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Luria Leslie Founou, Raspail Carrel Founou, Arshad Ismail, Mushal Allam, Sabiha Yusuf Essack
OBJECTIVES: The draft genome sequences of two Enterobacter aerogenes HN503E2II and PN108E5IIB isolated from two Cameroonian abattoirs, are reported here. METHODS: Genomic DNA of these isolates was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors and plasmids were identified. RESULTS: The whole genome sequencing revealed that both strains are similar with genomes of 4,878,638 and 4,794,257bp and encoded several resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, fosfomycin, phenicols, sulphonamides, trimethoprim, macrolide and tetracycline...
June 20, 2018: Journal of Global Antimicrobial Resistance
Wen Yang, Wei Jiang, Guo-Yue Zhong, Na-Na Liu, Qian Chen, Xiao-Yun Wang
In order to develop genomic-SSR markers for species of Saxifraga genus, a mixed plant genomic DNA sample was sequenced based on high-throughput Illumina MiSeq platform. According to genomic sequencing data, SSR loci were identified with MISA software, and then primers were designed with Primer 3 software. A total of 120 pairs of primers were randomly synthesized and amplified in genomic DNA of a few plant samples. Those primers who have yielded polymorphic bands and were considered easy to amplify were identified...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Miao Yu, Jing-Long Jiang, Xu-Ming Ren, Li Li, Cheng-Jin Jiao, Ling-Juan Yang, Hao Xu
The root rot disease is a common disease during the cultivation of Panax quinquefolius. In order to provide some clues for solving the root rot disease of P. quinquefolius, the relationship between rhizosphere soil fungal communities and root rot of P. quinquefolius was investigated in this study. The diversities and the changes of fungal communities structure in blank control group (group C), rhizosphere soil of healthy P. quinquefolius (group N) and occurrence of root rot in rhizosphere soil of P. quinquefolius (group R)were analyzed byusing the Illumina MiSeq high-throughput sequencing technology...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Yao-Ting Huang, Jan-Fang Cheng, Shi-Yu Chen, Yu-Kai Hong, Zong-Yen Wu, Po-Yu Liu
OBJECTIVES: Shewanella algae is an environmental marine bacteria and an emerging opportunistic human pathogen. Moreover, there are increasing reports of strains showing multi-drug resistance, particularly carbapenem-resistant isolates. Although S. algae have been found in bivalve shellfish aquaculture, there is very little genome-wide data on resistant determinants in S. algae from shellfish. In the study, we aimed to determine the whole genome sequence of carbapenem-resistant S. algae strain AC isolated from small abalone in Taiwan...
June 19, 2018: Journal of Global Antimicrobial Resistance
Luria Leslie Founou, Raspail Carrel Founou, Mushal Allam, Arshad Ismail, Sabiha Yusuf Essack
OBJECTIVES: We report here the draft genome sequence of E. coli strain HN503E1II isolated from a nasal sample of an abattoir worker in Cameroon. METHODS: Genomic DNA of E. coli was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors, plasmids and sequence types were identified. RESULTS: The genome comprised a circular chromosome of 4,674,201bp, with a 50...
June 19, 2018: Journal of Global Antimicrobial Resistance
Nicholas B Larson, Chen Wang, Jie Na, Ross A Rowsey, William Edward Highsmith, Nicole L Hoppman, Jean-Pierre Kocher, Eric W Klee
The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance...
June 22, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Fraser J Combe, Evelyn Taylor-Cox, Graeme Fox, Tommy Sandri, Nick Davis, Martin J Jones, Bradley Cain, David Mallon, W Edwin Harris
High-throughput sequencing tools promise to revolutionize many aspects of genetic research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called 'conservation genomics gap' (Shafer et al . 2015). The conservation genetics paradigm is that, basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al ...
June 2018: Journal of Genetics
S Quercia, F Freccero, C Castagnetti, M Soverini, S Turroni, E Biagi, S Rampelli, A Lanci, J Mariella, E Chinellato, P Brigidi, M Candela
BACKGROUND: Even if horses strictly depend on the gut microbiota for energy homeostasis, only a few molecular studies have focused on its characterisation and none on the perinatal gut microbial colonisation process. OBJECTIVES: To explore the perinatal colonisation process of the foal gut microbial ecosystem and the temporal dynamics of the ecosystem assembly during the first days of life. STUDY DESIGN: Longitudinal study. METHODS: Thirteen Standardbred mare-foal pairs were included in the study...
June 21, 2018: Equine Veterinary Journal
Anand Kumar, Anastasia N Vlasova, Loic Deblais, Huang-Chi Huang, Asela Wijeratne, Sukumar Kandasamy, David D Fischer, Stephanie N Langel, Francine Chimelo Paim, Moyasar A Alhamo, Lulu Shao, Linda J Saif, Gireesh Rajashekara
BACKGROUND: Human rotavirus (HRV) is a major cause of viral gastroenteritis in infants; particularly in developing countries where malnutrition is prevalent. Malnutrition perturbs the infant gut microbiota leading to sub-optimal functioning of the immune system and further predisposing infants to enteric infections. Therefore, we hypothesized that malnutrition exacerbates rotavirus disease severity in infants. METHODS: In the present study, we used a neonatal germ free (GF) piglets transplanted with a two-month-old human infant's fecal microbiota (HIFM) on protein deficient and sufficient diets...
June 22, 2018: BMC Gastroenterology
Rongxiao Che, Yongcui Deng, Fang Wang, Weijin Wang, Zhihong Xu, Yanbin Hao, Kai Xue, Biao Zhang, Li Tang, Huakun Zhou, Xiaoyong Cui
Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR...
October 15, 2018: Science of the Total Environment
Antoine Pierart, Camille Dumat, Arthur QuyManh Maes, Christophe Roux, Nathalie Sejalon-Delmas
The influence of biofertilization with arbuscular mycorrhizal fungi (AMF) on trace metal and metalloids (TM) - Pb, Cd and Sb - uptake by leek (Allium porrum L.) grown in contaminated soils was investigated. The effect of biofertilization on human bioaccessibility of the TM in the plants was also examined. Leek were cultivated in one soil with geogenic TM sources and one soil with anthropogenic TM, to assess the influence of pollutant origin on soil-plant transfer. Leek were grown for six months on these contaminated soils, with and without a local AMF based biofertilizer...
May 15, 2018: Science of the Total Environment
Annegret Lucke, Josef Böhm, Qendrim Zebeli, Barbara U Metzler-Zebeli
Dietary deoxynivalenol (DON) impairs the intestinal functions and performance in broiler chickens, whereas little is known about the effect of DON on the gastrointestinal microbiota. This study evaluated the impact of graded levels of dietary DON contamination on the cecal bacterial microbiota, their predicted metabolic abilities and short-chain fatty acid (SCFA) profiles in chickens. In using a single oral lipopolysaccharide (LPS) challenge we further assessed whether an additional intestinal stressor would potentiate DON-related effects on the cecal microbiota...
2018: Frontiers in Microbiology
Sebnem Kader, Mehmet Mutlu, Filiz Akturk Acar, Yakup Aslan, Aysenur Bahadır
OBJECTIVE: Herein, a neonate with congenital FVII deficiency is presented. BASIC METHOD: Diagnosis of congenital FVII deficiency was confirmed by genetic analysis using next-generation sequencing method (MiSeq-Illumina). RESULT: Our patient was found to have a novel homozygous mutation. CONCLUSION: Early diagnosis and treatment of congenital FVII deficiency can be crucial.
June 18, 2018: Blood Coagulation & Fibrinolysis: An International Journal in Haemostasis and Thrombosis
Akila Subramaniam, William J Van Der Pol, Travis Ptacek, Elena Lobashevsky, Cherry Neely, Joseph R Biggio, Elliot J Lefkowitz, Casey D Morrow, Rodney K Edwards
OBJECTIVES: To evaluate if midtrimester maternal serum contains microbial DNA and whether it differs between women with spontaneous preterm birth (SPTB) and those delivering at term. STUDY DESIGN: In this retrospective case-control study, we identified 20 healthy nulliparas with SPTB at 24-33 weeks of a nonanomalous singleton in 2014. Each case was matched by race/ethnicity to a control delivering at 39-40 weeks. Serum samples, collected at 15-20 weeks and stored at -80C , were thawed and DNA extracted...
June 18, 2018: Journal of Maternal-fetal & Neonatal Medicine
Jazelyn M Salvador, Dame Loveliness T Apaga, Frederick C Delfin, Gayvelline C Calacal, Sheila Estacio Dennis, Maria Corazon A De Ungria
Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results...
June 8, 2018: Forensic Science International. Genetics
Boyang Qiu, Kait Al, Ana M Pena-Diaz, George S Athwal, Darren Drosdowech, Kenneth J Faber, Jeremy P Burton, David B O'Gorman
BACKGROUND: Advances in DNA sequencing technologies have made it possible to detect microbial genome sequences (microbiomes) within tissues once thought to be sterile. We used this approach to gain insights into the likely sources of Cutibacterium acnes (formerly Propionibacterium acnes) infections within the shoulder. METHODS: Tissue samples were collected from the skin, subcutaneous fat, anterior supraspinatus tendon, middle glenohumeral ligament, and humeral head cartilage of 23 patients (14 male and 9 female patients) during primary arthroplasty surgery...
June 13, 2018: Journal of Shoulder and Elbow Surgery
Xiangkun Li, Gaige Liu, Shuli Liu, Kaili Ma, Lingwei Meng
The volatile fatty acids (VFAs) accumulation pattern and microbial community succession were studied during excess sludge (ES) alkaline fermentation at pH of 10.0 with expanded granular sludge blanket reactor over 5 cyclers. Microbial community shifted conspicuously as ES suffered alkaline fermentation. Both VFAs and acid-producing bacteria increased rapidly during the first 8 days fermentation time, and they showed a quite positive correlation relationship. In addition, soluble chemical oxygen demand (SCOD) also dramatically increased during the first 8 days, which implied 8 day was the optimum sludge retention time (SRT) for ES alkaline fermentation and VFAs accumulation time...
June 12, 2018: Journal of Environmental Management
Ruth E Timme, Hugh Rand, Maria Sanchez Leon, Maria Hoffmann, Errol Strain, Marc Allard, Dwayne Roberson, Joseph D Baugher
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions...
June 15, 2018: Microbial Genomics
Peng Wu, Guihao Zhang, Jie Zhao, Jiawei Chen, Yang Chen, Weina Huang, Jialei Zhong, Jiarong Zeng
Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be sterile has been overturned. Dysbiosis of the urinary microbiome has been revealed responsible for various urological disorders, including prostate cancer. The link between chronic inflammation, microbiome and solid tumors has been established for various neoplastic diseases. However, a detailed and comprehensive analysis of urinary microenvironment of bladder cancer has not been yet reported...
2018: Frontiers in Cellular and Infection Microbiology
Tiffany L Carson, Fuchenchu Wang, Xiangqin Cui, Bradford E Jackson, William J Van Der Pol, Elliot J Lefkowitz, Casey Morrow, Monica L Baskin
OBJECTIVE: Racial health disparities persist among black and white women for colorectal cancer. Understanding racial differences in the gut microbiota and related covariates (e.g., stress) may yield new insight into unexplained colorectal cancer disparities. METHODS: Healthy non-Hispanic black or white females (age ≥19 years) provided survey data, anthropometrics, and stool samples. Fecal DNA was collected and isolated from a wipe. PCR was used to amplify the V4 region of the 16SrRNA gene and 250 bases were sequenced using the MiSeq platform...
June 12, 2018: Psychosomatic Medicine
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