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Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro

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Created: Jul 27, 2016 at 12:36 a.m.
Last updated: Jan 02, 2018 at 8:20 p.m.
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This data was collected as part of a study to understand the connectivity and diversity of stream bacteria communities in streams flowing from high to low elevation through different types of urbanization and in different seasons. The dataset contains OTU (operational taxonomic units, the bacterial surrogate for species) abundance for bacteria at iUTAH aquatic GAMUT sites ( in three watersheds in September 2014. Briefly, water column samples were filtered onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced bacterial DNA (PCR-amplified using V4-region specific primers) using 454-pyrosequencing (an older sequencing method with more limitations). We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Schloss 2011 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for analysis is available at
There are three files; site and sample metadata (e.g. date sampled) is included in the file stream_design.txt, observed OTU counts by sample are in the .shared file, and the taxonomic classification of OTUs is in the .taxonomy file.

Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310.

Subject Keywords



Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
Place/Area Name:
Multiple Watersheds
North Latitude
East Longitude
South Latitude
West Longitude


Start Date:
End Date:


Additional Metadata

Name Value
Observed Variables Rank abundance
Variable Description Relative abundance of bacterial community taxa in water column
Data Collection Method Streamwater aseptically vacuum filtered in the field or lab using autoclaved Nalgene filter cups and 47 mm 0.2 um membrane filters, were stored on dry ice or liquid nitrogen until extracted with MoBIO PowerMax Soil DNA kits. PCR-amplified 16S rDNA samples were sequenced using BYU’s DNA Sequencing Center (454-Pyrosequencing or Hi-Seq).
Data Processing Method Sequences have been processed using MOTHUR (Schloss et al. 2009).


Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation iUTAH-innovative Urban Transitions and Aridregion Hydro-sustainability 1208732

How to Cite

Jones, E., Z. Aanderud (2018). Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro, HydroShare,

This resource is shared under the Creative Commons Attribution CC BY.


Erin Fleming Jones 6 years, 11 months ago

Illumina Hi-Seq samples from September 2014-October 2015 are also available on HydroShare.

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