Leptospiral sphingomyelinase Sph2 as a potential biomarker for diagnosis of leptospirosis

Leptospirosis is an underestimated infectious tropical disease caused by the spirochetes belonging to the genus Leptospira. Leptospirosis is grossly underdiagnosed due to its myriad symptoms, varying from mild febrile illness to severe haemorrhage. Laboratory tests for leptospirosis is an extremely important and potent way for disease diagnosis, as the clinical manifestations are very similar to other febrile diseases. Currently available diagnostic techniques are time-consuming, require expertise and sophisticated instruments, and cannot identify the disease at an early phase of infection. Early diagnosis of leptospirosis is the need of the hour while considering the severe complications after the infection and the rate of mortality after misdiagnosis. Secretion of Leptospira-specific sphingomyelinases in leptospirosis patient's urine within a few days of the onset of infection is quite common and is a virulence factor present only in pathogenic Leptospira species. Herein, the structural and functional importance of leptospiral sphingomyelinase Sph2 in leptospirosis pathogenesis, as well as the potential of screening urinary Sph2 for diagnosis and the scope for developing a rapid and easily affordable point-of-care test for urinary leptospiral sphingomyelinase Sph2 as an alternative to current diagnostic methods are discussed.

Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29T reveals its exopolysaccharide and pigment producing capabilities

Halomonas malpeensis strain YU-PRIM-29T is a yellow pigmented, exopolysaccharide (EPS) producing halophilic bacterium isolated from the coastal region. To understand the biosynthesis pathways involved in the EPS and pigment production, whole genome analysis was performed. The complete genome sequencing and the de novo assembly were carried out using Illumina sequencing and SPAdes genome assembler (ver 3.11.1) respectively followed by detailed genome annotation. The genome consists of 3,607,821 bp distributed in 18 contigs with 3337 protein coding genes and 53% of the annotated CDS are having putative functions. Gene annotation disclosed the presence of genes involved in ABC transporter-dependent pathway of EPS biosynthesis. As the ABC transporter-dependent pathway is also implicated in the capsular polysaccharide (CPS) biosynthesis, we employed extraction protocols for both EPS (from the culture supernatants) and CPS (from the cells) and found that the secreted polysaccharide i.e., EPS was predominant. The EPS showed good emulsifying activities against the petroleum hydrocarbons and its production was dependent on the carbon source supplied. The genome analysis also revealed genes involved in industrially important metabolites such as zeaxanthin pigment, ectoine and polyhydroxyalkanoate (PHA) biosynthesis. To confirm the genome data, we extracted these metabolites from the cultures and successfully identified them. The pigment extracted from the cells showed the distinct UV-Vis spectra having characteristic absorption peak of zeaxanthin (λmax 448 nm) with potent antioxidant activities. The ability of H. malpeensis strain YU-PRIM-29T to produce important biomolecules makes it an industrially important bacterium.

Oral microbial profile in oral cancer patients before and after radiation therapy in a cancer care center - A prospective study

Background:

Head and neck cancer is the sixth most common cancer reported worldwide. In many cases, the level of aggressiveness of therapy adopted in cancer patients may cause the alteration in oral microbiota; the emergence of potential pathogens may cause opportunistic infections in already immune-compromised individuals leading to increases in morbidity and mortality. Hence, this study was conducted to assess the oral microbial profile in oral cancer patients before and after radiotherapy.

Materials and Methods:

A total of 145 oral swabs were collected before radiotherapy (n = 96), 3 months postradiotherapy (n = 25), 6 months postradiotherapy (n = 12) and controls (n = 12). The samples were inoculated into brain–heart infusion broth and later in different media for bacterial isolation. The isolates were subjected to phenotypic characterization by automatic identification system.

Results:

Among the 96 samples studied from the preradiotherapy patient samples, Streptococcus species (n = 28) were the predominant isolate, followed by Staphylococcus species (n = 16), Enterobacter species (n = 6) and Enterococcus species (n = 6). Of the 25 samples studied 3 months after radiotherapy, Klebsiella pneumoniae (n = 4) was isolated and 12 samples studied after 6 months of radiotherapy Candida species (n = 4) and Pediococcus species (n = 3) were isolated. Among the control group (n = 12) screened, Streptococcus acidominimus (n = 3) is the predominant bacteria isolated.

Conclusion:

High prevalence of Streptococcus sp. was found in patients of oral cancer before radiotherapy, while Candida albicans and Klebsiella species and Pediococcus species are the significant pathogens isolated in postradiotherapy cancer patients.

Anti-biofilm and cytoprotective activities of quercetin against Pseudomonas aeruginosa isolates

Increase in infection with multidrug resistant Pseudomonas aeruginosa is a serious global challenge in healthcare. Pseudomonas aeruginosa is capable of causing human infection in various sites and complicates the infection due to its virulence factors. This study was aimed to investigate the effect of quercetin, a dietary flavonoid against the virulence factors of P. aeruginosa and its cell protective effects on epithelial cells. Bactericidal activity, anti-biofilm activity and effect on different virulence factors were carried out using standard methods by using five P. aeruginosa isolates. Cytotoxicity and cell protective effect of quercetin was evaluated by trypan blue dye exclusion assay. All the tested isolates were completely inhibited (100%) by quercetin at a concentration of 500 μg ml^-1 . It showed significant (P < 0·05) inhibitory effect on virulence factors including biofilm formation and showed significant protective effect on HEK 293T cells infected with P. aeruginosa strains. This study supports the role of quercetin against P. aeruginosa, by inhibiting virulence factors as well as its cytoprotective activity during bacterial infection either by attenuating the virulence or providing direct protective effect to the host cells. SIGNIFICANCE AND IMPACT OF THE STUDY: The increase in infections caused by opportunistic pathogen Pseudomonas aeruginosa is a serious concern in the health care system. This study describes the beneficial effects of a dietary flavonoid, quercetin against pathogenic P. aeruginosa strains and its protective effect against the P. aeruginosa infection in HEK 293T cells in vitro.

Adaptation and diversification in virulence factors among urinary catheter-associated Pseudomonas aeruginosa isolates

AIM

The aim of this study was to investigate the natural variation in the antibiotic sensitivity, biofilm formation and virulence among Pseudomonas aeruginosa isolated from the catheter-associated urinary tract infection (CAUTI) from a single centre.

METHODS AND RESULTS

Pseudomonas aeruginosa strains were isolated from the patients with CAUTI after obtaining informed consent. These isolates were identified by routine biochemical methods and 16S rRNA gene sequencing. Antibiotic sensitivity and virulence factors were measured using standard protocols. Crystal violet staining, scanning electron microscopy and confocal laser scanning microscopy were used for the biofilm studies. The extent of infectivity of the strains to induce cell lysis was studied in vitro using the Human Embryonic Kidney cells (HEK 293T). Association between virulence factors, biofilm formation and antibiotic resistance among the strains was analysed statistically. Among the 1266 patients admitted during the 2016-2017 period, 98 cases of CAUTI were reported and 18·36% (n = 18) was due to P. aeruginosa infection. Antibiogram showed that 94·4% of isolates were resistant to multiple antibiotics and 73·7% were carbapenem-resistant. All the isolates formed biofilm on different material surfaces with varying intensity (OD₅₈₀ ≥0·20-1·11). The biofilm intensity on silicone-latex material was significantly higher compared to the polystyrene surface (P > 0·05). All the strains were highly virulent and able to cause cell killing of HEK 293T cells with a rate ranging from 69·35 to 100% and showed very low sensitivity to healthy human serum.

CONCLUSIONS

Antibiotic sensitivity and association between the virulence factors and biofilm formation in the P. aeruginosa clinical strains showed complex natural diversity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the natural diversity and adaptation in virulence factors, biofilm formation and host-pathogen interaction among catheter-associated P. aeruginosa strains. The findings from the study urge for developing individualized drug strategy for targeting these multidrug-resistant pathogens.

Halomonas malpeensis sp. nov., isolated from rhizosphere sand of a coastal sand dune plant

A Gram-stain-negative, aerobic, non-endospore-forming organism, isolated from the rhizosphere sand of a coastal sand dune plant was studied for its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain YU-PRIM-29^T was grouped within the genus Halomonas and was most closely related to Halomonas johnsoniae (97.5 %). The 16S rRNA gene sequence similarity to other Halomonas species was <97.5 %. Strain YU-PRIM-29^T grew optimally at 28 °C (growth range, 10-36 °C), at a pH of 7-9 (growth range, pH 5.5-12.0) and in the presence of 0.5 to 5 % (w/v) NaCl (growth up to 20 % NaCl). The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Halomonas. The fatty acids C18 : 1ω7c and C16 : 0 were found as major compounds, followed by the hydroxylated fatty acid C12 : 0 3-OH. The quinone system consisted predominantly of ubiquinone Q-9. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In the polyamine pattern, spermidine was the predominant compound. The DNA G+C content was 64.8 mol%. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain YU-PRIM-29^T from its closest-related species. Hence, YU-PRIM-29^T represents a new species of the genus Halomonas, for which we propose the name Halomonas malpeensis sp. nov., with YU-PRIM-29^T (=LMG 28855^T=CCM 8737^T) as the type strain.

Characterization and Antibiotic Sensitivity Profile of Bacteria in Orofacial Abscesses of Odontogenic Origin

BACKGROUND

Odontogenic infections range from peripheral abscess to superficial and deep infections leading to severe infections in head and neck region. This study was aimed to assess bacterial isolates responsible for orofacial infection of odontogenic origin and their drug susceptibility patterns so as to provide better perceptive for the management of odontogenic infections.

METHODS

The study was made in a selected cohort of patients, irrespective of age and gender having moderate and severe orofacial infections of odontogenic origin admitted to Yenepoya University Hospital. Pus samples were collected and identification of bacteria was performed by 16S rRNA gene sequencing. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method.

RESULT

A total of 37 study subjects were included, with bacterial isolation rate of 31 (83.7 %). The mean age presented of all patients was 40.62. Of all, 24 (64.9 %) were males. Staphylococcus aureus, Enterobacter claocae subsp. dissolvens, Klebsiella quasipneumoniae subsp. similipneumoniae, Staphylococcus aureus subsp. anaerobius and Klebsiella pneumoniae subsp. ozaenae were the most prevalent isolates. Result showed that 58.6 % of the isolates were resistant to gentamicin, 52.5 % for ampicillin, 51.3 % for piperacillin; least resistant being 18.9 % for azithromycin.

CONCLUSION

High prevalence of bacterial isolates was found, Staphylococcus aureus being the dominant. Most of the bacteria were resistant to different classes of antibiotics. Appropriate antibiotics should be given based on the bacterial isolates, culture sensitivity and clinical course of the disease.

Functional and cell proliferative properties of an exopolysaccharide produced by Nitratireductor sp. PRIM-31

Exopolysaccharides (EPS) produced by bacteria are important source of natural biomolecules with therapeutic applications. In this study EPS produced by a strain PRIM-31 isolated from seawater from south west coast of India identified by 16S rRNA gene sequencing as Nitratireductor sp. was investigated for its biotechnological applications. The isolate produced 650 mg L(-1) EPS under optimum growth conditions. The purified EPS contained 58.3% carbohydrates with 7.08% uronic acid containing sugars, functional groups such as sulfate (2.68%) and trace amounts of proteins (0.65%). Molecular weight of the EPS was 90 kDa and monosaccharide composition was arabinose, glucose, xylose, glucuronic acid and galactose (6.6: 3.5: 2.1: 1.3: 1). The EPS displayed antioxidant activity in terms of total antioxidant capacity, ferric reducing power, scavenging of DPPH (IC50 390 μg mL(-1)) and superoxide radicals (IC50 340 μg mL(-1)). Cell proliferative activity of the EPS was evidenced by significant improvement in human dermal fibroblast (HDF) proliferation compared to control. Further, significant improvement (41%) in HDF cell migration was observed in in vitro scratch assay with EPS treatment. The EPS also showed antiproliferative activity against glioblastoma cells with an IC50 of 234.04 μg mL(-1). These functional properties of the EPS prospect its biotechnological applications.

Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov

Two Gram-stain-negative, non-endospore-forming, rod-shaped bacteria, strains CC-MHSW-5T and A1392, were isolated from water of coastal hot springs located in Taiwan and China, respectively, and investigated for their taxonomic position. The two strains shared identical 16S rRNA gene sequences, a DNA-DNA hybridization value >80 % and similar genomic DNA G+C contents (64.3 and 64.6 mol%), but showed different genomic fingerprint patterns generated by BOX-PCR and three random amplification polymorphic DNA PCRs. The strains shared highest 16S rRNA gene sequence similarities with the type strains of Chelativorans multitrophicus (96.7 and 96.1 %), Thermovum composti (96.2 and 96.1 %) and Chelativorans oligotrophicus (96.1 and 95.8 %). Phylogenetic trees (based on 16S rRNA and recA gene sequence comparisons) showed a distinct clustering of both strains with the type strains of species of the genus Chelativorans and T. composti Nis3T. The quinone systems of strains CC-MHSW-5T and Nis3T contained ubiquinone Q-10 as the major component. The major polyamine in both strains was sym-homospermidine. Putrescine, spermidine and, for strain CC-MHSW-5T, spermine were found in minor concentrations. Their polar lipid profiles consisted of phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The fatty acid profile contained major amounts of C18 : 1ω7c and C19 : 0 cyclo ω8c. On the basis of these results, the two strains are considered to represent a novel species of the genus Chelativorans , for which the name Chelativorans intermedius sp. nov. is proposed. The type strain is CC-MHSW-5T ( = CCM 8543T = LMG 28482T = DSM 29391T = CIP 110825T). Based on both genotypic and phenotypic characters, it is proposed that T. composti be reclassified within the genus Chelativorans as Chelativorans composti comb. nov.

Versatile properties of an exopolysaccharide R-PS18 produced by Rhizobium sp. PRIM-18

Exopolysaccharides (EPS) produced by bacteria have attracted scientific and industrial attention due to their multifunctional properties and relatively easier production. In this study, an EPS viz., R-PS18 produced by Rhizobium sp. PRIM-18 was characterized and its functional properties were assessed. Cell proliferative and in vitro wound healing activities of the EPS were established using human dermal fibroblast (HDF) cells. The isolate produced 2.1 g L(-1) purified EPS (molecular weight 9.33×10(6) Da) comprising of glucose, galactose, and mannose (6.1:1.8:1). Viscosity of 0.25% solution was 23.4 mPa s (shear rate 75 s(-1)) and it showed pseudoplastic and thixotropic behavior. High emulsification, iron chelation, and superoxide scavenging abilities were also observed. Significant increase in HDF cell proliferation and wound healing in vitro was achieved by R-PS18 treatment. Sulfation of R-PS18 significantly enhanced the cell proliferative and wound healing activities. In conclusion, these findings indicate potential applications of R-PS18.

Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant

A novel, Gram-staining-negative, rod-shaped, aerobic and motile bacterium, designated strain CC-SKC2(T), was isolated from the root tumor of a green bell pepper (Capsicum annuum var. grossum) plant in Taiwan. Cells were positive for oxidase and catalase activities and exhibited growth at 25-37 °C, pH 4.0-9.0 and tolerated NaCl concentrations up to 4.0 % (w/v). Strain CC-SKC2(T) is able to trigger nodulation in soybean (Glycine max Merr.), but not in Capsicum annuum var. grossum, red bean (Vigna angularis), sesbania (Sesbania roxburghii Merr.) or alfalfa (Medicago varia Martin.). The novel strain shared highest 16S rRNA gene sequence similarity to Rhizobium rhizoryzae KCTC 23652(T) and Rhizobium straminoryzae CC-LY845(T) (both 97.5 %) followed by Rhizobium lemnae L6-16(T) (97.3 %), Rhizobium pseudoryzae KCTC 23294(T) (97.1 %), and Rhizobium paknamense NBRC 109338(T) (97.0 %), whereas other Rhizobium species shared <96.7 % similarity. The DNA-DNA relatedness values of strain CC-SKC2(T) with R. rhizoryzae KCTC 23652(T), R. pseudoryzae KCTC 23294(T) and R. paknamense NBRC 109338(T) were 11.4, 17.2 and 17.0 %, respectively (reciprocal values were 11.1, 28.3 and 24.0 %, respectively). Phylogenetic analysis based on 16S rRNA, atpD and recA genes revealed a distinct taxonomic position attained by strain CC-SKC2(T) with respect to other Rhizobium species. The major fatty acids in strain CC-SKC2(T) were C16:0, C19:0 cyclo ω8c, C14:0 3-OH and/or C16:1 iso I and C18:1 ω7c and/or C18:1 ω6c. The polyamine pattern showed predominance of spermidine and moderate amounts of sym-homospermidine. The predominant quinone system was ubiquinone (Q-10) and the DNA G+C content was 60.5 mol%. On the basis of polyphasic taxonomic evidence presented here, strain CC-SKC2(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium capsici sp. nov. is proposed. The type strain is CC-SKC2(T) (=BCRC 80699(T) = JCM 19535(T)).

Carbon nanotube-reinforced hydroxyapatite composite and their interaction with human osteoblast in vitro

As a bone mineral component, hydroxyapatite (HA) has been an attractive bioceramic for the reconstruction of hard tissues. However, its poor mechanical properties, including low fracture toughness and tensile strength, have been a substantial challenge to the application of HA for the replacement of load-bearing and/or large bone defects. In this study, HA is reinforced with high-purity and well-functionalized multiwalled carbon nanotubes (MWCNTs; >99 wt%) having an average diameter of 15 nm and length from 10 to 20 μm. The cellular response of these functionalized CNTs and its composites were examined in human osteoblast sarcoma cell lines. Calcium nitrate tetrahydrate (Ca(NO3)2·4H2O) and diammonium hydrogen phosphate ((NH4)2HPO4) were used to synthesize HA in situ. MWCNTs were functionalized by heating at 100°C in 3:1 ratio of sulfuric acid and nitric acid for 60 min with stirring and dispersed in sodium dodecyl benzene sulfonate by sonication. HA particles were produced in MWCNTs solution by adding Ca(NO3)2·4H2O and (NH4)2HPO4 under vigorously stirring conditions. The composite was dried and washed in distilled water followed by heat treatment at 250°C to obtain CNT-HA powder. Physiochemical characterization of the composite material was carried out using Fourier transform infrared spectroscopy, field-emission scanning electron microscopy, energy-dispersive X-ray spectrometer, and X-ray diffractometer. Furthermore, this study investigates the cytotoxic effects of functionalized-MWCNTs (f-MWCNTs) and its composites with HA in human osteoblast sarcoma cell lines. Human osteoblast cells were exposed with different concentrations of f-MWCNTs and its composite with HA. The interactions of f-MWCNT and MWCNT-HA composites were analyzed by 3-(4,5–dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay. The results indicate no detrimental effect on survival or mitochondrial activity of the osteoblast cells. Cell viability decreased with an increase in CNT concentration indicating that MWCNTs and its composite can be cytotoxic at higher dosages. This result provides further evidence that the bionano interface can be developed for CNT-reinforced HA composites for load-bearing bone implants, drug delivery, and tissue engineering.

Anti-quorum sensing activity of flavonoid-rich fraction from Centella asiatica L. against Pseudomonas aeruginosa PAO1

BACKGROUND/PURPOSE

Inhibition of quorum sensing (QS), a cell-density dependent regulation of gene expression in bacteria by autoinducers is an attractive strategy for the development of antipathogenic agents.

METHODS

In this study, the anti-QS activity of the ethanolic extract of the traditional herb Centella asiatica was investigated by the biosensor bioassay using Chromobacterium violaceum CV026. The effect of ethyl acetate fraction (CEA) from the bioassay-guided fractionation of ethanol extract on QS-regulated violacein production in C. violaceum ATCC12472 and pyocyanin production, proteolytic and elastolytic activities, swarming motility, and biofilm formation in Pseudomonas aeruginosa PAO1 were evaluated. Possible mechanism of QS-inhibitory action on autoinducer activity was determined by measuring the acyl homoserine lactone using C. violaceum ATCC31532. Anti-QS compounds in the CEA fraction were identified using thin layer chromatography biosensor overlay assay.

RESULTS

Ethanol extract of C. asiatica showed QS inhibition in C. violaceum CV026. Bioassay-guided fractionation of ethanol extract revealed that CEA was four times more active than the ethanol extract. CEA, at 400 μg/mL, completely inhibited violacein production in C. violaceum ATCC12472 without significantly affecting growth. CEA also showed inhibition of QS-regulated phenotypes, namely, pyocyanin production, elastolytic and proteolytic activities, swarming motility, and biofilm formation in P. aeruginosa PAO1 in a concentration-dependent manner. Thin layer chromatography of CEA with biosensor overlay showed anti-QS spot with an Rf value that corresponded with that of standard kaempferol.

CONCLUSION

The anti-QS nature of C. asiatica herb can be further exploited for the formulation of drugs targeting bacterial infections where pathogenicity is mediated through QS.

Zeaxanthin biosynthesis by members of the genus Muricauda

Zeaxanthin, a C40xanthophyll carotenoid, has potential biological applications in nutrition and human health. In this study we characterized carotenoid composition in 5 taxonomically related marine bacterial isolates from the genus Muricauda. The pigment was characterized using high performance liquid chromatography (HPLC) and mass spectrometry, which confirmed the presence of all-trans-zeaxanthin. Muricauda strains produced zeaxanthin as a predominant carotenoid. M. flavescens JCM 11812(T) produced highest yield (4.4 +/- 0.2 mg L(-1)) when cultured on marine broth at 32 degrees C for 72 h. This is the first report on the presence of zeaxanthin among the majority of species from the genus Muricauda.

Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157T, and a lower sequence similarity to all other species of the genus Ruegeria . Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus Ruegeria . Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus Ruegeria , for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).

Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis

An aerobic, Gram-negative, rod-shaped bacterium with polar flagella, strain CC-AFH3(T), was isolated from an oil-contaminated site located in Kaohsiung county, Taiwan. Strain CC-AFH3(T) grew at 20-40 °C, pH 5.0-10.0 and <2 % (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain CC-AFH3(T) showed the greatest degree of similarity to Herbaspirillum soli SUEMI10(T) (96.5 %), H. aurantiacum SUEMI08(T) (96.3 %), H. canariense SUEMI03(T) (96.0 %), H. psychrotolerans PB1(T) (95.4 %) and members of other Herbaspirillum species (94.1-95.2 %), and lower similarity to members of other genera (<94 %). Phylogenetic analyses also positioned the novel strain in the genus Herbaspirillum as an independent lineage. The major fatty acids in strain CC-AFH3(T) were C10 : 0 3-OH, C12 : 0, C14 : 0 2-OH, C16 : 0, iso-C15 : 0 3-OH, C17 : 0 cyclo, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids of strain CC-AFH3(T) were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The predominant quinone was ubiquinone 8 (Q-8) and the DNA G+C content was 63.4 mol%. On the basis of 16S rRNA gene sequence analysis in combination with physiological and chemotaxonomic data, strain CC-AFH3(T) represents a novel species in a new genus, for which we propose the name Noviherbaspirillum malthae gen. nov., sp. nov.; the type strain of Noviherbaspirillum malthae is CC-AFH3(T) ( = BCRC 80516(T) = JCM 18414(T)). We also propose the reclassification of Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and 'Herbaspirillum psychrotolerans' as Noviherbaspirillum soli comb. nov. (type strain SUEMI10(T) = LMG 26149(T) = CECT 7840(T)), Noviherbaspirillum aurantiacum comb. nov. (type strain SUEMI08(T) = LMG 26150(T) = CECT 7839(T)), Noviherbaspirillum canariense comb. nov. (type strain SUEMI03(T) = LMG 26151(T) = CECT 7838(T)) and Noviherbaspirillum psychrotolerans comb. nov. (type strain PB1(T) = DSM 26001(T) = LMG 27282(T)), respectively. An emended description of Herbaspirillum seropedicae is also presented.

Hydrolysis of acid and alkali presoaked lignocellulosic biomass exposed to electron beam irradiation

In this study, synergetic effect of mild acid and alkali with electron beam irradiation (EBI) on the enzymatic hydrolysis of a selected grass biomass was assessed. Biomass samples prepared by soaking with 1% H2SO4, or 1% NaOH, were exposed to 75 and 150 kGy of EBI. Water presoaked biomass was used as control. Hydrolysis of pretreated samples was carried out using cellulase (15 FPU/g biomass) for 120 h. Structural changes were studied by FTIR and XRD analyses. Reducing sugar and glucose yields from enzymatic hydrolysis were significantly higher in acid and alkali presoaked EBI exposed samples. Theoretical glucose yield showed 40% increase from control in alkali presoaked EBI exposed (150 kGy) samples. Removal of hemicellulose, decreased crystallinity and structural changes were major factors for the combined treatment effect favoring the hydrolysis.

Bhargavaea ullalensis sp. nov., isolated from coastal sand

A Gram-positive-staining, aerobic, non-endospore-forming bacterium, isolated from Ullal coastal sand, Mangalore, Karnataka, India, on marine agar 2216, was studied in detail for its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain ZMA 19(T) was grouped into the genus Bhargavaea with high 16S rRNA gene sequence similarities to all currently described species of the genus Bhargavaea, Bhargavaea cecembensis (99.3 %), Bhargavaea beijingensis (98.8 %) and Bhargavaea ginsengi (98.6 %). GyrB amino acid sequence-based analysis supported the phylogenetic position and also distinguished strain ZMA 19(T) from the three other species of the genus Bhargavaea. Amino acid sequence similarities were only 85.6 to 89.5 % between strain ZMA 19(T) and the type strains of members of the genus Bhargavaea, which shared higher similarities among each other (93.0 to 96.2 %). The chemotaxonomic characterization supported the allocation of the novel strain to the genus Bhargavaea. The major menaquinone was MK-8. The polar lipid profile contained predominantly diphosphatidylglycerol and moderate amounts of phosphatidylglycerol. The diagnostic peptidoglycan diamino acid was lysine and the polyamine pattern contained spermidine and spermine. The major fatty acids were iso- and anteiso-branched fatty acids. DNA-DNA hybridization with the types strains Bhargavaea cecembensis LMG 24411(T), Bhargavaea beijingensis DSM 19037(T) and Bhargavaea ginsengi DSM 19038(T) resulted in values (reciprocal values in parentheses) of 26 % (29 %), 18 % (15 %) and 21 % (12 %), respectively. The results of physiological and biochemical tests allowed phenotypic differentiation of strain ZMA 19(T) from all other species of the genus Bhargavaea. Thus, ZMA 19(T) represents a novel species of this genus, for which the name Bhargavaea ullalensis sp. nov. is proposed, with ZMA 19(T) ( = LMG 27071(T) = CCM 8429(T)) as the type strain.

Stappia taiwanensis sp. nov., isolated from a coastal thermal spring

A beige-coloured, Gram-stain-negative, aerobic, non-motile moderately thermotolerant, rod-shaped organism, strain CC-SPIO-10-1(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on Marine Agar 2216. Based on 16S rRNA gene sequence analysis, this organism was grouped into the genus Stappia, showing 98.3 % sequence similarity to Stappia indica B106(T) and 98.2 % gene sequence similarity to Stappia stellulata IAM 12621(T). Ubiquinone Q-10 was the major respiratory quinone and C18 : 1ω7c and C18 : 1ω7c 11-methyl were detected as the major fatty acids. The hydroxylated fatty acid C18 : 0 3-OH was detected as well. Predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid AL1 and unidentified phospholipid PL1. Minor amounts of several unidentified lipids (PL2 and L1-L7) were present as well. The polyamine pattern contained the major compounds spermidine and spermine. Strain CC-SPIO-10-1(T) could be differentiated from the type strains of S. stellulata and S. indica by a set of biochemical tests. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain CC-SPIO-10(T) represents a novel species of the genus Stappia for which the name Stappia taiwanensis sp. nov. is proposed. The type strain is CC-SPIO-10 (T) ( = CCUG 59208(T) = LMG 25538 (T) = CCM 7757(T)).

Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring

A yellowish pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain CC-TBT-3T), was isolated on marine agar 2216 from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis of strain CC-TBT-3T showed a relatively low similarity (<95.5 %) to representatives of the genera Novosphingobium , Sphingosinicella and Sphingomonas of the Sphingomonadaceae , with the most related strain being the type strain of Novosphingobium soli . In addition to the relatively low 16S rRNA gene sequence similarity to members of established species, the isolate also showed some unique chemotaxonomic features, including the presence of some glycolipids with unusual chromatographic behaviour. The major components of the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and three unidentified glycolipids. The major respiratory quinone was ubiquinone Q-10. The polyamine pattern was characterized by the triamine sym-homospermidine as a major component. Although the predominant fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), the isolate did not show the typical hydroxyl fatty acids, such as C14 : 0 2-OH, C15 : 0 2-OH and C16 : 0 2-OH, found in members of the genera Novosphingobium , Sphingomonas and Sphingosinicella , but showed instead high amounts of C18 : 1 2-OH (12.0 %). The DNA G+C content of strain CC-TBT-3T was 63.4 mol%. 16S rRNA gene sequence, chemotaxonomic and physiological analyses revealed that strain CC-TBT-3T represents a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingomicrobium lutaoense gen. nov., sp. nov. is proposed; the type strain is of the type species S. lutoaense, CC-TBT-3T ( = DSM 24194T = CCM 7794T).

Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban)

A Gram-negative, coccoid-shaped bacterium, strain CC-CCM15-8(T), was isolated from a rhizosphere soil sample of the plant Crossostephium chinense (L.) Makino (Seremban) from Budai Township, Chiayi County, Taiwan. 16S rRNA gene sequence analysis clearly allocated strain CC-CCM15-8(T) to the Paracoccus cluster, showing highest similarities to the type strains of 'Paracoccus beibuensis' (98.8%), Paracoccus homiensis (97.6%), Paracoccus aestuarii (97.7%) and Paracoccus zeaxanthinifaciens (97.7%). The fatty acid profile, comprising C(18:1)ω7c as the major component and C(10:0) 3-OH as the characteristic hydroxylated fatty acid, supported the placement of strain CC-CCM15-8(T) within the genus Paracoccus. The polyamine pattern consisted of putrescine and spermidine as major components. Ubiqinone Q-10 was the major quinone type (95%); ubiquinone Q-9 was also detected (5%). The complex polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and unidentified phospholipids, lipids and glycolipids. Levels of DNA-DNA relatedness between strain CC-CCM15-8(T) and 'P. beibuensis' LMG 25871(T), P. aestuarii DSM 19484(T), P. zeaxanthinifaciens LMG 21993(T) and P. homiensis KACC 11518(T) were 24.9% (34.8%, reciprocal analysis), 15.7% (17.5%), 17.7% (23.4%) and 16.0% (25.4%), respectively. Physiological and biochemical test results allowed the phenotypic differentiation of strain CC-CCM15-8(T) from its closest relatives in the genus Paracoccus. Based on the data presented, it is concluded that strain CC-CCM15-8(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus rhizosphaerae sp. nov. is proposed. The type strain is CC-CCM15-8(T) (=LMG 26205(T)=CCM 7904(T)).

Microbulbifer taiwanensis sp. nov., isolated from coastal soil

A Gram-negative, non-spore-forming rod (CC-LN1-12(T)) was isolated from coastal soil samples of Lutao Island (Green Island), Taiwan, and its taxonomic position was studied. 16S rRNA gene sequence analysis showed that isolate CC-LN1-12(T) was grouped into the Microbulbifer cluster, with the highest similarities to Microbulbifer okinawensis ABABA23(T) (97.9 %), Microbulbifer maritimus TF-17(T) (97.7 %) and Microbulbifer donghaiensis CN85(T) (97.7 %), similarities to all other species of the genus Microbulbifer were lower than 96.8 %. The polyamine pattern contained the major compounds spermidine and cadaverine. The fatty acid profile, comprising the major fatty acids iso-C(15 : 0), iso-C(17 : 1)ω9c, C(18 : 1)ω7c and iso-C(11 : 0) 3-OH as the major hydroxylated fatty acid, supported the affiliation of strain CC-LN1-12(T) to the genus Microbulbifer. DNA-DNA hybridizations between strain CC-LN1-12(T) and Microbulbifer okinawensis ABABA23(T), M. donghaiensis CN85(T) and M. maritimus JCM 12187(T) resulted in relatedness values of 21.5 % (14.3 %, reciprocal analysis), 35.9 % (48.5 %, reciprocal analysis) and 48.1 % (52.1 %, reciprocal analysis), respectively. From these data, as well as from physiological and biochemical tests, strain CC-LN1-12(T) could be clearly differentiated from the most closely related species of the genus Microbulbifer. It is concluded that strain CC-LN1-12(T) represents a novel species, for which the name Microbulbifer taiwanensis sp. nov. is proposed. The type strain is CC-LN1-12(T) ( = LMG 26125(T) = CCM 7856(T)).

Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum

A Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T  = CCM 7756T).

Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

A beige-coloured, Gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1T, was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94 % sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C18 : 1ω7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1T was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1T represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1T ( = JCM 15068T = CCM 7767T).

Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems

A Gram-reaction-positive, rod-shaped bacterium, designated strain CC-VM-YT, was isolated from the faeces of the pill millipede Arthrosphaera magna Attems from India and was subsequently studied to determine its taxonomic position. Based on16S rRNA gene sequence similarities, the isolate clearly grouped with members of the genus Microbacterium. On the basis of pairwise comparisons of the 16S rRNA gene sequences, strain CC-VM-YT was most closely related to Microbacterium insulae DS-66T (98 %), Microbacterium hydrocarbonoxydans DSM 160809T (97.8 %) and Microbacterium hominis NBRC 15708T (97.9 %). The peptidoglycan contained the amino acids ornithine (Orn), alanine (Ala), glycine (Gly), homoserine (Hsr) and glutamic acid (Glu) in an approximate molar ratio of 1.0 : 0.8 : 2.2 : 0.8 : 0.3. In addition, substantial amounts of threo-3-hydroxy glutamic acid (Hyg) were detected, which is characteristic of peptidoglycan type B2β. The acyl type of the peptidoglycan was glycolyl. The menaquinones of strain CC-VM-YT were MK-13 (72 %), MK-12 (25 %) and MK-11 (3 %). The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. The fatty acid profile comprised anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids, which was congruent with fatty acid profiles of other members of the genus Microbacterium. The results of physiological and biochemical tests as well as DNA–DNA hybridizations with the most closely related species, M. insulae, M. hydrocarbonoxydans and M. hominis, revealed clear phenotypic and genotypic differences between strain CC-VM-YT and other members of the genus Microbacterium. Based on these results, strain CC-VM-YT ( = DSM 22421T  = CCM 7681T) represents a new species of the genus Microbacterium, for which the name Microbacterium arthrosphaerae sp. nov. is proposed.

Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond

A bacterial strain, designated an-8T, was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain an-8T were Gram-reaction-negative, aerobic, rod-shaped and non-motile, formed yellow-pigmented colonies and grew at 15–30 °C (optimum 25 °C), pH 7–8 (optimum pH 8.0) and in 0–1 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain an-8T belonged to the genus Flavobacterium and its most closely related neighbours were Flavobacterium terrigena DS-20T and Flavobacterium terrae R2A1-13T with sequence similarities of 95.1 and 94.9 %, respectively. Strain an-8T contained iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C16 : 0 3-OH, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 1 as the major fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylserine and several unidentified polar lipids. The G+C content of the genomic DNA was 39.8 mol%. On the basis of the phylogenetic and phenotypic data, strain an-8T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium macrobrachii sp. nov. is proposed. The type strain is an-8T ( = BCRC 17965T  = LMG 25203T).

Aquabacterium limnoticum sp. nov., isolated from a freshwater spring

A Gram-negative, facultatively anaerobic, short-rod-shaped, non-motile and non-spore-forming bacterial strain, designated ABP-4(T), was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Growth occurred at 20-40 °C (optimum, 30-37 °C), at pH 7.0-10.0 (optimum, pH 7.0-9.0) and with 0-3% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4(T), together with Aquabacterium fontiphilum CS-6(T) (96.4% sequence similarity), Aquabacterium commune B8(T) (96.1%), Aquabacterium citratiphilum B4(T) (95.5%) and Aquabacterium parvum B6(T) (94.7%), formed a deep line within the order Burkholderiales. Strain ABP-4(T) contained summed feature 3 (comprising C(16:1) ω7c and/or C(16:1) ω6c), C(18:1) ω7c and C(16:0) as predominant fatty acids. The major cellular hydroxy fatty acid was C(10:0) 3-OH. The major isoprenoid quinone was Q-8 and the DNA G+C content was 68.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and several uncharacterized phospholipids. The DNA-DNA relatedness of strain ABP-4(T) with respect to recognized species of the genus Aquabacterium was less than 70%. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ABP-4(T) represents a novel species in the genus Aquabacterium, for which the name Aquabacterium limnoticum sp. nov. is proposed. The type strain is ABP-4(T) (=BCRC 80167(T)=KCTC 23306(T)).

Supercritical carbon dioxide micronization of zeaxanthin from moderately thermophilic bacteria Muricauda lutaonensis CC-HSB-11T

Moderately thermophilic bacterial strain CC-HSB-11(T) (Muricauda lutaonensis), which was described recently from a coastal hot spring of Green Island, Taiwan, has been identified to produce zeaxanthin as a predominant xanthophyll by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Cell culture in bioreactor produced 3.12 ± 0.18 mg zeaxanthin L(-1) of culture. Micronization of zeaxanthin was achieved through supercritical carbon dioxide antisolvent precipitation method. Yield of zeaxanthin after the process was 53.4%. Dynamic light scattering assay determined the polydisperse existence of micronized particles of size 3 nm to 2 μm. Field emission scanning electron microscopy revealed distinct morphology and size distribution heterogeneity of particles. Integrity of zeaxanthin after the antisolvent process was assessed by LC-MS/MS. The technique capitalizes on the inherent ability of CC-HSB-11(T) to synthesize zeaxanthin and the work demonstrated feasibility of antisolvent precipitation method to produce microparticles exploiting a bacterial strain.

Stappia aquimarina sp. nov., isolated from seawater

A light-yellow pigmented bacterial strain designated SPIO-19(T) was isolated from seawater in Taiwan and was characterized using the polyphasic taxonomy approach. Strain SPIO-19(T) was Gram-negative, obligately aerobic, rod-shaped, motile by means of one polar flagellum and non-spore forming. Growth occurred at 15-42°C (optimum, 30-40°C), at pH 5.0-9.0 (optimum, pH 8.0) and with 0.5-9.0% NaCl (optimum, 1.0-5.0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SPIO-19(T) belonged to the genus Stappia and its closest neighbours were Stappia indica B106(T) and Stappia stellulata IAM 12621(T) with sequence similarities of 98.0% and 97.9%, respectively. Strain SPIO-19(T) contained C(18:1)ω7c as predominant fatty acid. The major isoprenoid quinone was Q-10 and the DNA G+C content was 64.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), phosphatidylcholine (PC), an uncharacterized aminolipid (AL) and an uncharacterized phospholipid (PL). The level of DNA-DNA relatedness of strain SPIO-19(T) to Stappia indica B106(T) and to Stappia stellulata IAM 12621(T) was 22.6 ± 2.8 % and 38.9 ± 3.8 %, respectively. On the basis of the genotypic and phenotypic data, strain SPIO-19(T) represents a new species in the genus Stappia, for which the name Stappia aquimarina sp. nov. is proposed. The type strain is SPIO-19(T) (=BCRC 80170(T) =LMG 25532(T)).

Gordonia humi sp. nov., isolated from soil

A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301T) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301T was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H2), minor amounts of MK-8(H2) and MK-7(H2). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis9, C16 : 0, C18 : 1 and tuberculostearic acid (10-methyl C18 : 0), supported the affiliation of strain CC-12301T to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301T from the most closely related Gordonia species. Strain CC-12301T therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301T (=DSM 45298T =CCM 7727T).

Arcicella aurantiaca sp. nov., isolated from stream water

A bacterial strain designated TNR-18T was isolated from stream water in southern Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-18T were Gram-stain-negative, strictly aerobic, non-motile and vibrioid, and the strain formed orange colonies. Growth occurred at 10–30 °C, with 0–0.2 % NaCl and at pH 6.0–10.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TNR-18T belonged to the genus Arcicella; its closest neighbours were Arcicella rosea TW5T and Arcicella aquatica NO-502T, with respective sequence similarities of 97.9 and 97.8 %. Predominant cellular fatty acids (>10 %) were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 37.7 %), C16 : 1 ω5c (13.0 %) and iso-C15 : 0 (11.1 %). The major respiratory quinone was MK-7. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The DNA G+C content was 39.9 mol%. On the basis of the phylogenetic and phenotypic data, strain TNR-18T should be classified as representing a novel species, for which the name Arcicella aurantiaca sp. nov. is proposed. The type strain is TNR-18T (=LMG 25207T =BCRC 17969T).

Terrimonas aquatica sp. nov., isolated from a freshwater spring

A yellow-pigmented bacterial strain, designated RIB1-6T, was isolated from a freshwater spring in Taiwan. Strain RIB1-6T was aerobic, Gram-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10–37 °C, at pH 7–8 and with 0–1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain RIB1-6T belonged to the genus Terrimonas and its two closest neighbours were Terrimonas ferruginea ATCC 13524T and Terrimonas lutea DYT (16S rRNA gene sequence similarity 97.4 % and 93.5 %, respectively). Strain RIB1-6T contained iso-C15 : 0 (33.4 %), iso-C17 : 0 3-OH (18.2 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 14.7 %) and iso-C15 : 1 (11.5 %) as the predominant fatty acids. The major isoprenoid quinone was MK-7. The DNA G+C content of strain RIB1-6T was 47.3 mol%. On the basis of the genotypic and phenotypic data, strain RIB1-6T represents a novel species in the genus Terrimonas, for which the name Terrimonas aquatica sp. nov. is proposed. The type strain is RIB1-6T (=BCRC 17941T=LMG 24825T).

Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli

A bacterial strain designated NAA16(T) was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Strain NAA16(T) was aerobic, Gram-staining-negative, rod-shaped, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 20-40 °C (optimum, 25 °C), at pH 7.0-8.0 (optimum, pH 7.5) and with up to 1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain NAA16(T) were Singularimonas variicoloris MN28(T), Sinobacter flavus CW-KD 4(T) and Solimonas soli DCY12(T), with respective sequence similarities of 96.7, 96.6 and 96.2 %. Phylogenetic trees reconstructed from 16S rRNA gene or rpoB sequences (encoding the β-subunit of the RNA polymerase) revealed that the novel strain NAA16(T) and these three closest relatives formed an independent phylogenetic clade within the Gammaproteobacteria. Strain NAA16(T) contained C₁₆:₀, C₁₈:₁ω7c and summed feature 3 (C₁₆:₁ω7c and/or C₁₆:₁ω6c) as predominant fatty acids and possessed phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids. The major isoprenoid quinone was Q-8. The DNA G+C content of strain NAA16(T) was 66.2 mol%. The taxonomic relationship of strain NAA16(T), Singularimonas variicoloris DSM 15731(T), Sinobacter flavus DSM 18980(T) and Solimonas soli LMG 24014(T) was clarified by means of a direct experimental comparison. Based on phenotypic, chemotaxonomic and phylogenetic data, the descriptions of the genus Solimonas and its type species Solimonas soli are emended. Members of the genus are Gram-negative, oxidase- and catalase-positive, aerobic or facultatively anaerobic and chemo-organotrophic. Chemotaxonomically, members of the genus Solimonas possess Q-8 as the major respiratory quinone, C₁₆:₀ and C₁₈:₁ω7c as predominant fatty acids and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids; the DNA G+C content is 64.9-68.4 mol%. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, allowed us to assign strain NAA16(T) to the genus Solimonas within the novel species Solimonas aquatica sp. nov. (type strain NAA16(T)  = BCRC 17835(T)  = LMG 24500(T)). The reclassification of Sinobacter flavus as Solimonas flava comb. nov. (type strain CW-KD 4(T)  = DSM 18980(T)  = KCTC 12881(T)  = CCTCC AB 206145(T)) and Singularimonas variicoloris as Solimonas variicoloris comb. nov. (type strain MN28(T)  = DSM 15731(T)  = LMG 22844(T)) is also proposed.

Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera

A Gram-negative, heterotrophic, marine bacterium, designated strain SW-11(T), was isolated from the reef-building coral Isopora palifera in Kenting, Taiwan. Cells were rods and were motile by a single polar flagellum. The strain grew at 10-45 °C (optimum, 30-35 °C), at pH 7.0-8.0 (optimum, pH 7.5) and with 2.0-4.0 % NaCl (optimum, 2.5-3.0 %). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unknown phospholipids. Isoprenoid quinones consisted of ubiquinone 9 (78.8 %) and ubiquinone 8 (21.1 %). Major cellular fatty acids were summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c; 22.3 %), C(17 : 1)ω8c (13.4 %), summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c; 13.1 %), C(16 : 0) (10.3 %) and anteiso-C(17 : 1)ω9c (10.0 %). The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis indicated that strain SW-11(T) belongs to the class Gammaproteobacteria and is a member of the order Alteromonadales. Strain SW-11(T) shared 93.2 % 16S rRNA gene sequence similarity with Teredinibacter turnerae T7902(T) and 92.1 % with Saccharophagus degradans 2-40(T), and can be further distinguished from these two related strains by distinct patterns of fatty acid content and differences in the polar lipid profile, the ability to utilize different compounds as carbon sources, the ability to degrade various compounds and differences in enzyme activities. The phylogenetic data and those from physiological, morphological and chemotaxonomic characterizations indicate that strain SW-11(T) represents a novel species and genus, for which the name Pseudoteredinibacter isoporae gen. nov., sp. nov. is proposed. The type strain of Pseudoteredinibacter isoporae is SW-11(T) ( = BCRC 17935(T)  = LMG 25246(T)).

Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring

The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.

Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei

A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117T, was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C18 : 1 ω7c, C19 : 0 cyclo ω8c, C16 : 0 and C18 : 0 were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117T was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117T is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117T (=BCRC 17964T =CCM 7684T).

Chitinibacter alvei sp. nov., isolated from stream water

A Gram-negative, aerobic bacterium, designated strain TNR-14T, was isolated from water of a stream located in southern Taiwan. Cells were rod-shaped and motile by means of a polar flagellum. The isolate exhibited optimum growth at 20 °C, at pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter and was related most closely to the type strain of Chitinibacter tainanensis (96.0 % similarity). The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 54.03 %) and C16 : 0 (27.22 %). The DNA G+C content of strain TNR-14T was 57.5 mol%. The results of physiological and biochemical tests and chemotaxonomic data allowed the clear phenotypic differentiation of the new isolate from Chitinibacter tainanensis. Strain TNR-14T is therefore considered to represent a novel species of the genus Chitinibacter, for which the name Chitinibacter alvei sp. nov. is proposed. The type strain is TNR-14T (=LMG 25206T =DSM 22217T =BCRC 17968T).

Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).

Georgenia soli sp. nov., isolated from iron-ore-contaminated soil in India

A Gram-positive actinobacterium (CC-NMPT-T3T) was isolated from iron-ore-contaminated soil near New Mangalore Port, Karnataka, India. Based on 16S rRNA gene sequence similarity studies, strain CC-NMPT-T3T belongs to the genus Georgenia and is most closely related to Georgenia muralis (98.6 %), Georgenia ruanii (97.4 %) and Georgenia thermotolerans (97.4 %). The peptidoglycan is of the type A4α l-Lys←l-Glu. The predominant isoprenoid quinone is menaquinone MK-8(H4) and the polar lipid profile is composed of the predominant compound diphosphatidylglycerol, moderate amounts of a phosphatidylinositol-mannoside, phosphatidylinositol and minor amounts of another phosphatidylmannoside and phosphatidylglycerol. The major fatty acids of strain CC-NMPT-T3T are anteiso-C15 : 0 and iso-C15 : 0. The results of DNA–DNA hybridizations, and physiological and biochemical tests allowed a clear phenotypic differentiation of strain CC-NMPT-T3T from all other Georgenia species. Strain CC-NMPT-T3T represents a novel species, for which the name Georgenia soli sp. nov. is proposed. The type strain is CC-NMPT-T3T (=DSM 21838T=CCM 7658T).

Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei

Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209T, CC-12309T and CC-5209T) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209T and CC-12309T were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1 %16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5 %. The third strain (CC-5209T) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209T, CC-12309T and CC-5209T consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA–DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209T and CC-12309T from M. halotolerans and other closely related Microbacterium species. Strain CC-5209T could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209T (=DSM 21798T=CCM 7686T)], Microbacterium humi sp. nov. [type strain CC-12309T (=DSM 21799T=CCM 7687T)] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209T (=DSM 22185T=CCM 7688T)].

Virgibacillus soli sp. nov., isolated from mountain soil

A Gram-positive bacterium (strain CC-YMP-6(T)) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6(T) clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6(T) were iso-C(15 : 0) and anteiso-C(15 : 0). The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6(T) from all recognized species of the genus Virgibacillus. Strain CC-YMP-6(T) is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6(T) (=DSM 22952(T)=CCM 7714(T)).

Deefgea chitinilytica sp. nov., isolated from a wetland

A bacterial strain, designated Nsw-4(T), was isolated from a water sample of Niao-Song Wetland Park in Taiwan and was characterized by using a polyphasic taxonomic approach. Strain Nsw-4(T) was Gram-negative, aerobic, ivory-coloured, rod-shaped and motile by means of a polar flagellum. Growth occurred at 15-37 degrees C, pH 6.0-8.0 and 0-2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Deefgea and that its closest neighbour was Deefgea rivuli WB 3.4-79(T) (96.9 %). The results of physiological and biochemical tests allowed the clear phenotypic differentiation of this isolate from D. rivuli WB 3.4-79(T). The major fatty acids were C16 : 1omega7c and C16 : 0. The G+C content of the genomic DNA was 53.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain Nsw-4(T) should be classified as representing a novel species and the second member of the genus Deefgea, for which the name Deefgea chitinilytica sp. nov. is proposed. The type strain is Nsw-4(T) (=BCRC 17934(T)=LMG 24817(T)).

Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata

A Gram-negative, aerobic, rod-shaped bacterium, designated strain CL-33(T), was isolated from the encrusting pore coral Montipora aequituberculata collected from seawater off the coast of southern Taiwan. 16S rRNA gene sequence analysis showed that the strain clustered closely with Endozoicomonas elysicola MKT110(T) (96.7 % similarity). The novel strain required NaCl for growth and exhibited optimal growth at 25 degrees C and in the presence of 2-3 % NaCl. Predominant cellular fatty acids were summed feature 3 (C(16 : 1)omega7c and/or C(16 : 1)omega6c; 39.6 %), summed feature 8 (C(18 : 1)omega7c and/or C(18 : 1)omega6c; 32.8 %) and C(16 : 0) (12.0 %). The DNA G+C content of strain CL-33(T) was 50.0 mol%. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of this isolate from E. elysicola. It is evident from the genotypic, phenotypic and chemotaxonomic data presented that strain CL-33(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas montiporae sp. nov. is proposed. The type strain is CL-33(T) (=LMG 24815(T) =BCRC 17933(T)).

Microlunatus soli sp. nov., isolated from soil

A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (strain CC-12602(T)) was isolated from a spawn used for growing the edible mushroom Agaricus brasiliensis in the laboratory. On the basis of 16S rRNA gene sequence analysis, strain CC-12602(T) was shown to belong to the genus Microlunatus and was related most closely to the type strains of Microlunatus ginsengisoli (96.1 % similarity), M. phosphovorus (95.9 %), M. panaciterrae (95.8 %) and M. aurantiacus (95.5 %). The quinone system comprised menaquinone MK-9(H4) as the major component and the polyamine pattern consisted of spermidine and spermine as major compounds. The predominant polar lipids were phosphatidylglycerol and unknown phospholipid PL3. Moderate amounts of diphosphatidylglycerol, an unknown glycolipid and three unknown phospholipids and minor amounts of an unknown phospholipid and a polar lipid were detected. The peptidoglycan type was A3gamma', based on LL-2,6-diaminopimelic acid with an interpeptide bridge consisting of a single glycine residue and a second glycine residue at position 1 of the peptide subunit. Peptidoglycan structure and major fatty acids (anteiso-C(15 : 0), iso-C(16 : 0) and iso-C(15 : 0)) supported the affiliation of strain CC-12602(T) to the genus Microlunatus. The results of physiological and biochemical tests allowed strain CC-12602(T) to be differentiated phenotypically from recognized Microlunatus species. Strain CC-12602(T) is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus soli sp. nov. is proposed. The type strain is CC-12602(T) (=DSM 21800(T) =CCM 7685( T)).

Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond

A non-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain GR13(T), was isolated using nutrient agar from a water sample from a pond used for the culture of soft-shell turtles (Trionyx sinensis), Pingtung County, Taiwan. 16S rRNA gene sequence studies indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella. Its closest neighbours were Vogesella indigofera ATCC 19706(T) and Vogesella perlucida DS-28(T) (both with 97.4 % gene sequence similarity). The novel isolate could be distinguished from these species by several phenotypic characteristics. The predominant fatty acids were summed feature 3 (C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH; 60 %), C(16 : 0) (13.6 %) and C(18 : 1)omega7c (12.5 %). The DNA G+C content of strain GR13(T) was 63 mol%. The DNA-DNA hybridization values for the novel strain with V. indigofera and V. perlucida were <25 %. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain GR13(T) represents a novel species in the genus Vogesella, for which the name Vogesella lacus sp. nov. is proposed. The type strain is GR13(T) (=BCRC 17836(T)=LMG 24504(T)).