title: ABFU5
organism: invertebrate gut metagenome
description: Gut microbiome community from abalone fed a formulated feed and fresh Ulva
attributes.tag: host
attributes.value: Haliotis midae
attributes.tag: isolation_source
attributes.value: Abalone (20-30g) from a controlled seven month laboratory trial where abalone were fed a formulated feed and fresh Ulva
attributes.tag: collection_date
attributes.value: 2012-08-20
attributes.tag: geo_loc_name
attributes.value: South Africa: Marine Research Aquarium (MRA) in Cape Town
attributes.tag: lat_lon
attributes.value: 33.91 S 18.38 E
attributes.tag: ref_biomaterial
attributes.value: Impact of Ulva as a functional ingredient in formulated feeds on the gut microbiome of farmed Haliotis midae
attributes.tag: rel_to_oxygen
attributes.value: not applicable
attributes.tag: samp_collect_device
attributes.value: At the end of the seven month feeding trial, abalone were starved for 48 hours prior to sample collection to standardise the fed state of individual abalone and limit the food-associated/transient bacteria. To sample the gut, abalone were euthanized using a sterile scalpel blade to perform a complete transverse section below the level of the cerebral ganglia, whereafter abalone were shucked (removed from the shell) by cutting the abductor muscle as close as possible to the shell. Once shucked, the abalone were mounted on a pre-sterilized dissection tray and the gastrointestinal tract of each animal was carefully removed using a sterile scalpel and tweezers, and stored in a 2 mL centrifuge tube and immediately flash frozen using liquid nitrogen. All dissection equipment was sterilized with 100% ethanol after each dissection to prevent any cross-contamination between samples.
attributes.tag: samp_mat_process
attributes.value: Total genomic DNA was extracted using a QIAamp Fast DNA Stool Mini Kit (Cat#51604) using 150 – 200 mg of ground abalone intestinal sample. The 16S V3-V4 hypervariable gene region (ca. 460bp) was polymerase chain reaction (PCR) amplified using the 16S_341F (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG) and 16S_805R (GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC) primer pair and next-generation sequencing was conducted at the University of the Western Cape (UWC) on an Illumina MiSeq sequencer (paired-end, 2x250bp).
attributes.tag: samp_size
attributes.value: 150 – 200 mg of ground abalone intestinal sample
attributes.tag: source_material_id
attributes.value: ABFU5
attributes.tag: BioSampleModel
attributes.value: Metagenome or environmental