18020 Sablefish GI microbiome & histology (Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments) Data Set Published / External 17938 Migrated from Resource Enhancement and Utilization Technologies Division Project Completed 2012-06-01 2019-05-15 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. Laboratory data Loaded by batch 4302, 01-31-2013 18:57 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 Theme Alternative feeds Theme aquaculture Theme fish diet Theme microbiome Theme sablefish Spatial Montlake Spatial NWFSC Montlake Instrument Instrument Not Applicable Platform Animal and Plant Collection Device Northwest Fisheries Science Center Seattle WA USA Data Set Spreadsheet Table (digital) Instrument Not Applicable Platform Not Applicable Animal and Plant Collection Device 56814 Comparative bacterial and archaeal gastrointestinal abundances from sablefish on different diets Published / External Planned 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. Spreadsheet Yes PARR 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. 1 phylum text Yes No Active bacterial or archaeal phylum name. Units for values are NA. text NA NA 2 class text Yes No Active bacterial or archaeal class name. Units for values are NA. text NA NA 3 order text Yes No Active bacterial or archaeal order name. Units for values are NA. text NA NA 4 family text Yes No Active bacterial or archaeal family name. Units for values are NA. text NA NA 5 genus text Yes No Active bacterial or archaeal genus name. Units for values are NA. text NA NA 6 species text Yes No Active bacterial or archaeal species name. Units for values are NA. text NA NA 7 representative_gene text Yes No 0 Active DNA sequence representative of taxon. Units for values are NA. text NA CATG 8 49b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 9 50b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 10 53b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 11 59b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 12 60b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 13 72b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 14 74b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 15 77b.1 number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 16 77b.2 number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 17 78b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 18 79b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 19 80b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 20 84b number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 21 corn number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 22 flax number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 23 ref number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 24 56a number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 25 74a number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 26 54c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 27 56c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 28 60c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 29 70c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 30 71c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 31 77c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 32 79c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 33 80c number No No 0 Active relative within-sample abundance for taxon. Units for values are NA. number NA 0 - 720 Data Steward 2015-10-01 Person Rhodes, Linda D Linda.Rhodes@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3279 206-860-3467 Distributor 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Metadata Contact 2015-10-01 Organization Northwest Fisheries Science Center NWFSC nmfs.nwfsc.metadata@noaa.gov https://ror.org/05r7z1k40 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov NWFSC Home Online Resource Originator 2015-10-01 Person Rhodes, Linda D Linda.Rhodes@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3279 206-860-3467 Point of Contact 2015-10-01 Person Rhodes, Linda D Linda.Rhodes@noaa.gov 2725 Montlake Blvd East Seattle WA 98112 206-860-3279 206-860-3467 -122.3062 -122.3062 47.6449 47.6449 NWFSC Montlake: NWFSC Montlake molecular biology & histology labs Range 2012-05-01 2013-04-30 Unclassified Submit request by email or telephone NA https://www.webapps.nwfsc.noaa.gov/apex/parr/comparative_bacterial_and_archaeal_gastrointestinal_abundances_from_sablefish_on_different_diets/data/page/ 2015-10-01 Organization Northwest Fisheries Science Center https://ror.org/05r7z1k40 Comparative bacterial and archaeal gastrointestina 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. https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/tables/table/comparative_bacterial_and_archaeal_gastrointestinal_abundances_from_sablefish_on_different_diets 2015-10-01 Organization Northwest Fisheries Science Center https://ror.org/05r7z1k40 Comparative bacterial and archaeal gastrointestina 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. https://www.webapps.nwfsc.noaa.gov/apex/parrdata/inventory/datasets/dataset/7390 Sablefish GI microbiome & histology Online Resource Web site NWFSC Dataset Information page. Raw & refined classification & abundance data from array analysis & histology analysis Spreadsheet Medium Process & sample negative controls included; sample concentrations adjusted to a standard range Yes 10 Yes No No 0 days No Delay No Archiving Intended 365 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. sample signals are standardized before comparisons 56814 Entity gov.noaa.nmfs.inport:18020 SysAdmin InPortAdmin 2013-01-31T18:57:58 SysAdmin InPortAdmin 2026-03-04T19:17:17 2019-06-04 Northwest Fisheries Science Center NWFSC 2725 Montlake Boulevard East Seattle WA 98112 USA 206-860-3200 https://www.nwfsc.noaa.gov 1001 Public No No 2019-06-04 1 Year 2020-06-04