Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR

2016 ◽  
Vol 109 (8) ◽  
pp. 1161-1166 ◽  
Author(s):  
Joshua R. Stokell ◽  
Timothy J. Hamp ◽  
Todd R. Steck
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Bacterial Abundance ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Toxic Cyanobacterial Bloom Triggers in Missisquoi Bay, Lake Champlain, as Determined by Next-Generation Sequencing and Quantitative PCR

Life ◽  
2015 ◽  
Vol 5 (2) ◽  
pp. 1346-1380 ◽  
Author(s):  
Nathalie Fortin ◽  
Valentina Munoz-Ramos ◽  
David Bird ◽  
Benoît Lévesque ◽  
Lyle Whyte ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Cyanobacterial Bloom ◽  
Next Generation ◽  
Lake Champlain ◽  
Generation Sequencing

scholarly journals Digital PCR—An Emerging Technology with Broad Applications in Microbiology

2019 ◽  
Vol 66 (1) ◽  
pp. 117-123 ◽  
Author(s):  
Stephen J Salipante ◽  
Keith R Jerome
Keyword(s):  
Next Generation Sequencing ◽  
Quantitative Pcr ◽  
Clinical Microbiology ◽  
Clinical Laboratory ◽  
Digital Pcr ◽  
Emerging Technology ◽  
Next Generation ◽  
Powerful Technique ◽  
Advantages And Disadvantages ◽  
Generation Sequencing

Abstract BACKGROUND The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR. CONTENT Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing. SUMMARY dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

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 Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment

2013 ◽  
Vol 79 (13) ◽  
pp. 4181-4185 ◽  
Author(s):  
Janet A. Lambert ◽  
Apoorv Kalra ◽  
Cristina T. Dodge ◽  
Susan John ◽  
Jack D. Sobel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Vaginosis ◽  
Quantitative Pcr ◽  
Broad Spectrum ◽  
Vaginal Microbiota ◽  
Next Generation ◽  
Healthy Women ◽  
Before And After ◽  
Generation Sequencing

ABSTRACTDeep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.

scholarly journals Minimal Residual Disease Detection by Next-Generation Sequencing in Multiple Myeloma: A Comparison With Real-Time Quantitative PCR

2021 ◽  
Vol 10 ◽  
Author(s):  
Qiumei Yao ◽  
Yinlei Bai ◽  
Shaji Kumar ◽  
Elaine Au ◽  
Alberto Orfao ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Next Generation Sequencing ◽  
Real Time ◽  
Quantitative Pcr ◽  
Residual Disease ◽  
Next Generation ◽  
Real Time Quantitative Pcr ◽  
Allele Specific ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Here we compared clonotype identification by allele-specific oligonucleotide real-time quantitative-PCR (ASO RQ-PCR) and next-generation sequencing (NGS) in 80 multiple myeloma patients. ASO RQ-PCR was applicable in 49/55 (89%) and NGS in 62/78 (80%). Clonotypes identified by both methods were identical in 33/35 (94%). Sensitivity of 10−5 was confirmed in 28/29 (96%) by NGS while sensitivity of RQ-PCR was 10−5 in 7 (24%), 5 × 10−5 in 15 (52%), and 10−4 in 7 (24%). Among 14 samples quantifiable by ASO RQ-PCR, NGS yielded comparable results in 12 (86%). Applicability of NGS can be improved if immunoglobulin heavy-chain incomplete DJ primers are included.

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