Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field.

An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).

Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G + C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and ß chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n = 3), followed by Tabrizicola (72.3%‒73.7%, n = 5), and Gemmobacter(72.3%‒73.5%, n = 7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T = BCRC 81286T = JCM 34182T).

Niabella agricola sp. nov., isolated from paddy soil.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative, orange-coloured bacterium (designated strain CC-SYL272T) isolated from paddy soil. Cells were observed to be strictly aerobic, non-motile and non-spore-forming rods, exhibiting positive catalase and oxidase. Strain CC-SYL272T was found to grow optimally at 20-40 °C, pH 6.0-8.0 and NaCl 0-2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CC-SYL272T belongs to the genus Niabella, family Chitinophagaceae, and is most closely related to Niabella pedocola (97.8 %) followed by Niabella drilacis (97.2 %) and established a distinct taxonomic lineage associated with these species. The highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-SYL272T versus Niabella species (69.1-83.5 %, n=8). The mean digital DNA-DNA hybridization (dDDH) value obtained for strain CC-SYL272T against N. pedocola was 27.3 %. The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The major polyamines were putrescine and sym-homospermidine. The dominating cellular fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and C16 : 1 ω6c/C16 : 1 ω7c. The draft genome (6.25 Mb) of strain CC-SYL272T spanned three contigs having 47.1 mol% DNA G+C content, 5087 protein-encoding genes, 10 rRNA genes and 44 tRNA genes. The genome harboured genes involved in the depolymerization of both animal and plant polysaccharides. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH and the phylogenomic placement, strain CC-SYL272T is considered to represent a novel species of the genus Niabella, affiliated to the family Chitinophagaceae, for which the name Niabella agricola sp. nov. is proposed. The type strain is CC-SYL272T (=BCRC 81319T=JCM 34758T).

Agrilactobacillus fermenti sp. nov. isolated from fermented vegetable residue.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive fermentative bacterium, designated strain CC-MHH1034T, isolated from a fermented vegetable residue. Cells of strain CC-MHH1034T were facultatively anaerobic, non-motile, and non-spore-forming rods, exhibiting positive catalase, oxidase and protease activities. Optimal growth occurred at 30 °Ð¡ and pH 6.0. Strain CC-MHH1034T shared the highest 16S rRNA gene sequence similarities with Agrilactobacillus composti (95.9 %) followed by Agrilactobacillus yilanensis (95.1 %) and established a distinct taxonomic lineage associated with these species. Highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-MHH1034T versus Agrilactobacillus (71.1-71.6 %, n=2) followed by Ligilactobacillus (66.5-66.8 %, n=2), Lactobacillus (64.1-65.8 %, n=4). The mean digital DNA-DNA hybridization (dDDH) value obtained for strain CC-MHH1034T against Agrilactobacillus was 19.2-19.5 % (n=2). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, four unidentified glycolipids, four unidentified phospholipids and one unidentified lipid. The major polyamine was sym-homospermidine and meso-diaminopimelic acid was detected as the cell-wall peptidoglycan. The dominating cellular fatty acids (>5 %) included C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 1 ω9c. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH, and the phylogenomic placement, strain CC-MHH1034T is considered to represent a novel species of the genus Agrilactobacillus, affiliated to the family Lactobacillaceae, for which the name Agrilactobacillus fermenti sp. nov. is proposed. The type strain is CC-MHH1034T (=BCRC 81220T=JCM 33476T).

Pusillimonas faecipullorum sp. nov., isolated from the poultry manure.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST705T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST705T were aerobic, Gram-stain-negative, non-motile, non-spore-forming rods, displaying positive reactions for catalase, oxidase and ß-glucosidase. Optimal growth occurred at 30 °C and pH 8. Strain CC-YST705T shared the highest (> 96.0%) pair-wise 16S rRNA gene sequence similarity with Pusillimonas noertemannii (96.7%), followed by Pusillimonas caeni (96.6%), Eoetvoesia caeni (96.1%) and Paracandidimonas soli (96.0%), and formed a distinct phyletic lineage associate with the clade that accommodated Pusillimonas species. The draft genome (3.1 Mb) having 57.4 mol % G + C content contained genes involved in the catabolism of aromatic hydrocarbons. The orthologous average nucleotide identity (OrthoANI) values were 62.8-73.1% (n = 8), 72.6 (n = 1), 71.5% (n = 1) compared within the type strains of the genera Pusillimonas, Eoetvoesia and Paracandidimonas, respectively. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C12:0, C16:0, C17:0 cyclo, C19:0 cyclo ω8c and 2 C14:0 3OH/iso-C16:1 I. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST705T is considered to represent a novel species of the genus Pusillimonas, for which the name Pusillimonas faecipullorum sp. nov. is proposed. The type strain is CC-YST705T (= BCRC 81285 T = JCM 34168 T).

Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640T, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °Ð¡ and pH 7. Strain CC-CFT640T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n=1) followed by Hypericibacter (89.4-90.0 %, n=2), Reyranella (88.8-89.8 %, n=5) and Nitrospirillum (89.2-89.4 %, n=2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (n=1), 74.0-74.6 % (n=2), 67.5-68.3 % (n=2) when compared within the type strains of the genera Enhydrobacter, Reyranella and Niveispirillum, respectively. The dominant cellular fatty acids (>5 %) included C16 : 0, iso-C17 : 1 ω10c, C19 : 0 cyclo ω8c, C18 : 1 2-OH and C18 : 1 ω7c/C18 : 1 ω6c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640T is considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640T (=BCRC 81219T=JCM 33507T).

Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501T, harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501T were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501T was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501T shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781T. Draft genome sequence (3.83 Mb) of strain CC-CFT501T revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C16:0, C18:0, C10:0 3-OH, C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501T is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501T (= BCRC 81218T = JCM 33506T).

Agricultural management and cultivation period alter soil enzymatic activity and bacterial diversity in litchi (Litchi chinensis Sonn.) orchards.

BACKGROUND: Agricultural management and temporal change including climate conditions and soil properties can result in the alteration of soil enzymatic activity and bacterial community, respectively. Therefore, different agricultural practices have been used globally to explore the soil quality. In this study, the temporal variations in soil property, enzymatic activity, and bacterial community at three successive trimester sampling intervals were performed in the soil samples of litchi orchards that were maintained under conventional and sustainable agricultural practices. RESULTS: Agricultural management found to significantly influence arylsulfatase, ß-glucosidase, and urease activities across time as observed by repeated-measures analysis of variance. Shannon and Simpson diversity indices, and the relative abundance of predominant Acidobacteria and Proteobacteria were significantly influenced by temporal change but not agricultural management. This suggested that soil enzymatic activity was more susceptible to the interaction of temporal change and agricultural management than that of the bacterial community. Multiple regression analysis identified total nitrogen, EC, and phosphorus as the significant predictors of acid phosphatase, arylsulfatase, and ß-glucosidase for explaining 29.5-39% of the variation. Moreover, the soil pH and EC were selected for the SOBS, Chao, ACE, and Shannon index to describe 33.8%, 79% of the variation, but no significant predictor was observed in the dominant bacterial phyla. Additionally, the temporal change involved in the soil properties had a greater effect on bacterial richness and diversity, and enzymatic activity than that of the dominant phyla of bacteria. CONCLUSIONS: A long-term sustainable agriculture in litchi orchards would also decrease soil pH and phosphorus, resulting in low ß-glucosidase and urease activity, bacterial richness, and diversity. Nevertheless, application of chemical fertilizer could facilitate the soil acidification and lead to adverse effects on soil quality. The relationship between bacterial structure and biologically-driven ecological processes can be explored by the cross-over analysis of enzymatic activity, soil properties and bacterial composition.

Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °Ð¡, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696T contained C16:0, C18:0, C18:1ω7c 11-methyl and C18:1ω6c/ C18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696T=BCRC 81284T=JCM 34167T) is proposed.

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, ß-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.

Aeromicrobium terrae sp. nov., isolated from a maize field.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486T, isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486T were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °Ð¡, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486T associated with Aeromicrobium panacisoli (97.0 % sequence identity), Aeromicrobium lacus (97.0 %), Aeromicrobium erythreum (96.8 %) and Aeromicrobium alkaliterrae (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % (n=11) compared within the type strains of the genus Aeromicrobium. Strain CC-CFT486T contained C16 : 0, C17 : 0, C17 : 1 ω8c and C18 : 1 ω9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486T contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486T is proposed to represent a novel Aeromicrobium species, for which the name Aeromicrobium terrae sp. nov. (type strain CC-CFT486T=BCRC 81217T=JCM 33499T).

Senescence-Mediated Redox Imbalance in Liver and Kidney: Antioxidant Rejuvenating Potential of Green Tea Extract.

This study investigates the catechin composition and protective effect of green tea extract on senescence-mediated redox imbalance in the livers and kidneys of aged mice. The results showed that the seven catechins in the green tea extract analyzed in this study could be completely separated within 30 min and the main components of catechins in green tea extract were EGCG, EGC and ECG. In terms of the anti-senescence effects of green tea extract, green tea extract supplementation at doses of 125, 625 and 1250 mg/kg for 4 weeks significantly alleviated the senescence-mediated redox imbalance, as exhibited from significantly (p < 0.05) reduced thiobarbituric acid-reactive substances (TBARS) and protein carbonyls levels in the serum, and increased glutathione (GSH) and total thiols contents in the plasma. Additionally, hepatic and renal protein carbonyls levels were significantly diminished (p < 0.05) and the activities of superoxide dismutase (SOD), catalase, glucose-6-phosphate dehydrogenase (G6PD), glutathione peroxidase (GSH-Px) and glutathione reductase (GSH-Rd) in the liver and kidney were remarkably elevated (p < 0.05). Overall, these results clearly show that green tea extract exhibits extremely potent protective effects against senescence-mediated redox imbalance in the livers and kidneys of mice by inhibiting oxidative damage of lipids and proteins and increasing the activities of antioxidant enzymes in organs.

Comparison of 4 sinus augmentation techniques for implant placement with residual alveolar bone height ≤3 mm.

This study compared implant outcomes following maxillary sinus floor augmentation (MSFA) in edentulous patients with a residual alveolar bone height ≤3 mm. Four techniques were evaluated: 1-stage bone-added osteotome sinus floor elevation procedure (BAOSFE) with simultaneous implant placement; 2-stage BAOSFE with delayed implant placement; 1-stage lateral window sinus floor elevation with simultaneous implant placement; and 2-stage lateral window sinus floor elevation with delayed implant placement. Patients were followed for 18 to 72 months (mean: 52.5 months) after prosthesis placement. Data were analyzed with cone-beam computed tomography. A total of 96 implants from 71 patients were analyzed; pretreatment, there were no significant differences between patients. Total implant survival was 98.9%. The mean residual bone height was significantly higher in the 1-stage BAOSFE group than the other groups (P < .01); 1 implant in this group failed at 3 months. There was no significant difference in total bone height gain between groups. However, the bone height gain of 1st sinus lifting with 2-stage BAOSFE was significantly lower than the 2-stage lateral window procedure (P < .01). There was no prosthesis failure. The favorable implant outcomes suggest these 1-stage and 2-stage MSFA procedures should be considered as alternative treatment options for patients with extremely atrophic posterior maxilla.

Cerasibacillus terrae sp. nov., isolated from maize field, and emended description of Cerasibacillus quisquiliarum Nakamura et al. 2004.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480T, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480T were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °Ð¡, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480T associated with Cerasibacillus quisquiliarum (97.2 % sequence identity), Virgibacillus soli (95.7 %), Virgibacillus carmonensis (95.4 %) and Virgibacillus byunsanensis (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480T and C. quisquiliarum were 74.2 and 20.1 %, respectively. Strain CC-CFT480T contained iso-C15:0, C16:1 ω7c alcohol and iso-C17:1 ω10c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480T is proposed to represent a novel Cerasibacillus species, for which the name Cerasibacillus terrae sp. nov. (type strain CC-CFT480T=BCRC 81216T=JCM 33498T).

Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber.

A bacterial strain CC-CTC003T was isolated from a synthetic wooden board. Cells of strain CC-CTC003T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003T belonged to the genus Flavobacterium and was most closely related to Flavobacterium cerinum (95.3 % sequence identity), Flavobacterium maris (94.9 % sequence identity), Flavobacterium qiangtangense (94.8 %) and Flavobacterium subsaxonicum (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003T and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with F. cerinum was 19.4 %. Strain CC-CTC003T contained C15 : 0, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c) and summed feature 9 (C16 : 0 10-methyl / iso-C17 : 1 ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003T (=BCRC 81146T=JCM 32838T).

Description of Azoarcus nasutitermitis sp. nov. and Azoarcus rhizosphaerae sp. nov., two nitrogen-fixing species isolated from termite nest and rhizosphere of Ficus religiosa.

A polyphasic taxonomic approach was used to characterise two presumably novel bacteria, designated strains CC-YHH838T and CC-YHH848T isolated from termite nest and rhizosphere of Ficus religiosa, respectively. These two nitrogen-fixing strains were observed to be Gram-staining-negative, aerobic rod, and colonies were yellowish in color. Growth of strains was observed at 20-37 °C, pH 7-8, and in the presence of 1-2% NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YHH838T and CC-YHH848T associated with Thauera hydrothermalis (97.1% sequence identity), and formed a separate branch with Azoarcus indigens (95.4%), Aromatoleum aromaticum (96.2%), and lower sequence similarity to other species. The calculation of OrthoANI values pointed out strains CC-YHH838T and CC-YHH848T gave 78.9% and 79.8% compared to Thauera hydrothermalis, respectively. The major fatty acids (> 5%) were C16:0, C17:0 cyclo, C10:0 3-OH, C16:1ω7c/C16:1ω6c and C18:1ω7c/C18:1ω6c. The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminophospholipid and phospholipids; the predominant polyamines were putrescine and spermidine. The predominant respiratory system was ubiquinone (Q-8) and the DNA G + C contents were 61.4 ± 0.1 mol% and 60.2 ± 1.3 mol%, respectively. Based on the phylogenetic and polyphasic comparisons, strains CC-YHH838T and CC-YHH848T are proposed to represent two novel species within the genus Azoarcus in the family Rhodocyclaceae, for which the name Azoarcus nasutitermitis sp. nov. (type strain CC-YHH838T = BCRC 81059T = JCM 32001T) and Azoarcus rhizosphaerae sp. nov. (type strain CC-YHH848T = BCRC 81060T = JCM 32002T) were proposed.

Protective Effects of Rosmarinic Acid against Selenite-Induced Cataract and Oxidative Damage in Rats.

Cataracts are the major cause of blindness and are associated with oxidative damage of the lens. In the present study, the aim was to evaluate the protective effects of rosmarinic acid on selenite-induced cataractogenesis in Sprague-Dawley rat pups. The animals were randomly divided into five groups, each of which consisted of 10 rat pups. Group I served as normal control (vehicle administration). For testing cataract induction, animals of Groups II, III, IV, and V were administered a single subcutaneous injection of sodium selenite (2.46 mg/kg body weight) on postpartum day 12. After sodium selenite intoxication, Group II served as control selenite. From the 11th day through the 17th day, Groups III-V received rosmarinic acid intraperitoneally at doses of 5, 10, and 50 mg/kg, respectively. On postpartum day 24, the rat pups were examined for cataract formation, and the lenses were isolated for further analysis of proteins and oxidative damage indicators. Selenite caused significant (p < 0.05) cataract formation. Through the effects of selenite, the protein expressions of filensin and calpain 2 were reduced, and the calcium concentrations, the level of lipid peroxidation (TBARS), and inflammation indicators (iNOS, COX-2, and NFκB) were upregulated. Furthermore, the protein expression of the antioxidant status (Nrf2, SOD, HO-1, and NQO1), the antioxidant enzymes activities (GSH-Px, GSH-Rd, and catalase), and the GSH levels were downregulated. In contrast, treatment with rosmarinic acid could significantly (p < 0.05) ameliorate cataract formation and oxidative damage in the lens. Moreover, rosmarinic acid administration significantly increased the protein expressions of filensin, calpain 2, Nrf2, SOD, HO-1, and NQO1, the antioxidant enzymes activities, and the GSH level, in addition to reducing the calcium, lipid peroxidation, and inflammation indicators in the lens. Taken together, rosmarinic acid is a prospective anti-cataract agent that probably delays the onset and progression of cataracts induced by sodium selenite.

Anti-fibrotic effect of rosmarinic acid on inhibition of pterygium epithelial cells.

AIM: To investigate the anti-fibrosis effect of rosmarinic acid (RA) in pterygium epithelial cells (PECs) to determine if RA is a potent agent for treating pterygium. METHODS: The PECs (1×104 cells/mL) were treated with 100 µmol/L of RA for 1, 3 and 6h. After RA treatment, the cell viability was determined by staining with acridine orange/DAPI and analysis via a NucleoCounter NC-3000. The protein expression levels of type I collagen, transforming growth factor beta-1 (TGF-ß1), TGF-ß type II receptor (TGF-ßRII), p-Smad1/5, p-Smad2, p-Smad3, and Smad4 of the cell lysates were measured by Western blot analysis. RESULTS: The cell viability of PECs was significantly decreased after RA treatment (P<0.01). As the result, RA reduced the protein expression of type I collagen and TGF-ß1 of PECs. Additionally, RA also inhibited TGF-ß1/Smad signaling by decreasing the protein expressions of TGF-ßRII, p-Smad1/5, p-Smad2, p-Smad3, and Smad4. CONCLUSION: This study demonstrate that RA could inhibit fibrosis of PECs by down-regulating type I collagen expression and TGF-ß1/Smad signaling. Therefore, RA is a potent therapeutic agent for the treatment of pterygium.

Nephroprotective effect of electrolyzed reduced water against cisplatin-induced kidney toxicity and oxidative damage in mice.

BACKGROUND: Cisplatin is a potent chemotherapeutic drug for cancer therapy, but it has serious side effects in clinical treatment, particularly nephrotoxicity. The purpose of this study was to evaluate the protective effect of electrolyzed reduced water (ERW) on renal injury caused by cisplatin. METHODS: Animals were divided into four groups as follows: normal control group, cisplatin control group, ERW control group and ERW + cisplatin group. Each group comprised 10 animals, which were orally treated with normal saline or ERW daily companion by administration of one dose of cisplatin for 28 days. Animals in the cisplatin group received an intraperitoneal single-dose injection of cisplatin (20 mg/kg body weight) as a single i.p. dose on the 25th day of the experiment. We determined the hydration state in urine and the level of serum markers of kidney function, the levels of glutathione (GSH) and thiobarbituric acid-reactive substances (TBARS) levels and the activities of glutathione peroxidase (GPx), glutathione reductase (GR), catalase (CAT) and superoxidase dismutase (SOD) in kidney and histopathological changes. RESULTS: After administration of ERW, the reduced urinary osmolality was increased and elevated Na+, K+, Mg2+ and Ca2+ levels in urine were significantly decreased in cisplatin-induced renal injury mice. Besides, the results demonstrated that significantly decreased elevated serum levels of creatinine and blood urea nitrogen (BUN) and the levels of TBARS in the kidneys that were induced by cisplatin. Moreover, ERW treatment was also found to markedly increase (p < 0.05) the activities of GPx, GR, CAT and SOD, and to increase GSH content in the kidneys. Histopathology showed that ERW protects against cisplatin-induced renal injury to both the proximal and distal tubules. CONCLUSION: ERW exhibits potent nephroprotective effects on cisplatin-induced kidney damage in mice, likely due to both the increase in antioxidant-defense system activity and the inhibition of lipid peroxidation.

Inhibitory effects of rosmarinic acid on pterygium epithelial cells through redox imbalance and induction of extrinsic and intrinsic apoptosis.

Pterygium is a common tumor-like ocular disease, which may be related to exposure to chronic ultraviolet (UV) radiation. Although the standard treatment for pterygium is surgical intervention, the recurrence rate of pterygium is high when no effective inhibitory drug is used after surgery. Rosmarinic acid (RA) is a polyphenol antioxidant with many biological activities, including anti-UV and anti-tumor properties. This study aimed to examine the inhibitory effects of RA on pterygium epithelial cells (PECs). Methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay was used to examine the cell cytotoxicity of PECs after RA treatment. A fluorescent probe, DCFH-DA (2',7'-dichlorofluorescin diacetate), was stained with PECs to measure intracellular reactive oxygen species (ROS) levels. Antioxidant activity assays were used to measure the levels of superoxide dismutase (SOD) and catalase (CAT) in PECs. Western blot analysis was used to determine the protein expression of nuclear factor E2-related factor 2 (Nrf2), heme oxygenase 1 (HO-1), quinone acceptor oxidoreductase 1 (NQO1), and apoptosis-associated proteins. RA significantly reduced the cell viability of the PECs. Treatment with RA remarkably increased the Nrf2 protein expression levels in the nucleus, HO-1 and NQO1 protein expression levels, and the activities of SOD and CAT. As a result, intracellular ROS levels in PECs were decreased. Additionally, the induction of extrinsic apoptosis on PECs by RA was associated with increasing expressions levels of Fas, Fas-associated protein with death domain (FADD), tumor necrosis factor-alpha (TNF-α), and caspase 8 protein. Moreover, the induction of intrinsic apoptotic cell death in PECs was confirmed through upregulation of cytochrome c, Bax, caspase 9, and caspase 3 and downregulation of Bcl-2 and pro-caspase 3. Our study demonstrated that RA could inhibit the viability of PECs through regulation of extrinsic and intrinsic apoptosis pathways. Therefore, RA may have potential as a therapeutic medication for pterygium.