EMA-amplicon-based taxonomic characterisation of the viable bacterial community present in untreated and SODIS treated roof-harvested rainwater

2019 ◽  
Vol 5 (1) ◽  
pp. 91-101 ◽  
Author(s):  
André Strauss ◽  
Brandon Reyneke ◽  
Monique Waso ◽  
Thando Ndlovu ◽  
Casparus J. Brink ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
Post Treatment ◽  
Next Generation ◽  
Ethidium Monoazide ◽  
Generation Sequencing

Illumina next generation sequencing coupled with ethidium monoazide bromide (EMA) was used to characterise and compare the viable bacterial community present in roof-harvested rainwater pre- and post-treatment.

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China

2017 ◽  
Vol 82 (4) ◽  
pp. 960-968 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Fan-Zhu Li ◽  
Jiyeon Lee ◽  
Jisu Kang ◽  
Seong-Il Lim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
Northeast China ◽  
Next Generation ◽  
Community Structures ◽  
Generation Sequencing

scholarly journals Bacterial abundance and community composition in green, brown and red water from intensive catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Karunia Adetera Nungki Wijayanti ◽  
Indah Istiqomah ◽  
Murwantoko Murwantoko
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Water Samples ◽  
Bacterial Abundance ◽  
Rrna Gene ◽  
Next Generation ◽  
Aquaculture System ◽  
Generation Sequencing

Abstract. Wijayanti KAN, Istiqomah I, Murwantoko. 2021. Bacterial abundance and community composition in green, brown and red water from intensive Catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia. Biodiversitas 22: 3677-3684. Catfish (Clarias sp.) is an important aquaculture commodity in Indonesia and cultured in an intensive system. Microorganisms play an important role in maintaining water quality of aquaculture system. The objective of this study was to determine the bacterial abundance and community composition of green, brown and red water collected from intensive catfish culture ponds in Yogyakarta using next-generation sequencing method. The water samples were collected from intensive catfish culture ponds with different colors, namely green, brown and red ponds located in Yogyakarta. The DNA from water samples was extracted using DNA extraction kit and used as template for 16S rRNA amplification. The V3-V4 hypervariable regions of the 16S rRNA gene were amplified apply for next-generation sequencing technology. This study could explore effectively the bacterial community in water samples. The bacterial communities in this catfish culture water showed higher bacterial richness compared to the other aquaculture system. The diversity of the green, brown and red catfish culture water ponds was similar with the number OTUs of the green, brown and red water samples, which were 1269; 1387 and 1323 OTUs respectively. The 694 OTUs (34.42%) were common core microbiomes in all catfish culture ponds, the 212 OTUs (10.51%) are present on green and brown water ponds, the 182 OTUs (9.02%) were on green and red water ponds, and the 183 OTUs (9.07%) were present on green and brown water ponds. However, the composition of the bacterial community was different. The most dominant phylum in green and brown water ponds was Proteobacteria with relative abundance in green water and brown water 71.6% and 47.0% respectively, whereas, the most dominant phylum in red water was Firmicutes (29.5%). The dominance of Firmicutes phylum in red water ponds may be caused by application of probiotic bacteria, the high organic content, and low oxygen concentration.

scholarly journals Next Generation Sequencing of Tumor and Matched Plasma Samples: Identification of Somatic Variants in ctDNA From Ovarian Cancer Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Ana Barbosa ◽  
Pedro Pinto ◽  
Ana Peixoto ◽  
Joana Guerra ◽  
Manuela Pinheiro ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Next Generation Sequencing ◽  
Molecular Profiling ◽  
Post Treatment ◽  
Plasma Samples ◽  
Next Generation ◽  
Somatic Variant ◽  
Treatment Naïve ◽  
Ctdna Analysis ◽  
Generation Sequencing

Genetic testing to detect somatic alterations is usually performed on formalin-fixed paraffin-embedded tumor samples. However, tumor molecular profiling through ctDNA analysis may be particularly interesting with the emergence of targeted therapies for ovarian cancer (OC), mainly when tumor is not available and biopsy is not viable, also allowing representation of multiple neoplastic subclones. Using a custom panel of 27 genes, next-generation sequencing (NGS) was performed on tumor and matched plasma samples from 96 OC patients, which were combined in two groups (treatment naive and post-treatment). Overall, at least one somatic variant present in the tumor sample was also detected in the matched plasma sample in 35.6% of the patients, a percentage that increased to 69.6% of the treatment naive patients and 83.3% of those with stage IV disease, showing the potential of ctDNA analysis as an alternative to identify somatic variants in these patients, namely those that have predictive value for targeted therapy. In fact, of the two treatment-naive patients with somatic BRCA1 variants identified in tumor samples, in one of them we detected in ctDNA a BRCA1 somatic variant that was present in the tumor with a VAF of 53%, but not in the one that had a VAF of 5.4%. We also showed that ctDNA analysis has a complementary role to molecular unraveling of inter- and intra-tumor heterogeneity, as exemplified by one patient diagnosed with bilateral OC in which different somatic variants from both tumors were detected in ctDNA. Interestingly, as these bilateral tumors shared a rare combination of two of the three variants identified in ctDNA, we could conclude that these morphologically different tumors were clonally related and not synchronous independent neoplasias. Moreover, in the post-treatment group of patients with plasma samples collected after surgery, those with detectable somatic variants had poor prognosis when compared with patients with no detectable somatic variants, highlighting the potential of ctDNA analysis to identify patients at higher risk of recurrence. Concluding, this study demonstrated that somatic variants can be detected in plasma samples of a significant proportion of OC patients, supporting the use of NGS-based ctDNA testing for noninvasive tumor molecular profiling and to stratify patients according to prognosis.

scholarly journals Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach

2021 ◽  
Vol 37 (6) ◽  
pp. 521-532
Author(s):  
Mahesh Adhikari ◽  
Sang Woo Kim ◽  
Hyun Seung Kim ◽  
Ki Young Kim ◽  
Hyo Bin Park ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
South Korea ◽  
Genomic Dna ◽  
Soil Samples ◽  
Community Diversity ◽  
Next Generation ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Cultivated Soils

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

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