scholarly journals Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Marina Panek ◽  
Hana Čipčić Paljetak ◽  
Anja Barešić ◽  
Mihaela Perić ◽  
Mario Matijašić ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Dna Extraction ◽  
Next Generation ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Sequencing Technologies ◽  
Generation Sequencing

Isolation of Desulfovibrio spp. from human gut microbiota using a next‐generation sequencing directed culture method

2019 ◽  
Vol 68 (6) ◽  
pp. 553-561 ◽  
Author(s):  
Y.‐R. Chen ◽  
L.‐Z. Zhou ◽  
S.‐T. Fang ◽  
H.‐Y. Long ◽  
J.‐Y. Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Culture Method ◽  
Next Generation ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Generation Sequencing

scholarly journals Optimisation of sample storage and DNA extraction for human gut microbiota studies​

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiota ◽  
Dna Extraction ◽  
Personalised Medicine ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Reliable Solution

Abstract Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Studying the gut virome in the metagenomic era: challenges and perspectives

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Sanzhima Garmaeva ◽  
Trishla Sinha ◽  
Alexander Kurilshikov ◽  
Jingyuan Fu ◽  
Cisca Wijmenga ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Human Health ◽  
Next Generation ◽  
Human Gut ◽  
Sequencing Technologies ◽  
Quantum Leap ◽  
Complex Ecosystem ◽  
Technical Challenges ◽  
Generation Sequencing

Abstract The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.

Confusion about the species richness of human gut microbiota

2015 ◽  
Vol 6 (5) ◽  
pp. 657-659 ◽  
Author(s):  
E. Avershina ◽  
K. Rudi
Keyword(s):  
Species Richness ◽  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Next Generation ◽  
Human Gut ◽  
Future Directions ◽  
High Profile ◽  
Potential Sources ◽  
Sequencing Studies ◽  
Generation Sequencing

A key message from a range of high profile next generation sequencing studies on the human microbiota is that it composes a tremendously rich community of more than 1000 species within each one of us. Although more recent studies have shown estimates of between 100 and 200 species per individual, this has not yet been made clear in the literature. Currently, the most widely accepted estimate of species richness is therefore five to ten times too high. Here, we will review the different estimates of species richness in the literature, address potential sources of artefacts, the reluctance to correct these, and provide suggestions for future directions.

scholarly journals Rapid whole-genome mutational profiling using next-generation sequencing technologies

2008 ◽  
Vol 18 (10) ◽  
pp. 1638-1642 ◽  
Author(s):  
D. R. Smith ◽  
A. R. Quinlan ◽  
H. E. Peckham ◽  
K. Makowsky ◽  
W. Tao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mutational Profiling ◽  
Generation Sequencing

The application of next-generation sequencing technologies to drug discovery and development

2011 ◽  
Vol 16 (11-12) ◽  
pp. 512-519 ◽  
Author(s):  
Peter M. Woollard ◽  
Nalini A.L. Mehta ◽  
Jessica J. Vamathevan ◽  
Stephanie Van Horn ◽  
Bhushan K. Bonde ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Next Generation ◽  
Drug Discovery And Development ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Daniela Barros-Silva ◽  
C. Marques ◽  
Rui Henrique ◽  
Carmen Jerónimo
Keyword(s):  
Dna Methylation ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Epigenetic Modification ◽  
Response To Therapy ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Prognosis And Prediction ◽  
Novel Biomarkers ◽  
Generation Sequencing

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

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