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Short Citation:
Northwest Fisheries Science Center, 2022: Sablefish GI microbiome & histology - Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments, https://www.fisheries.noaa.gov/inport/item/18020.

Item Identification

Title: Sablefish GI microbiome & histology - Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments
Short Name: Sablefish GI microbiome & histology (Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments)
Status: Completed
Creation Date: 2012-06-01
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

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

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
None Alternative feeds
None aquaculture
None fish diet
None microbiome
None sablefish

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None Montlake
None NWFSC Montlake

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
None Instrument Not Applicable

Platform Keywords

Thesaurus Keyword
UNCONTROLLED
None Animal and Plant Collection Device

Physical Location

Organization: Northwest Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Spreadsheet
Data Presentation Form: Table (digital)

Support Roles

Data Steward

CC ID: 849257
Date Effective From: 2015-10-01
Date Effective To:
Contact (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

Distributor

CC ID: 849258
Date Effective From: 2015-10-01
Date Effective To:
Contact (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
URL: NWFSC Home

Metadata Contact

CC ID: 849256
Date Effective From: 2015-10-01
Date Effective To:
Contact (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
URL: NWFSC Home

Originator

CC ID: 849260
Date Effective From: 2015-10-01
Date Effective To:
Contact (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

Point of Contact

CC ID: 849259
Date Effective From: 2015-10-01
Date Effective To:
Contact (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

Extents

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 849266
W° Bound: -122.3062
E° Bound: -122.3062
N° Bound: 47.6449
S° Bound: 47.6449
Description

NWFSC Montlake: NWFSC Montlake molecular biology & histology labs

Extent Group 1 / Time Frame 1

CC ID: 849265
Time Frame Type: Range
Start: 2012-05-01
End: 2013-04-30

Access Information

Security Class: Unclassified
Data Access Procedure:

Submit request by email or telephone

Data Access Constraints:

NA

Distribution Information

Distribution 1

CC ID: 849262
Start Date: 2019-05-15
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.

Distribution 2

CC ID: 849261
Start Date: 2019-05-15
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.

URLs

URL 1

CC ID: 849263
URL: https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/7390
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

Technical Environment

Description:

Spreadsheet

Data Quality

Accuracy:

Medium

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
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.

Lineage

Lineage Statement:

sample signals are standardized before comparisons

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity Comparative bacterial and archaeal gastrointestinal abundances from sablefish on different diets

Catalog Details

Catalog Item ID: 18020
GUID: gov.noaa.nmfs.inport:18020
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 Last Review Date: 2019-06-04
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2020-06-04