Project description:Pseudomonas putida has attracted much interest for its environmental, industrial, biotechnological, and clinical importance. Here, we report the complete genome sequence of the type strain P. putida NBRC 14164. This genome sequence will assist to further elucidate the molecular mechanisms of the characteristic traits among strains belonging to the species P. putida.
Project description:Pseudomonas putida KF715 (NBRC 110667) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report a complete genome sequence of the KF715 strain, which comprises a circular chromosome and four plasmids. Biphenyl catabolic genes were located on the largest plasmid, pKF715A.
Project description:Schistosomiasis, also generally known as snail fever, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. In Hong Kong and mainland China, the freshwater snail Biomphalaria straminea has been introduced and has the potential to transmit intestinal schistosomiasis caused by S. mansoni, a parasite of man which has a wide distribution in Africa and parts of the New World, especially Brazil. The first identification of B. straminea in Hong Kong dates back to the 1970s, and its geographical distribution, phylogenetic relationships, and infection status have not been updated for more than 30 years. Thus, this study aims to reveal the distribution and current infection status of B. straminea in contemporary Hong Kong.Snails were collected from different parts of Hong Kong from July 2016 to January 2017. Both anatomical and molecular methods were applied to identify B. straminea. Cytochrome c oxidase subunit 1 (cox1), internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), and 16S ribosomal DNA (rDNA) were sequenced from individual snails and analyzed. To detect the presence of S. mansoni, both biopsy and PCR analyses were carried out.Using both anatomical and molecular analyses, this study demonstrated the existence of black- and red-coloured shell B. straminea in different districts in the New Territories in Hong Kong, including places close to the mainland China border. None of the B. straminea (n = 87) investigated were found to be infected with S. mansoni when tested by biopsy and PCR. The Hong Kong B. straminea are genetically indistinguishable, based on the chosen molecular markers (cox1, ITS1-5.8S-ITS2, and 16S rDNA), and are similar to those obtained in mainland China and South America.Biomphalaria straminea is now well established in freshwater habitats in Hong Kong. No evidence of infection with S. mansoni has been found. Surveillance should be continued to monitor and better understand this schistosomiasis intermediate host in mainland China and Hong Kong.
Project description:Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces hygroscopicus subsp. hygroscopicus into the NBRC culture collection. An average nucleotide identity analysis confirmed that the taxonomic identification is correct. The genome sequence will serve as a valuable reference for genome mining to search new secondary metabolites.
Project description:Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is able to degrade various types of n-alkanes. Here, we report the complete genome of strain NBRC 101098.
Project description:BACKGROUND:Biomphalaria straminea is an invasive vector in China, posing a significant threat to public health. Understanding the factors affecting the establishment of this snail is crucial to improve our ability to manage its dispersal and potential risk of schistosomiasis transmission. This study sought to determine the spatial distribution of B. straminea in mainland China and whether environmental factors were divergent between places with and without B. straminea. METHODS:A malacological survey of B. straminea was conducted in Guangdong Province, China. Snails were identified using anatomical keys. Water and sediment samples were taken, and their physicochemical properties were analyzed using national standard methods. Landscape and climatic variables were also collected for each site. We compared the environmental characteristics between sites with and without B. straminea using Mann-Whitney U test. We further used generalized linear mixed models to account for seasonal effects. RESULTS:B. straminea was found at six sites, including one in Dongguan and five in Shenzhen. Probability map found a hot spot of B. straminea distribution at Shenzhen and Hong Kong. Sites occupied by B. straminea were characterized by higher median altitude, mean annual precipitation and moderate temperature. Water with snails had higher median concentrations of total nitrogen, nitrate and nitrites, ammoniacal nitrogen, calcium, zinc and manganese but lower dissolved oxygen and magnesium. Sediments with snails had higher median copper, zinc and manganese. B. straminea was associated with maximum temperature of the warmest month (pMCMC <?0.001) and sediment zinc (pMCMC <?0.001). CONCLUSIONS:B. straminea is distributed in Shenzhen and its surrounding areas in Guangdong, China. Sites with and without B. straminea differed in the maximum temperature of the warmest month and sediment zinc. Surveillance should be continued to monitor the dispersal of this snail in China.
Project description:Strain 113P3 was isolated from activated sludge and identified as a polyvinyl alcohol (PVA)-degrading Pseudomonas species; it was later reidentified as Sphingopyxis species. Only three genes are directly relevant to the metabolism of PVA and comprise the pva operon, which was deposited as accession no. AB190228. Here, we report the complete genome sequence of strain 113P3, which has been conserved as a stock culture (NBRC 111507) at the Biological Resource Center, National Institute of Technology and Evaluation (NITE) (Tokyo, Japan). The genome of strain 113P3 is composed of a 4.4-Mb circular chromosome and a 243-kb plasmid. The whole finishing was conducted in silico except for four PCRs. The sequence corresponding to AB190288 exists on the chromosome.
Project description:Schistosomiasis is a snail-borne parasitic disease and is endemic in many tropical and subtropical countries. Biomphalaria straminea, an intermediate host for Schistosoma mansoni, is native to the southeastern part of South America and has established in other regions of South America, Central America and southern China during the last decades. S. mansoni is endemic in Africa, the Middle East, South America and the Caribbean. Knowledge of the potential global distribution of this snail is essential for risk assessment, monitoring, disease prevention and control.A comprehensive database of cross-continental occurrence for B. straminea was compiled to construct ecological models. We used several approaches to investigate the distribution of B. straminea, including direct comparison of climatic conditions, principal component analysis and niche overlap analyses to detect niche shifts. We also investigated the impacts of bioclimatic and human factors, and then used the bioclimatic and footprint layers to predict the potential distribution of B. straminea at global scale. We detected niche shifts accompanying the invasions of B. straminea in the Americas and China. The introduced populations had enlarged its habitats to subtropical regions where annual mean temperature is relatively low. Annual mean temperature, isothermality and temperature seasonality were identified as most important climatic features for the occurrence of B. straminea. Additionally, human factors improved the model prediction (P<0.001). Our model showed that under current climate conditions the snail should mostly be confined to the tropic and subtropic regions, including South America, Central America, Sub-Saharan Africa and Southeast Asia.Our results confirmed that niche shifts took place in the invasions of B. straminea, in which bioclimatic and human factors played an important role. Our model predicted the global distribution of B. straminea based on habitat suitability, which would help for prioritizing monitoring and management efforts for B. straminea control in the context of ongoing climate change and human disturbances.
Project description:BACKGROUND:Schistosomiasis is a common parasitic disease designated as a neglected tropical disease by the World Health Organization. Schistosomiasis mansoni is a form of the disease that is caused by the digenean trematode Schistosoma mansoni, transmitted through Biomphalaria spp. as an intermediate host. Biomphalaria was introduced to Hong Kong, China in aquatic plants shipments coming from Brazil and the snail rapidly established its habitats in southern China. Earlier studies of Biomphalaria spp. introduced to southern China identified the snails as Biomphalaria straminea, one of the susceptible species implicated in S. mansoni transmission in South America. However, recent molecular investigations also indicated the presence of another South American species, B. kuhniana, which is refractory to infection. As such, it is important to identify accurately the species currently distributed in southern China, especially with emerging reports of active S. mansoni infections in Chinese workers returning from Africa. METHODS:We combined morphological and molecular taxonomy tools to precisely identify Biomphalaria spp. distributed in Guangdong Province, southern China. In order to clearly understand the molecular profile of the species, we constructed a phylogeny using mtDNA data (COI and 16S rRNA sequences) from six populations of Biomphalaria spp. from Shenzhen City in Guangdong Province. In addition, we examined the external morphology of the shell and internal anatomy of the reproductive organs. RESULTS:Both morphological and molecular evidences indicated a close affinity between Biomphalaria spp. populations from Guangdong and B. straminea from Brazil. The shell morphology was roughly identical in all the populations collected with rounded whorls on one side and subangulated on the other, a smooth periphery, an egg-shaped aperture bowed to one side, and a deep umbilicus. The shape and number of prostate diverticula (ranged from 11.67 to 17.67) in Guangdong populations supports its close affinity to B. straminea rather than B. kuhniana. Molecular analysis did not conflict with morphological analysis. Little genetic differentiation was observed within Biomphalaria populations collected. Phylogenetic analysis of COI and 16S rRNA haplotypes from snails collected and B. straminea sequences from Brazil and China using Bayesian inference revealed that Guangdong populations were clustered in one clade with B. straminea from Hong Kong of China and B. straminea from Brazil indicating their close affinity to each other. CONCLUSIONS:Data obtained in the current study clearly show that the populations of Biomphalaria spp. investigated are B. straminea, and we assume that those snails were either introduced via passive dispersal from Hong Kong of China or as a result of multiple introduction routes from Brazil.