Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach

CONTEXT

The COVID-19 (coronavirus disease 19) pandemic brought on by the SARS-CoV-2 outbreak (severe acute respiratory syndrome coronavirus 2) has stimulated the exploration of various available chemical compounds that could be used to treat the infection. This has driven numerous researchers to investigate the antiviral potential of several bioactive compounds from medicinal plants due to their reduced adverse effects compared to chemicals. Some of the bioactive compounds used in folklore treatment strategies are reported as effective inhibitors against the proliferative and infective cycles of SARS-CoV-2. The secondary metabolites from plants are generally used to treat various diseases due to their intact medicinal properties. The present study analyzes the inhibitory potential of phytochemicals from medicinal plants like Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera against SARS-CoV-2 by molecular docking.

METHODS

Ten druggable protein targets from SARS-CoV-2 are docked against the phytochemicals from the selected medicinal plants. The phytocompounds astragalin, isoquercetin, and 5-hydroxy-7-methoxy-6-c-glycosy flavone were found to have lower binding energy depicting their inhibitive potential compared with the reported inhibitors that are used in the treatment of SARS-CoV-2 infection. The phytocompounds found to have the least binding energy were selected for further analyses. To assess the compounds' potential as drugs, their ADMET characteristics were also examined. Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera six possible compounds were separately screened for ADME and toxicity characteristics; then, the results were analyzed. To assess the impact of the phytocompound binding on the dynamics of SARS-CoV-2 ribonuclease protein NSP15, microsecond-level all atomistic molecular dynamics simulations were performed, and their dynamics were analyzed. Microsecond-level molecular dynamics simulations of both the ligands complexed with NSP15 revealed that the ligand induces allosteric effects on NSP15, which could lead to destabilization of NSP15 hexameric interface and loss of RNA binding. The low binding energy exhibited by the phytochemicals from Lantana camera, Sphaeranthus indicus, and Nelumbo nucifera against the protein targets of SARS-CoV-2 showed inhibitory potential by the selected molecules. Their predicted interference of the enzymes involved in the molecular mechanisms aiding the proliferation of SARS-CoV-2 indicated the inhibitive ability of the phytochemicals.

Outcomes of ab-interno irrigating goniectomy with trabectome in primary and secondary glaucoma from a single center in India

Purpose

This study was done to report intermediate-term outcomes of irrigating goniectomy with trabectome (trabectome) surgery among different types of glaucoma eyes from a single center in India using a cross-sectional, longitudinal, observational study design.

Methods

Fifty-three patients (58 eyes) with glaucoma who underwent irrigating goniectomy with trabectome between January 2019 and February 2020 were included. Pre-operative data included age, gender, eye laterality, specific diagnosis, number of anti-glaucoma medications (AGMs), prior glaucoma surgeries, visual acuity, and intraocular pressure (IOP) on medical treatment. Post-operative data included IOP changes during the follow-up till 1-year, number of AGMs, any complications, or additional surgical intervention required. Success was defined as IOP ≤ 21 mmHg and ≥ 20% reduction of IOP from pre-operative IOP with no additional glaucoma surgery.

Results

The cohort included 58 eyes (male 53.4% and female 46.6%) ranging from 0.6 to 81 years of age. The average baseline IOP was 23.4 ± 10.2 mmHg and reduced significantly with surgery to 14.1 ± 5.3 mmHg at 1-year follow-up. The AGMs reduced from 2.4 ± 1.4 pre-surgery to 1.6 ± 1.4 at 1-year follow-up. Four eyes required additional glaucoma surgeries for IOP control. The success rate of trabectome with phacoemulsification (88%) was discernibly higher than with trabectome alone (67%). Intra-operatively, significant blood reflux was noticed in 27 eyes, of which only one required tamponading with a viscoelastic agent.

Conclusion

This study concludes that irrigating goniectomy with trabectome has good efficacy and safety in both pediatric and adult cases of glaucoma in terms of IOP control, reduction in AGMs, and low incidence of complications in the Indian population.

Bio-corrosion impacts on mechanical integrity of ZM21 Mg for orthopaedic implant application processed by equal channel angular pressing

The mechanical integrity of rolled ZM21 Mg was improved by equal channel angular pressing (ECAP) to function as a potential biodegradable bone screw implant. Electron backscattered diffraction (EBSD) revealed deformed grains of 45 µm observed in rolled ZM21 Mg. They were transformed to equiaxed fine grains of 5.4 µm after 4^th pass ECAP. The yield strength of rolled and ECAPed ZM21 Mg alloys were comparable. In contrast, 4^th pass ZM21 Mg exhibited relatively higher elongation when compared to rolled sample. The mechanical properties of rolled and ECAPed ZM21 Mg were dependant on both grain refinement and crystallographic texture. The rolled and 4^th pass ECAPed tensile samples exhibited nonlinear deterioration of mechanical properties when tested after 7, 14, 21 and 28 days immersion in Hank's solution. The evaluation signifies that regardless their processing condition, ZM21 Mg alloys are suitable for surgical areas that requires high mechanical strength. In addition, the 4^th pass ECAP samples were viable to MG-63 cells proving themselves to be promising candidates for future in vivo studies.

Pregnancy Outcomes Post-bariatric Surgery-a Single-Centre Retrospective Study from India

BACKGROUND

Bariatric surgery presently is the best possible intervention for treatment of severe obesity and its related conditions. This study presents retrospective data on the pregnancy outcomes of Indian patients who underwent bariatric surgery before conception.

METHODOLOGY

This is a single-centre retrospective, observational study. Data on demographics, pre-surgery weight, body mass index (BMI), types of bariatric surgery, weight at conception, weight gain during pregnancy, type of delivery and the health of the baby were collected and analysed to study the weight loss pattern and pregnancy outcomes in female patients of childbearing potential.

RESULTS

The study included 34 women of childbearing potential (BMI>30 kg/m²) who underwent bariatric surgery. The study population was followed up from the time of surgery until 1-year post-delivery of the baby. The mean weight gain during the pregnancy was 14.9±5.4 kg. Twenty-three underwent LSCS, and the rest had normal delivery with mean baby weight of 2.5±0.4 kg. Six babies required neonatal intensive care. In our series, only 4 of 35 cohorts that are only 11% had substantial weight retention (range 5-13 kg) at the end of 12 months which is significantly lower than the normal cohorts who did not undergo bariatric surgery.

CONCLUSION

Bariatric surgery improves fertility with safe pregnancy and its outcomes in terms of preeclampsia, eclampsia, gestational diabetes, premature rupture of the membranes (PROM), postpartum haemorrhage (PPH) and puerperal sepsis in women with childbearing potential and safe for offspring in terms of shoulder dystocia, macrosomia, birth asphyxia and perinatal mortality. However, they should be well aware of the risks associated with bariatric surgery especially the mal-absorptive procedures.

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations

BACKGROUND

The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

RESULTS

The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

CONCLUSIONS

Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.

Bioresponsive supramolecular hydrogels for hemostasis, infection control and accelerated dermal wound healing

Injectable, drug-releasing hydrogel scaffolds with multifunctional properties including hemostasis and anti-bacterial activity are essential for successful wound healing; however, designing ideal materials is still challenging. Herein, we demonstrate the fabrication of a biodegradable, temperature-pH dual responsive supramolecular hydrogel (SHG) scaffold based on sodium alginate/poly(N-vinyl caprolactam) (AG/PVCL) through free radical polymerization and the subsequent chemical and ionic cross-linking. A natural therapeutic molecule, tannic acid (TA)-incorporated SHG (AG/PVCL-TA), was also fabricated and its hemostatic and wound healing efficiency were studied. In the AG/PVCL-TA system, TA acts as a therapeutic molecule and also substitutes as an effective gelation binder. Notably, the polyphenol-arm structure and diverse bonding abilities of TA can hold polymer chains through multiple bonding and co-ordinate cross-linking, which were vital in the formation of the mechanically robust AG/PVCL-TA. The SHG formation was successfully balanced by varying the composition of SA, VCL, TA and cross-linkers. The AG/PVCL-TA scaffold was capable of releasing a therapeutic dose of TA in a sustained manner under physiological temperature-pH conditions. AG/PVCL-TA displayed excellent free radical scavenging, anti-inflammatory, anti-bacterial, and cell proliferation activity towards the 3T3 fibroblast cell line. The wound healing performance of AG/PVCL-TA was further confirmed in skin excision wound models, which demonstrated the potential application of AG/PVCL-TA for skin regeneration and rapid wound healing.

Isoeugenol suppresses multiple quorum sensing regulated phenotypes and biofilm formation of Pseudomonas aeruginosa PAO1

The potential strategy to prevent bacterial pathogenicity is disabling quorum sensing circuits with structural mimicking molecules. Here, we analyzed a synthetic molecule isoeugenol, for inhibition of quorum sensing regulated phenotype and biofilm formation. Isoeugenol was an effective inhibitor, i.e., more than 70% of virulence factors were inhibited including pyocyanin, rhamnolipid, exopolysaccharide, swarming motility and biofilm formation. Interestingly, these quorum sensing regulated phenotypes in Pseudomonas aeruginosa PAO1 were inhibited without affecting the planktonic cells. Moreover, the presence of isoeugenol exhibited more than 70% inhibition of biofilm formation through inhibition of the quorum sensing systems. Furthermore, docking studies suggest that isoeugenol bound to the quorum sensor regulators such as LasI, LasR PqsE and SidA with considerable binding interactions. Our results demonstrate the utility of isoeugenol as a blocker of quorum sensing, which will be functioning as an antivirulence compound.

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.

Is weight regaining significant post laparoscopic Roux-en-Y gastric bypass surgery? - A 5-year follow-up study on Indian patients

Background

Laparoscopic Roux-en-Y gastric bypass (RYGB) has been proven to induce significant weight loss and remission of related co-morbidities in patients with morbid obesity. The long-term follow-up data show weight regain or failure to achieve complete remission of type 2 diabetes mellitus (T2DM) in some patients. In this study, we report weight loss patterns and remission of T2DM in patients with morbid obesity during a 5-year follow-up after RYGB.

Objective

The objective was to evaluate outcomes during the follow-up on excess weight loss (EWL) and remission of T2DM after laparoscopic RYGB among Indian patients.

Setting

The study was conducted in a tertiary care hospital, Kerala, India.

Materials and Methods

This is a retrospective study in patients who underwent surgery between 2007 and 2010. The patient demographics, pre- and post-operative body mass index (BMI), co-morbidities and EWL were recorded from the medical records. These data were compared between pre-operative and follow-up intervals till 5 years using statistical approaches.

Results

The study included 157 patients (91 males and 66 females) having a mean pre-operative BMI of 47.91 ± 7.01 kg/m². A significant reduction in the BMI was observed at each follow-up point (P < 0.01) till 5 years after the surgery. The mean percentage of EWL increased from 34.57% ± 12.62% to 71.50% ± 15.41% from 3 months to 5 years after the surgery. Twelve per cent (n = 19) of patients achieved normal BMI (<25 mg/kg²) by 3^rd year after the surgery. However, the remission of T2DM was achieved in >50% of patients within a year of surgery. During the 5^th year, weight regain (1-22 kg) was observed in 36.70% (n = 58) patients, and recurrence of T2DM was observed in two patients.

Conclusions

The long-term durability of RYGB in the study population was satisfactory with significant weight loss and remission of T2DM.

Demineralization of tooth enamel following radiation therapy; An in vitro microstructure and microhardness analysis

Objective

The objective of this study is to evaluate the effects of radiotherapy doses on mineral density and percentage mineral volume of human permanent tooth enamel.

Materials and Methods

Synchrotron radiation Xray microcomputed tomography (SRμCT) and microhardness testing were carried out on 8 and 20 tooth samples, respectively. Enamel mineral density was derived from SRμCT technique using ImageJ software. Microhardness samples were subjected to Vickers indentations followed by calculation of microhardness and percentage mineral volume values using respective mathematical measures. Data were analyzed using paired t-test at a significance level of 5%. Qualitative analysis of the enamel microstructure was done with two-dimensional projection images and scanned electron micrographs using μCT and field emission scanning electron microscopy, respectively.

Results

Vickers microhardness and SRμCT techniques showed a decrease in microhardness and an increase in mineral density, respectively, in postirradiated samples. These changes were related to mineral density variation and alteration of hydroxyapatite crystal lattice in enamel surface. Enamel microstructure showed key features such as microporosities and loss of smooth homogeneous surface. These indicate tribological loss and delamination of enamel which might lead to radiation caries.

Conclusions

Tooth surface loss might be a major contributing factor for radiation caries in head-and-neck cancer patients prescribed to radiotherapy. Such direct effects of radiotherapy cause enamel abrasion, delamination, and damage to the dentinoenamel junction. Suitable measures should, therefore, be worked out to protect nontarget oral tissues such as teeth while delivering effective dosages to target regions.

Bacterial cross talk with gut microbiome and its implications: a short review

Human gut microbiota exists in a complicated symbiotic relationship which postulates to impact health and disease conditions on the host. Interestingly, the gut microbiome shows different mechanisms to regulate host physiology and metabolism including cell-to-cell communications. But microbiota imbalance is characterized to change in the host normal functioning and lead to the development and progression of major human diseases. Therefore, the direct cross talk through the microbial metabolites or peptides suggests the evidence of host health and disease. Recent reports highlight the adaptation signals/small molecules promoting microbial colonization which allows modulating immunity of host and leads to pathogen colonization. Moreover, quorum sensing peptides are also evident in the involvement of host disease conditions. Here, we review the current understanding of the gut microbiota cross talk with mammalian cells through metabolites and peptides. These studies are providing insight into the prediction of signature molecules which significantly provide information for the understanding of the interaction for precision medicine applications.

A novel exopolysaccharide from marine bacterium Pantoea sp. YU16-S3 accelerates cutaneous wound healing through Wnt/β-catenin pathway

Natural polysaccharides with versatile properties are the potential candidates for wound healing applications. In this study, an exopolysaccharide, EPS-S3, isolated from a marine bacteria Pantoea sp. YU16-S3 was evaluated for its wound-healing abilities by studying the key molecular mechanisms in vitro and in vivo. Basic characterisation showed EPS-S3 as a heteropolysaccharide with glucose, galactose, N-acetyl galactosamine and glucosamine. The molecular weight of EPS-S3 was estimated to be 1.75 × 10⁵ Da. It showed thermal stability up to 200 °C and shear-thickening non-Newtonian behaviour. It was biocompatible with dermal fibroblasts and keratinocytes and showed cell adhesion and cell proliferation properties. EPS-S3 facilitated cell migration in fibroblasts, induced rapid transition of cell cycle phases and also activated macrophages. In vivo experiments in rats showed the re-epithelialization of injured tissue with increased expression of HB-EGF, FGF, E-cadherin and β-catenin in EPS-S3 treatment. The results indicate that EPS-S3 modulates healing process through Wnt/β-catenin pathway due to its unique characteristics. In conclusion, EPS-S3 biosynthesized by the marine bacterium is a potential biomolecule for cutaneous wound healing applications.

The whole-genome sequence analysis of Enterobacter cloacae strain Ghats1: insights into endophytic lifestyle-associated genomic adaptations

Enterobacter cloacae is normally considered to be an opportunistic human pathogen. Here, we report on the whole-genome sequence of an endophytic E. cloacae, strain "Ghats1", isolated from leaves of the medicinal plant Coscinium fenestratum Gaertn. Functional analysis of the Ghats1 genome revealed an enrichment for genes involved in the uptake and exchange of nutrients, for chemotaxis and for plant colonization. Unexpectedly though, there were no ORFs belonging to the "virulence factors and antibiotic resistance". Moreover, the presence of hydrolytic enzymes and motility functions reveals the characteristics of an endophyte lifestyle of a bacterium that can colonize and adapt to plant environment. These results provide a better understanding of an endophytic lifestyle through plant-microbe interaction, which can be further exploited as a biocontrol agent.

Seven-Year Outcomes of Laproscopic Sleeve Gastectomy in Indian Patients with Different Classes of Obesity

BACKGROUND

The aim of the study was to assess the long-term outcome in terms of weight loss and remission of comorbidities among the patients who had undergone LSG in an Indian setting.

METHODS

This is a retrospective observational study of patients (BMI > 30 kg/m²) who underwent LSG having a minimum 6 months of follow-up data. Based on preoperative BMI, patients were grouped as class 1, 30 < BMI < 35 kg/m²; class 2, 35 < BMI < 40 kg/m²; and class 3, BMI > 40 kg/m². Data on BMI and %EWL between three classes and among genders at different follow-up points for 7 years were compared.

RESULT

Study included 95 patients (mean age of 33.7 ± 11 years), and the preoperative mean BMI was 40.2 ± 5.1 kg/m². At one year of surgery, 85.5% patients achieved > 50%EWL. The highest mean %EWL was found in class 1 (66.19%), followed by class 2 (56.73%) and class 3 (46.59%) at the sixth month follow-up. At the seventh year, %EWLs were 85.11% (class 1), 76.69% (class 2), and 62.98% (class 3) and the mean BMIs were 25.13 ± 3.09 kg/m² (class 1), 26.86 ± 2.12 kg/m² (class 2), and 31.07 ± 3.39 kg/m² (class 3) and were significantly different (p < 0.05). At the last follow-up, though, the males showed slight weight regain; however, there were no statistical differences between the genders (p = 0.065).

CONCLUSION

Outcome from LSG was better in patients with BMI < 40 kg/m² compared to the patients with BMI > 40 kg/m². Remission of obesity-related comorbidities was observed with LSG in all groups and gender did not influence the outcome significantly.

Tetrandrine isolated from Cyclea peltata induces cytotoxicity and apoptosis through ROS and caspase pathways in breast and pancreatic cancer cells

Tetrandrine is a bisbenzylisoquinoline alkaloid known to exhibit anticancer activity against different cancers. In the present study, the cytotoxic effect of tetrandrine isolated from Cyclea peltata on pancreatic (PANC-1) and breast (MDA-MB-231) cancer cells was evaluated in vitro with an attempt to understand the role of tetrandrine on the generation of reactive oxygen species (ROS) and caspase activation. Results demonstrate the dose- and time-dependant cytotoxic effect of tetradrine on both MDA-MB-231 and PANC-1 cells with IC₅₀ values ranging between 51 and 54 μM and 22 and 27 μM for 24 h and 48 h of incubation respectively. In addition, treatment of MDA-MB-231 and PANC-1 cells with tetrandrine showed the shrunken cytoplasm and damaged cell membrane in a dose- and time-dependant manner under the microscope. Also, tetrandrine treatment revealed an elevated levels of reactive oxygen species and increased activities of caspase-8, -9 and -3 confirming the apoptosis of cells through both extrinsic death receptor and intrinsic caspase activation. Therefore, the present study suggests the apoptosis of cells with the activation of caspase pathways mainly intrinsic pathway as a downstream event of tetrandrine-induced ROS generation. Hence, reactive oxygen species-mediated caspase activation pathway may be potentially targeted with the use of tetrandrine to treat breast and pancreatic cancers.

A bioactive exopolysaccharide from marine bacteria Alteromonas sp. PRIM-28 and its role in cell proliferation and wound healing in vitro

Marine bacteria secrete exopolysaccharides (EPS) with unique structural and functional properties and serve as a source of newer bioactive biopolymers. This study reports an EPS produced by a marine bacterium identified as Alteromonas sp. PRIM-28 for its bioactivities. The EPS was characterised using standard methods and tested for its bioactivities using in vitro models. EPS-A28 is an anionic heteropolysaccharide with a molecular weight of 780 kDa and exists as triple helical structure in aqueous solution. Monosaccharide composition is mannuronic acid, glucose and N-acetyl glucosamine repeating units in the ratio 1:3.67:0.93. The FT-IR spectra showed the presence of sulphate, phosphate and uronic acid residues. The thermal analysis showed partial degradation of the EPS-A28 at 190 °C and 40% of residues were stable up to 800 °C. It showed biocompatibility and induced proliferation and migration of dermal fibroblasts (HDF) and keratinocytes. EPS-A28 could increase the S-phase of cell cycle. The proliferative property of the EPS-A28 was established by the increased expression of fibroblast proliferation marker (Ki-67) also its capability of binding to cell surface. It also induced nitric oxide and arginase synthesis in macrophages. These findings suggest that EPS-A28 can be potentially used as a multifunctional bioactive polymer in wound care.

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.

Study on the morphological and biocompatible properties of chitosan grafted silk fibre reinforced PVA films for tissue engineering applications

The current study delineates the preparation of novel chitosan grafted silk fibre reinforced Poly (vinyl alcohol) (PVA) composite films with desirable properties. Although silk fibroin has been extensively used for various biomedical applications, its properties could be further re-tailored for its suitability in the field of regenerative medicine. Chitosan was successfully grafted over silk, via acylation with succinic anhydride and thereby the fibres were incised and used for the preparation of the films. The grafted silk fibre reinforced PVA films were subjected to FTIR studies, microscopic analysis by atomic force microscopy (AFM) and optical microscopy techniques, X-ray diffraction (XRD) analysis and further evaluated for in vitro biocompatibility studies. The composite films demonstrated improved surface roughness with increasing concentration of the fibre and its dispersion in the polymer matrix was observed. Furthermore, in vitro biocompatibility and cellular behaviour such as adhesion and proliferation of mouse fibroblasts as well as astrocyte cells was studied and the results showed improved proliferative activity, when compared to the pristine PVA films. These results were further supported by the results confirmed by MTT assay demonstrating the films to be non-toxic. The efficiency and feasibility of the films to be used for tissue engineering, was further evaluated by haemocompatibility studies using human erythrocytes, thus making them a potential material to be used for biomedical applications.

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.

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.

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.

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.

Inhibition of quorum sensing in Chromobacterium violaceum by Syzygium cumini L. and Pimenta dioica L

OBJECTIVE

To investigated into the anti-quorum sensing (QS) activity of Syzygium cumini L. (S. cumini) and Pimenta dioica L. (P. dioica) using Chromobacterium violaceum (C. violaceum) strains.

METHODS

In this study, anti-QS activity of ethanol extract of Syzygium cumini L. and Pimenta dioica L. were screened using C. violaceum CV026 biosensor bioassay. By bioassay guided fractionation of S. cumini and P. dioica, ethyl acetate fraction (EAF) with strong anti-QS activity was separated. Inhibition of QS regulated violacein production in C. violaceum ATCC12472 by EAF was assessed at different concentrations. The effect of EAF on the synthesis of autoinducer like N-acyl homoserine lactone (AHL) was studied in C. violaceum ATCC31532 using its mutant C. violaceum CV026 by standard methods.

RESULTS

EAF inhibited violacein production in C. violaceum ATCC12472 in a concentration dependent manner without significant reduction in bacterial growth. Complete inhibition of violacein production was evidenced in 0.75-1.0 mg/mL concentration of EAF without inhibiting the synthesis of the AHL. TLC biosensor overlay profile of EAF revealed two translucent spots in S. cumini and P. dioica that inhibited C6-AHL mediated violacein production in C. violaceum CV026.

CONCLUSIONS

This study indicates the anti-QS activity of the tested medicinal plants against C. violaceum.

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.

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)).

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)).

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.

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)).

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)).

Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle

The taxonomic status of a pale-yellow-coloured bacterial isolate from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile that was characteristic for the genus Sphingobium, consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids and the lack of 3-OH fatty acids, ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone, and a polar lipid pattern that consisted of the predominant compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, sphingoglycolipid and an unknown glycolipid. Spermidine was the major polyamine component. The genotypic and phenotypic data (physiology and fatty acid and polar lipid profiles) showed that the isolate merits classification as representing a novel species of the genus Sphingobium, for which the name Sphingobium rhizovicinum sp. nov. is proposed. The type strain is CC-FH12-1T (=CCM 7491(T)=BCRC 17770T) [corrected]

Application of wastewater from paper and food seasoning industries with green manure to increase soil organic carbon: a laboratory study

This laboratory scale experiment was designed to study the suitability of organic wastes from paper and food seasoning industries to improve the soil organic carbon for rice cultivation. Lignin-rich wastewater from paper industry and nitrogen-rich effluent from a food industry at suitably lower concentrations were used at two levels of green manure to enhance the soil organic carbon fraction over time. Both the groups of soils with or without Sesbania were incubated under submerged condition at 25 degrees C for 15 days. Wastewaters from paper industry (WP), food industry (WS), and a combination of WP+WS were added separately to both the treatment groups in flasks. After 103 days of incubation, from all the three treatments and control, total organic carbon and alkali-soluble organic carbon fractions were analyzed. Results indicated that in all the three treatments containing green manure amended with industrial wastewaters, the organic carbon content increased significantly. The alkali-soluble organic carbon fraction was increased by 59% in the soil amended with green manure containing WS and by 31% in the treatment without green manure compared to control. The paper mill waste water namely, WP, increased the organic carbon only in the soil containing green manure by 63%. The combined treatment of WP+WS with green manure increased alkali-soluble organic carbon fraction by 90% compared to control, while in the treatment without green manure, the organic carbon increase was 71%. Overall, the combined treatment WP+WS with green manure could increase the alkali-soluble organic carbon fraction more than all other treatments. Hence, wastewater rich in organics from paper and food industries can be efficiently used to temporarily increase the soil organic carbon content.

Chromobacterium aquaticum sp. nov., isolated from spring water samples

Strain CC-SEYA-1T, a motile, Gram-negative, non-violet-pigmented bacterium, was isolated on nutrient agar from spring-water samples collected from Yang-Ming Mountain, Taipei County, Taiwan. 16S rRNA gene sequence studies showed that the strain clustered with Chromobacterium violaceum (96.8 % similarity) and Chromobacterium subtsugae (96.5 % similarity), followed by Aquitalea magnusonii (95.8 % similarity). The fatty acid profile was slightly different from those reported for C. violaceum, C. subtsugae and A. magnusonii. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolate from the described Chromobacterium species. It is evident from the data obtained that the strain should be classified as a novel species in the genus Chromobacterium. The name proposed for this taxon is Chromobacterium aquaticum sp. nov.; the type strain is CC-SEYA-1T (=CCUG 55175T=BCRC 17769T).

Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil

A bacterial isolate from a sample of oil-contaminated soil was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constituted a distinct phyletic line within the genus Pseudoxanthomonas, displaying >3.7 % sequence divergence with respect to recognised Pseudoxanthomonas species. The genus assignment was confirmed by a chemotaxonomic analysis, which revealed the presence of a fatty acid profile characteristic of members of the genus Pseudoxanthomonas (straight-chain saturated, unsaturated and branched-chain fatty acids of the iso/anteiso type and 3-hydroxylated fatty acids) and the presence of a ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The novel isolate was distinguishable from other members of the genus Pseudoxanthomonas on the basis of a combination of phenotypic properties. The genotypic and phenotypic data show that the strain represents a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas spadix sp. nov. is proposed. The type strain is IMMIB AFH-5(T) (=DSM 18855(T)=CCUG 53828(T)).

Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste

A yellow-pigmented, Gram-negative, rod-shaped bacterium (strain CC-YY255(T)) was isolated from compost generated from food waste collected from Kinmen County, Taiwan. 16S rRNA gene sequence analysis indicated that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Luteimonas; its closest neighbour was the type strain of Luteimonas mephitis (94.4 % sequence similarity). The isolate was distinguished from Luteimonas mephitis on the basis of several phenotypic properties. The organism utilized glucose, maltose, gentiobiose, melibiose and turanose and only a few organic acids (acetate, propionate) and amino acids (L-alanyl glycine, glycyl L-aspartic acid and glycyl L-glutamic acid) as substrates. The fatty acid profile was slightly different from that reported for Luteimonas mephitis. It is evident from the genotypic, chemotaxonomic and physiological data presented that strain CC-YY255(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas composti sp. nov. is proposed. The type strain is CC-YY255(T) (=CCUG 53595(T)=CIP 109311(T)=BCRC 17598(T)).

Lysobacter defluvii sp. nov., isolated from municipal solid waste

A bacterial isolate obtained from soil from a municipal landfill site in India was characterized using a polyphasic taxonomic approach. The colonies of the isolate were found to be yellow and highly mucoid. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constitutes a distinct phyletic line within the genus Lysobacter, displaying >3 % sequence divergence with respect to recognized Lysobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile characteristic of members of the genus Lysobacter and consisting of saturated, unsaturated, straight-chain and branched-chain fatty acids as well as iso-C(11 : 0) 3-OH as hydroxylated fatty acid, and the presence of an ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The genotypic and phenotypic data show that strain IMMIB APB-9(T) merits classification as representing a novel species of the genus Lysobacter, for which the name Lysobacter defluvii sp. nov. is proposed. The type strain is IMMIB APB-9(T) (=CCUG 53152(T)=DSM 18482(T)).

Detection of filamentous genus Gordonia in foam samples using genus-specific primers combined with PCR – denaturing gradient gel electrophoresis analysis

A nested-PCR amplification combined with denaturing gradient gel electrophoresis (PCR–DGGE) approach was used to detect and identify Gordonia populations from wastewater treatment plant foam samples. The PCR-amplified region (position 722–1119) by specifically designed primers G699F and G1096R covered the hypervariable region of the Gordonia 16S rRNA gene sequence. This approach successfully distinguished Gordonia species to the interspecies level. The differential ability of PCR–DGGE analysis was effectively used to separate 12 Gordonia species belonging to different 16S rRNA gene-based phylogenetic lineages into 8 groups. Based on this method, the minimum limit of Gordonia detection was 5 × 104CFU·g–1in the seeded soil samples. The PCR–DGGE bands obtained were excised and identified by sequence analysis. Gordonia polyisoprenivorans , Gordonia amicalis , DGGE type II Gordonia species, and an uncertain Gordonia species dominated the activated sludge foam samples. Results of this study indicate that the detection and analyses of genus Gordonia within a complex microbial community could be accomplished using the PCR–DGGE approach to a larger extent, with certain limitations. Detection of diverse Gordonia populations in foam samples from wastewater treatment plants revealed the significant role of Gordonia in biological foaming during wastewater treatment. The nested-PCR amplification and DGGE can be used as a diagnostic tool for the early detection of foaming incidents in wastewater treatment plants using Gordonia as indicator organism.

Williamsia serinedens sp. nov., isolated from an oil-contaminated soil

The taxonomic status of a bacterium designated strain IMMIB SR-4(T) isolated from an oil-contaminated soil sample was characterized by using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that on pyrolysis GC produce C(16 : 0) and C(18 : 0) fatty acids, and dihydrogenated menaquinone with nine isoprene units as the predominant menaquinone. The generic assignment was confirmed by 16S rRNA gene sequence analysis. Comparative analysis of the 16S rRNA gene sequence showed that strain IMMIB SR-4(T) formed a distinct phyletic line within the genus Williamsia, displaying sequence similarities of 95.5-98.1 % with the type strains of recognized Williamsia species. Strain IMMIB SR-4(T) was distinguished from the type strains of recognized species of the genus Williamsia based on a set of phenotypic features. The genotypic and phenotypic data indicated that strain IMMIB SR-4(T) represents a novel species of the genus Williamsia, for which the name Williamsia serinedens sp. nov. is proposed. The type strain is IMMIB SR-4(T) (=DSM 45037(T)=CCUG 53151(T)).

Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant

The taxonomic status of a bacterial isolate from the sludge of a wastewater treatment plant was characterized by using a polyphasic taxonomic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Gordonia, fatty acids C16 : 0 and C18 : 0 (found by pyrolysis gas chromatography) and a dihydrogenated menaquinone with nine isoprene units [MK-9(H2)] as the predominant menaquinone. The genus assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that the novel isolate constitutes a hitherto unknown subline within the genus Gordonia, displaying 95.9 to 97.6 % gene sequence similarity to the recognized species of the genus. The novel isolate was distinguished from the type strains of phylogenetically related species by using a set of phenotypic features. The genotypic and phenotypic data show that the new strain merits classification as a novel species of the genus Gordonia, for which the name Gordonia malaquae sp. nov. is proposed. The type strain is IMMIB WWCC-22T (=DSM 45064T=CCUG 53555T).

Effect of free and encapsulated Pseudomonas putida CC-FR2-4 and Bacillus subtilis CC-pg104 on plant growth under gnotobiotic conditions

A study was performed to investigate the efficiency of microbial inoculants after encapsulating in alginate supplemented with humic acid on plant growth. Two promising plant growth promoting rhizobacteria were identified by 16S rDNA sequencing as Pseudomonas putida CC-FR2-4 and Bacillus subtilis CC-pg104, which were further characterized by biochemical analyses and inoculated to Lectuca sativa L. seedlings as free cells and entrapped in beads. Significant increase in shoot height after 21 days of growth was observed with encapsulated CC-pg104 inoculated plants. Highest increase in root length was observed with CC-pg104 free-cell inoculated plants, followed by plants inoculated with encapsulated CC-pg104. Results clearly demonstrated that inoculation of the encapsulated bacterial isolates promoted plant growth similar to their respective free cells and could be a novel and feasible technique for application in agricultural industry.

Gordonia soli sp. nov., a novel actinomycete isolated from soil

A soil isolate, strain CC-AB07T, was characterized using a polyphasic approach. This organism had chemotaxonomic and morphological properties consistent with its classification in the genusGordonia. 16S rRNA gene sequence analysis showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genusGordonia, its closest neighbours being the type strains ofGordonia alkanivorans,Gordonia amicalis,Gordonia bronchialis,Gordonia desulfuricans,Gordonia polyisoprenivoransandGordonia rhizosphera. The novel isolate was distinguished from all of these type strains using a range of phenotypic properties and bygyrBgene sequence analysis. It was evident from the genotypic and phenotypic data that strain CC-AB07Tshould be classified as representing a novel species in the genusGordonia, for which the nameGordonia solisp. nov. is proposed. The type strain is CC-AB07T(=BCRC 16810T=DSM 44995T).

Pseudolabrys taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from soil

A Gram-negative, short rod-shaped micro-organism (CC-BB4T) was isolated on nutrient agar from soil from Sinshe in Taichung County, Taiwan. Analysis of the 16S rRNA gene sequence demonstrated that this isolate was novel, as it showed <92 % similarity to the sequences of species of the genera Labrys, Beijerinckia and Methylocystis. The micro-organism did not utilize methylamine or methanol as a substrate, but was able to use several organic acids. The fatty acid profile was different from those reported for the genera Labrys, Beijerinckia, Methylocystis, Angulomicrobium, Methylorhabdus and Methyloarcula. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, strain CC-BB4T represents a novel genus, for which the name Pseudolabrys gen. nov. is proposed. The type species is Pseudolabrys taiwanensis sp. nov., and the type strain of P. taiwanensis is CC-BB4T (=CCUG 51779T=CIP 108932T).

Encapsulation of plant growth-promoting bacteria in alginate beads enriched with humic acid

The key to achieving successful, reproducible results following the introduction of beneficial microbes into soil relies on the survival rate of the inoculated bacteria in a heterogeneous soil environment and hence an improved encapsulation method was developed. Owing to the constraints associated with the inoculum formulation, in this study, encapsulation of a plant growth promoting bacteria (PGPB) isolate Bacillus subtilis CC-pg104 was attempted with alginate by enriching the bead microenvironment with humic acid. High viability of the encapsulated bacteria was observed with minimum cell loss upon storage for 5 months. Steady and constant cell release from the bead was observed for 1 week at different pH. Encapsulated cells remained active as evidenced by their ability to solubilize calcium phosphate in vitro. Successful plant growth promotion of lettuce by the encapsulated bacteria under gnotobiotic and sterile environment was also achieved. Feasibility of this improved encapsulation technique is mainly due to the dual benefits of humic acid to microbe and plant and its chemical properties allowing an easy mixing with alginate without interfering in the formation of the alginate gel beads by cross-linking with Ca2+ ions. Thus, the encapsulation method described in this study can be effectively used to protect the PGPB inoculum from adverse conditions of the soil for their successful establishment in the rhizosphere.