QIIME allows analysis of high-throughput community sequencing data

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...

Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...

Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?

One option is ...

16S rRNA amplicon sequencing (Illumina MiSeq, V3-V4 region) to assess community structure.

Record of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater). Young fry arrived at Solbergstranda 2015-02-05 17:20.

Spreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).

Spreadsheet columns are:

• Date (YYYY-MM-DD)
• Day (day zero is the day before first feeding with new feed)
• Inputter (person entering data into Excel)
• Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
• Section (tanks were divided in half using perforated walls)
• Treatment (explained in sheet "treatments")

...

At the GenoSysFat startup meeting 2015-04-22, Dominic Nanton of EWOS described the feeds they made for GenoSysFat.

Describes recipes with linseed oil (LNO) and palm oil (PO) to provide the 18:3n-3 precursor to EPA and DHA and match saturation of 100% fish oil (FO) control diet at ca 0.7 mass% EPA+DHA.

Page 2: Overview Page 3-4: Description of feeds. Feed no., Code, Initial fish weight (g), Feed size (mm), Fish number (3000), Feed (kg) Page 5-7: Feed formulations. Feed number, Feed name, Feed size ...

A file which combine previous metabolomics samples ID to new sample ID file (https://fairdomhub.org/data_files/1330)

FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand Sept 2015.

(Knut Rudi --> Jon Olav Vik 20160126, email subject "metadata for alle fisk".)

File contents look like this:

OTU_1 1..446 -GTCC---GCCCTACGGGAT... OTU_2 1..446 -GTCC--GCCC-TACGGGAT... ... OTU_439 1..472 ----ATGTCACCTACGGGAT...

FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand January 2016.

Gut microbiota analysis of fish sampled in january 2016. The data is found in row 335-548 and downwards (Sheet 1). The first 16 colums contain information about the fish, and the following columns (From R to AJO) each represent an OTU (Operational taxonomic unit) with the given taxonomy for each OTU presented in the bottom row. Sequencing depth was kept at 13000 sequences per sample, thus the numbers presented in the OTU columns represent the number of sequences matching the specific OTU from the ...

Gut microbiota analysis of the fish whose gross phenotypes are listed in https://fairdomhub.org/data_files/1244. Besides identification of the fish, the data are a 130 x 435 matrix showing amounts of operational taxonomic units (OTUs), one row per fish and one column per OTU (https://en.wikipedia.org/wiki/Operational_taxonomic_unit). Sequences that characterize each OTU are in https://fairdomhub.org/data_files/1317. Amounts are measured as the number out of 2000 sequences examined that contain a ...

Combined taxonomy table of abundance of OTUs (Operational Taxonomy Units) in both freshwater and saltwater samples from 16S V3-V4 Illumina sequencing of gut microbiota. Primers used for sequencing are given in https://fairdomhub.org/sops/270 The OTUs are presented in number of counts per sample (n=349). Each row represent one sample. Raw data are available in the Sequence Read Archive database under accession number SRP119730 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP119730).