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expected bacteria in hatchery water #122

Closed emmats closed 6 years ago

emmats commented 6 years ago

I need to make a fasta file of sequences from bacterial taxonomic groups that one would expect to find in Taylor hatchery water. Any candidates? I can go through the literature and choose them, but I am wondering if anyone has information on the Taylor hatchery more specifically.

sr320 commented 6 years ago

Not specifically but here are some resources...

Metagenomic Profiling of Microbial Composition and Antibiotic Resistance Determinants in Puget Sound http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048000

Metagenomic_Profiling_of_Microbial_Composition_and_Antibiotic_Resistance_Determinants_in_Puget_Sound_1FBB4682.png PubMed_Central__Figure_2__PLoS_One__2012__7_10___e48000__Published_online_2012_Oct_29__doi_ _10_1371_journal_pone_0048000_1FBB4742.png

Metagenome Sequence Accession

Sequence data for the Puget Sound dataset is available through the Metagenomics RAST (MG-RAST) server (http://metagenomics.anl.gov/) under the MG-RAST identification numbers 4460178.3, 4460179.3, 4460180.3, 4460182.3, 4460188.3, 4460189.3 and 4460190.3.

Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (Crassostrea gigas) Microbiota from the Puget Sound Region in the United States http://genomea.asm.org/content/5/23/e00468-17.full

This is the first study analyzing Pacific oyster microbiota in the Puget Sound estuarine system using a next-generation sequencing method. Taxonomic analysis indicated that Tenericutes, Chlamydiae, Proteobacteria, and Firmicutes were the most abundant phyla. Small numbers of operational taxonomic units (OTUs) belonging to the Vibrio genus were detected in all the oyster microbiome samples. Accession number(s).Raw sequences were deposited to the NCBI SRA database under accession no. SRP075291. Filtered and assembled sequences are also publicly available on the MG-RAST server under the project ID mgp15218 and MG-RAST ID mgm4666675.3 to mgm4666698.3.

emmats commented 6 years ago

That should be a good start. Thanks!