Sablefish GI microbiome & histology - Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments
Northwest Fisheries Science Center
Data Set
(DS)
| ID: 18020
| Published / External
Created: 2013-01-31
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Last Modified: 2022-08-09
Project (PRJ) | ID: 17938
ID: 18020
Data Set (DS)
* Discovery• First Pass
» Metadata Rubric
Item Identification
* » Title | Sablefish GI microbiome & histology - Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments |
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Short Name | Sablefish GI microbiome & histology (Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments) |
* Status | Completed |
Creation Date | 2012-06-01 |
Revision Date | |
• Publication Date | 2019-05-15 |
* » Abstract |
Sustainable culture of sablefish (Anoplopoma fimbria) is an active research area at NWFSC, with a primary objective of rearing a human food source under healthy, economic, and sustainable conditions. Development of sustainable feed for juvenile fish through replacement of marine fish oils is key for economic and ecological viability of sablefish culture. This project intends to analyze the GI microbiome of juvenile sablefish, comparing three feeds (corn oil, linseed oil, BioOregon BioBrood) used in a National Marine Aquaculture Initiative (NMAI)-funded project examining the effects of substitute lipids on growth, production composition, and lipid bioconversion. Community DNA from GI mucus and luminal contents will be extracted, quantified, and quality checked. DNA will be submitted for analysis by a microbial phylogenetic microarray bearing over a million probes for classifying more than 59,000 bacterial taxa. Second Genome, a company with exclusive licensing for this phylogenetic microarray, will conduct the the analysis for classification, relative abundance, & ordination. Complementary to microbiome analysis, morphological changes in gastrointestinal tissues will be assessed for each fish by light microscopic histology (collaboration with Mark Myers). Although this is a stand-alone project, the objective is for the microbiome approach to become an integral component of finfish nutrition research. Raw & refined classification & abundance data from array analysis & histology analysis. |
* Purpose |
Laboratory data |
Notes |
Loaded by batch 4302, 01-31-2013 18:57 |
Other Citation Details | |
• Supplemental Information |
Subject to Public Access to Research Results (PARR): Yes Peer Reviewed Publication: Dietary effects on sablefish gastrointestinal microbiome & histology. Peer reviewed publication Presentation: Microbiome of Sablefish under Different Dietary Regimens. Aquaculture meeting presentation Report: Report to NOAA Aquaculture Program. Funding report |
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Keywords
Theme Keywords
Thesaurus | Keyword |
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None | Alternative feeds |
None | aquaculture |
None | fish diet |
None | microbiome |
None | sablefish |
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* Spatial Keywords
Thesaurus | Keyword |
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None | Montlake |
None | NWFSC Montlake |
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None | Instrument Not Applicable |
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Thesaurus | Keyword |
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None | Animal and Plant Collection Device |
Physical Location
• » Organization | Northwest Fisheries Science Center |
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• » City | Seattle |
• » State/Province | WA |
• Country | USA |
• » Location Description |
Data Set Information
* Data Set Scope Code | Data Set |
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• Data Set Type | Spreadsheet |
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» Data Presentation Form | Table (digital) |
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Support Roles
* » Support Role | Data Steward |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Rhodes, Linda D |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Linda.Rhodes@noaa.gov |
Phone | 206-860-3279 |
Fax | 206-860-3467 |
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* » Support Role | Distributor |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Organization | Northwest Fisheries Science Center (NWFSC) |
Address |
2725 Montlake Boulevard East Seattle, WA 98112 USA |
Email Address | nmfs.nwfsc.metadata@noaa.gov |
Phone | 206-860-3200 |
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URL | http://www.nwfsc.noaa.gov |
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* » Support Role | Metadata Contact |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Organization | Northwest Fisheries Science Center (NWFSC) |
Address |
2725 Montlake Boulevard East Seattle, WA 98112 USA |
Email Address | nmfs.nwfsc.metadata@noaa.gov |
Phone | 206-860-3200 |
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URL | http://www.nwfsc.noaa.gov |
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* » Support Role | Originator |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Rhodes, Linda D |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Linda.Rhodes@noaa.gov |
Phone | 206-860-3279 |
Fax | 206-860-3467 |
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* » Support Role | Point of Contact |
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* » Date Effective From | 2015-10-01 |
Date Effective To | |
Person | Rhodes, Linda D |
Address |
2725 Montlake Blvd East Seattle, WA 98112 |
Email Address | Linda.Rhodes@noaa.gov |
Phone | 206-860-3279 |
Fax | 206-860-3467 |
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Extents
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Extent Group 1
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Extent Group 1 / Geographic Area 1
* » W° Bound | -122.3062 |
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* » E° Bound | -122.3062 |
* » N° Bound | 47.6449 |
* » S° Bound | 47.6449 |
* » Description |
NWFSC Montlake: NWFSC Montlake molecular biology & histology labs |
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* » Time Frame Type | Range |
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* » Start | 2012-05-01 |
End | 2013-04-30 |
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Access Information
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* » Security Class | Unclassified |
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• Data Access Policy | |
» Data Access Procedure |
Submit request by email or telephone |
• » Data Access Constraints |
NA |
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Distribution Information
Start Date | 2019-05-15 |
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End Date | Present |
» Download URL | https://www.webapps.nwfsc.noaa.gov/apex/parr/comparative_bacterial_and_archaeal_gastrointestinal_abundances_from_sablefish_on_different_diets/data/page/ |
Distributor | Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present) |
File Name | Comparative bacterial and archaeal gastrointestina |
Description |
These data were derived from a feeding study with juvenile sablefish, comparing plant-based feeds (flax, corn) with fish-based feed (reference). Intestinal microbiomes were determined by hybridization of a gastronintesntial DNA microarray. |
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Review Status |
Start Date | 2019-05-15 |
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End Date | Present |
» Download URL | https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/comparative_bacterial_and_archaeal_gastrointestinal_abundances_from_sablefish_on_different_diets |
Distributor | Northwest Fisheries Science Center (NWFSC) (2015-10-01 - Present) |
File Name | Comparative bacterial and archaeal gastrointestina |
Description |
These data were derived from a feeding study with juvenile sablefish, comparing plant-based feeds (flax, corn) with fish-based feed (reference). Intestinal microbiomes were determined by hybridization of a gastronintesntial DNA microarray. |
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URLs
URL | https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/7390 |
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Name | Sablefish GI microbiome & histology |
URL Type | Online Resource |
File Resource Format | Web site |
Description |
NWFSC Dataset Information page. Raw & refined classification & abundance data from array analysis & histology analysis |
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» Quality Control Procedures Employed |
Process & sample negative controls included; sample concentrations adjusted to a standard range |
Data Management
» Have Resources for Management of these Data Been Identified? | Yes |
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» Approximate Percentage of Budget for these Data Devoted to Data Management | 10 |
» Do these Data Comply with the Data Access Directive? | Yes |
» Is Access to the Data Limited Based on an Approved Waiver? | No |
» If Distributor (Data Hosting Service) is Needed, Please Indicate | No |
» Approximate Delay Between Data Collection and Dissemination | 0 days |
» If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed |
No Delay |
» Actual or Planned Long-Term Data Archive Location | No Archiving Intended |
» If To Be Determined, Unable to Archive, or No Archiving Intended, Explain |
Data is in a non-standard format for archiving |
» Approximate Delay Between Data Collection and Archiving | 365 |
» How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive? |
The Northwest Fisheries Science Center facilitates backup and recovery of all data and IT components which are managed by IT Operations through the capture of static (point-in-time) backup data to physical media. Once data is captured to physical media (every 1-3 days), a duplicate is made and routinely (weekly) transported to an offsite archive facility where it is maintained throughout the data's applicable life-cycle. |
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sample signals are standardized before comparisons |
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Child Items
Rubric scores updated every 15m
Score | Type | Title |
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Entity (ENT) | Comparative bacterial and archaeal gastrointestinal abundances from sablefish on different diets | |
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Item Type | Relationship Type | Title |
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Catalog Details
Catalog Item ID | 18020 |
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Metadata Record Created By | SysAdmin InPortAdmin |
Metadata Record Created | 2013-01-31 18:57+0000 |
Metadata Record Last Modified By | SysAdmin InPortAdmin |
» Metadata Record Last Modified | 2022-08-09 17:11+0000 |
Metadata Record Published | 2019-06-04 |
Owner Org | NWFSC |
Metadata Publication Status | Published Externally |
Do Not Publish? | N |
Metadata Workflow State | Published / External |
Metadata Last Review Date | 2019-06-04 |
Metadata Review Frequency | 1 Year |
Metadata Next Review Date | 2020-06-04 |
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