Additional file 1 of Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs

Additional file 1. Rarefaction sequencing curves and total read counts. Rarefaction curves before (A) and following (B) filtration to remove taxonomic assignation out-with desired 16S microbial SILVA results. Clear plateaus are seen suggesting adequate sequencing depth was achieved at a depth of 150...

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Bibliographic Details
Main Authors: Morag Clinton (11678457), Adam J. Wyness (10170055), Samuel A. M. Martin (8994104), Andrew S. Brierley (11678460), David E. K. Ferrier (9526432)
Format: Still Image
Language:unknown
Published: 2021
Subjects:
Microbiology
Experimental design
Sampling methodology
Gill microbiota
Microbial assemblages
Aquaculture
Atlantic salmon
Veterinary microbiology
Online Access:https://doi.org/10.6084/m9.figshare.16986720.v1
Description
Summary:Additional file 1. Rarefaction sequencing curves and total read counts. Rarefaction curves before (A) and following (B) filtration to remove taxonomic assignation out-with desired 16S microbial SILVA results. Clear plateaus are seen suggesting adequate sequencing depth was achieved at a depth of 1500 sequences from swab and biopsy samples. Accompanying table illustrates the total unfiltered read counts seen in curve A, as well as read counts as specific filtration steps towards final filtered read counts. Filtration steps were as follows 1) Removal of sequences unassigned to bacteria; 2) Removal of sequences assigned to archaea; 3) Removal of sequences assigned to mitochondria; 4) Removal of sequences assigned to chloroplasts; 5) Removal of sequences not taxonomically assigned below kingdom level.

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