Article
Biochemical Research Methods
Dylan G. Maghini, Eli L. Moss, Summer E. Vance, Ami S. Bhatt
Summary: Utilizing a combination of short-read metagenomic sequencing and long-read sequencing, high-quality bacterial genomes can be obtained from the complex human gut microbiome, with some challenges to overcome.
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Engineering, Environmental
Martin Hjorth Andersen, Lisette Thomsen, Mikkel Stokholm-Bjerregaard, Susan Hove Hansen, Mads Albertsen, Per Halkjaer Nielsen, Soren Eriksen
Summary: The partial nitritation/anammox process is a popular approach for removing nitrogen from sidestreams, but it requires extensive surveillance and monitoring due to its sensitivity to disturbances. In this study, we utilized online sensor data and Nanopore DNA sequencing to monitor the microbial community and detect system disturbances in two full-scale deammonification reactors over a year. DNA surveillance revealed unexpected variations in anammox bacteria, and the composition and dynamics of the surrounding community indicated causes for occasional process disturbances. Monitoring the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) could potentially optimize reactor operation. The use of frequent DNA sequencing was found to be an important supplement to online sensor data for process surveillance and control.
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Genetics & Heredity
Rohia Alili, Eugeni Belda, Phuong Le, Thierry Wirth, Jean-Daniel Zucker, Edi Prifti, Karine Clement
Summary: The study introduced a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of the human gut microbiome using Oxford Nanopore sequencing technology. It proposed rapid personalized whole-genome profiling of target microbiome species through simulations and validation with actual samples, providing new insights for the clinical application of gut microbiome analysis technology.
Article
Microbiology
Polona Rajar, Achal Dhariwal, Gabriela Salvadori, Roger Junges, Heidi Aaro amdal, Dag Berild, Drude Fugelseth, Ola Didrik Saugstad, Ulrik Lausten-Thomsen, Gorm Greisen, Kirsti Haaland, Fernanda Cristina Petersen
Summary: This study aimed to develop an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and characterization of microbiome and resistome.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Genetics & Heredity
Laura K. White, Jay R. Hesselberth
Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Katlijn De Meulenaere, Wim L. Cuypers, Julia M. Gauglitz, Pieter Guetens, Anna Rosanas-Urgell, Kris Laukens, Bart Cuypers
Summary: This study investigates the potential of nanopore adaptive sampling to enrich Plasmodium falciparum reads during sequencing, and the results show that adaptive sampling mode can significantly enrich the reads of P. falciparum. By sequencing patient blood samples, adaptive nanopore sequencing can efficiently enrich and sequence the genome of P. falciparum, simplifying the timeline from blood collection to parasite sequencing. This technology can be used for monitoring genetic markers or generating nearly complete genomes, and its mobility makes it easily applicable on-site in endemic areas.
Article
Microbiology
Heleen Delbeke, Ingele Casteels, Marie Joossens
Summary: The purpose of this study was to compare and interpret published studies on ocular microbiome using different DNA extraction protocols. The results showed that the choice of extraction protocol significantly affected the microbial composition and abundance.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Eliane Bou Orm, Stephane Sauvagere, Janick Rocher, Jean-Charles Benezet, Sandrine Bayle, Christian Siatka, Anne Bergeret, Luc Malhautier
Summary: The industrial hemp plant Cannabis sativa is a valuable source of vegetable fiber for textiles and biocomposites. The methodological aspects of nucleic acid extraction from hemp stems have been poorly studied, despite their crucial importance for studying microbial communities. A comparative analysis of three extraction protocols revealed that the Genosol procedure showed the highest yields in terms of DNA quantity and quality, making it suitable for studying bacterial and fungal populations in retted hemp stems.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Computer Science, Information Systems
Wenjie Hu, Yuxin Zhang, Hongrui Zhang, Weigang Chen
Summary: This paper proposes a hardware accelerator for accelerating the recognition of DNA sequencing barcodes using a barcode identification scheme combining cyclic shifting with dynamic programming. The experimental results demonstrate that the accelerator can achieve a speedup of two orders of magnitude for longer barcodes.
Article
Multidisciplinary Sciences
Anna Czmil, Michal Wronski, Sylwester Czmil, Marta Sochacka-Pietal, Michal Cmil, Jan Gawor, Tomasz Wolkowicz, Dariusz Plewczynski, Dominik Strzalka, Michal Pietal
Summary: This paper introduces a novel bioinformatics tool called NanoForms, which helps people without bioinformatics knowledge to process their raw genome sequencing data. Through collaboration between experimentalists and bioinformaticians, a free web server has been established to facilitate the processing and analysis of raw prokaryotic genome data from Oxford Nanopore.
Article
Microbiology
Kang Il Jun, Baek-Lok Oh, Narae Kim, Joo Young Shin, Jangsup Moon
Summary: This study demonstrates the potential of nanopore amplicon sequencing in rapidly and accurately identifying pathogens in infectious endophthalmitis, providing a more efficient alternative to conventional culture studies.
INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY
(2021)
Article
Dentistry, Oral Surgery & Medicine
Alessio Buonavoglia, Fausto Zamparini, Gianvito Lanave, Francesco Pellegrini, Georgia Diakoudi, Andrea Spinelli, Maria Stella Lucente, Michele Camero, Violetta Iris Vasinioti, Maria Giovanna Gandolfi, Vito Marte, Carlo Prati
Summary: This study evaluated microbial communities in root canals using Nanopore sequencing and analyzed their relationship with peri-radicular inflammatory diseases. The results showed the presence of various microorganisms in root canals, which were closely related to clinical and endodontic conditions. Future studies should further evaluate these conditions and identify their role in inducing bone damage and local systemic diseases to better understand the relationship between microbes and endodontic pathologies.
JOURNAL OF ENDODONTICS
(2023)
Article
Public, Environmental & Occupational Health
Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, Maria-Eugenia Guazzaroni
Summary: Nanopore sequencing shows potential for community profiling in healthcare settings, although lower throughput may be a limitation. The use of single-use Flongle flowcells in nanopore sequencing runs can provide valuable insights into community composition.
FRONTIERS IN PUBLIC HEALTH
(2021)
