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The Influence of Different High Fidelity DNA Polymerase on 16S rRNA Sequencing
Assessing differences due to high fidelity DNA polymerase to downstream 16S rRNA gene survey results. Variations in number of OTUs and chimera prevalence were found to be high... -
Surface seawater from coral reefs and aquaria Raw sequence reads
Samples were used to examine the performance of V4 SSU rRNA gene primers. -
DNA extraction comparison testing 2019-2020
Our DNA extraction protocol is years old, and we want to compare new extraction methods to address outstanding issues. For more details, check out the motivation and... -
PPIT: an R package for inferring microbial taxonomy from nifH sequences
Amplicon sequencing of metabolic marker genes provides targeted snapshots of community metabolic potential. However, inferring microbial taxonomy from metabolic marker gene... -
Every base matters: assessing small subunit rRNA primers for marine microbiom...
Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and... -
Experimental manipulation of fish host microbiomes
Host-associated microbiomes provide excellent means to explore eco-evolutionary processes that influence microbiome recruitment and dynamics of species compositions. Especially... -
Investigation of the Coral Microbiome
This study was conducted to profile the prokaryotic diversity associated with seven different scleractinian coral species collected from the Caribbean and Pacific. In addition,... -
Comparison of samples and mock communities amplified with single-base variati...
This study is a comparison of marine environmental and marine mock community samples amplified with different versions of a commonly used universal forward primer 515. A... -
Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
Human activities are driving up atmospheric carbon dioxide concentrations at an unprecedented rate, perturbing the ocean's carbonate buffering system, lowering oceanic pH, and... -
Single-cell view of deep-sea microbial activity and intracommunity heterogeneity
Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth.... -
Conservation of genomic information in multiple displacement amplified low-qu...
Marine invertebrates and their microbiomes have been a rich source of bioactive compounds and interesting genomic features. However, factors such as which species and tissue are... -
ESP deployed about 1-2 km from catalina island. Sampled 1 to 2 times per day ...
"Short time-scale observations are valuable for understanding microbial influence on nutrient and energy cycles. We assessed dynamics in relative abundance and potential... -
Contributions of environmental and maternal transmission to the assembly of l...
Characterization of fungal communities of seeds and leaves of Switchgrass (Panicum virgatum) along with the characterization of aerially dispersed fungi as sources of leaf... -
Metagenomic and metatranscriptomic sequencing and assembly of Photogranules
Understanding the microbial succession and algae-bacteria interaction during photogranulation process -
Comparative analysis of fish eDNA reveals higher sensitivity achieved through...
Comparative analysis of fish eDNA reveals</p><p>higher sensitivity achieved through sequence-based metabarcoding -
synthetic metagenome Raw sequence reads
The goal of the study is to identify the RNA-protein binding motifs used by the G. kaustauphilus S15 and to understand how specific or general the binding site can be. This data... -
Earth Microbiome Project Multi-omics (EMP500)
The Earth Microbiome Project Multi-omics component (EMP500) involves amplicon and shotgun metagenomic sequencing and metabolomic profiling of over five hundred microbial... -
ECOLOGY OF AEROBIC ANOXYGENIC PHOTOTROPHS IN THE ADRIATIC SEA (ADRISAAF)
Bacteria, as the most diverse trophic group, make up the base of the marine food web. Aerobic anoxygenic phototrophs (AAP) are widespread in the environment and account for up... -
Comparative analysis of amplicon and metagenomic sequencing methods reveals k...
Background: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These... -
Microbial ecology of coral-dominated reefs in the Federated States of Micronesia
We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding seven islands and atolls (Yap, Woleai, Olimarao,...