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed rose-colored colonies. Optimal growth occurred at 30 °C, pH 7 and with 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that CAR-16T represented a member of the family Cytophagaceae and formed a phylogenetic lineage in the genus Aquirufa. CAR-16T was most closely related to Aquirufa nivalisilvae 59G-WUEMPELT with a 99.7 % 16S rRNA gene sequence similarity. CAR-16T showed 71.2-79.5 % average nucleotide identity and 17.8-21.7 % digital DNA-DNA hybridization identity with the strains of other species of the genus Aquirufa. The major fatty acids of strain CAR-16T were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c and/or iso-C15 : 0 2-OH). The polar lipid profile consisted of a mixture of phosphatidylethanolamine and several uncharacterized aminophospholipids, phospholipids and lipids. The major isoprenoid quinone was MK-7. The genomic DNA G+C content of CAR-16T was 38.8 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, CAR-16T should be classified as representing a novel species of the genus Aquirufa, for which the name Aquirufa rosea sp. nov. is proposed. The type strain is CAR-16T (=BCRC 81153T=LMG 30923T=KCTC 62869T).

American cutaneous leishmaniasis in French Guiana: a retrospective comparison between liposomal amphotericin B and meglumine antimoniate

New World cutaneous leishmaniasis (CL) is endemic in many countries of Latin America, including French Guiana 1 . While pentamidine is the first-line treatment against Leishmania guyanensis in this territory 2 , pentavalent antimonials such as meglumine antimoniate (MA) are recommended in case of L. braziliensis or pentamidine-resistant strains of other species 2 . Liposomal amphotericin B (L-AmB) (Ambisome ®) is widely used against fungi and visceral leishmaniasis 3 . However, data concerning its efficacy in New World CL are scarce and contradictory 4-7 . Due to a shortage in MA, the Cayenne Hospital started using L-AmB as an alternative in 2015. We conducted a retrospective study to compare efficacy and safety of L-AmB and MA in patients treated for CL.

Diversity and occurrence of methylotrophic yeasts used in genetic engineering.

Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the 1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level. The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate- derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues. Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataea representatives prevail. Despite the phylogenetic gap between the genus Ogataea and the genus Komagataella representatives, it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There exist expression systems based on other strains of the genus Komagataella as well as the genus Candida. The potential of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented around the world both in nature and in urban environments, it may reasonably be expected that new expression systems for recombinant proteins based on strains obtained in other regions of the globe will appear.

Sphingobium algorifonticola sp. nov., isolated from a cold spring.

Strain TLA-22T, isolated from a cold spring in Taiwan, was characterized using a polyphasic taxonomy approach. Cells were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a single polar flagellum, rod-shaped and formed bright yellow colonies. Optimal growth occurred at 20-25 °C, pH 6-6.5, and in the presence of 0.5 % NaCl. The major fatty acids of TLA-22T were C18 : 1 ω7 c and C17 : 1ω6c. The predominant hydroxy fatty acids were C15 : 0 2-OH and C14 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sphingoglycolipid, an unidentified aminophospholipid, an unidentified phospholipid and three unidentified lipids. TLA-22T contained spermidine as the major polyamine and putrescine as the minor component. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of TLA-22T was 63.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that TLA-22T was a mem,ber of a phylogenetic lineage including members of the genus Sphingobium. TLA-22T was most closely related to Sphingobium aromaticiconvertens RW16T, with a 97.4 % 16S rRNA gene sequence similarity. TLA-22T showed 74.8-75.7 % average nucleotide identity and 20.1-22.0 % digital DNA-DNA hybridization identity with the strains of other species of the genus Sphingobium. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TLA-22T should be classified as representing a novel species of the genus Sphingobium, for which the name Sphingobium algorifonticola sp. nov. is proposed. The type strain is TLA-22T (=BCRC 81097T =LMG 30309T=KCTC 62189T).