Quantitative assessment of shotgun metagenomics and 16S rDNA amplicon sequencing in the study of human gut microbiome

I Laudadio, V Fulci, F Palone, L Stronati… - OMICS: A Journal of …, 2018 - liebertpub.com
The analysis of microbiota composition in humans, animals, and built environments is
important because of emerging roles and applications in a broad range of disease and …

[HTML][HTML] Characterization of shallow whole-metagenome shotgun sequencing as a high-accuracy and low-cost method by complicated mock microbiomes

W Xu, T Chen, Y Pei, H Guo, Z Li, Y Yang… - Frontiers in …, 2021 - frontiersin.org
Characterization of the bacterial composition and functional repertoires of microbiome
samples is the most common application of metagenomics. Although deep whole …

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

R Ranjan, A Rani, A Metwally, HS McGee… - … and biophysical research …, 2016 - Elsevier
The human microbiome has emerged as a major player in regulating human health and
disease. Translational studies of the microbiome have the potential to indicate clinical …

[HTML][HTML] Shallow shotgun sequencing reduces technical variation in microbiome analysis

AJ La Reau, NB Strom, E Filvaroff, K Mavrommatis… - Scientific reports, 2023 - nature.com
The microbiome is known to play a role in many human diseases, but identifying key
microbes and their functions generally requires large studies due to the vast number of …

[HTML][HTML] Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

J Mas-Lloret, M Obón-Santacana, G Ibáñez-Sanz… - Scientific data, 2020 - nature.com
The gut microbiome has a fundamental role in human health and disease. However,
studying the complex structure and function of the gut microbiome using next generation …

[HTML][HTML] Characterization of the gut microbiome using 16S or shotgun metagenomics

J Jovel, J Patterson, W Wang, N Hotte… - Frontiers in …, 2016 - frontiersin.org
The advent of next generation sequencing (NGS) has enabled investigations of the gut
microbiome with unprecedented resolution and throughput. This has stimulated the …

[HTML][HTML] An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

DM O'Sullivan, RM Doyle, S Temisak, N Redshaw… - Scientific Reports, 2021 - nature.com
Despite the advent of whole genome metagenomics, targeted approaches (such as 16S
rRNA gene amplicon sequencing) continue to be valuable for determining the microbial …

[PDF][PDF] Assessment of fecal DNA extraction protocols for metagenomic studies

F Yang, J Sun, H Luo, H Ren, H Zhou, Y Lin… - …, 2020 - academic.oup.com
Background Shotgun metagenomic sequencing has improved our understanding of the
human gut microbiota. Various DNA extraction methods have been compared to find …

Evaluating the information content of shallow shotgun metagenomics

B Hillmann, GA Al-Ghalith, RR Shields-Cutler, Q Zhu… - Msystems, 2018 - Am Soc Microbiol
Although microbial communities are associated with human, environmental, plant, and
animal health, there exists no cost-effective method for precisely characterizing species and …

[HTML][HTML] Impact of DNA extraction method on variation in human and built environment microbial community and functional profiles assessed by shotgun …

H Sui, AA Weil, E Nuwagira, F Qadri, ET Ryan… - Frontiers in …, 2020 - frontiersin.org
Both the host microbiome and the microbiome of the built environment can have profound
impacts on human health. While prior studies have suggested that the variability introduced …