Viral metagenomics from mammalian feces (Sciuridae)

Knowledge graph centered on Viral metagenomics from mammalian feces (Sciuridae) with 30 nodes and 116 connections. Top connected: Rocky Mountain Biological Laboratory, Gothic, Marmota, Yellow-bellied Marmot, Beetles.

Method synopsis

A comprehensive protocol for extracting, amplifying, sequencing and analyzing viral DNA from fecal samples to identify microviral genomes. Uses rolling circle amplification followed by high-throughput sequencing and bioinformatic analysis.

Synthesized from method descriptions across 2 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Microvirus Genomes Identified in Fecal Samples from Yellow - Bellied Marmots (2022), Microbiology Resource Announcements. Implementations in other papers (listed below) may differ.

1. Fecal sample collection
   Fecal samples were collected from three yellow-bellied marmots with identification numbers 8189-7849 (Mar1), 7828-8390 (Mar2), and 8265-6223 (Mar3) living in the upper East River Valley, in and around the Rocky Mountain Biological Laboratory near Crested Butte, CO, USA
   Quantities: Three fecal samples from three individual marmotsDuration: Collection dates were 18, 21, and 22 May 2018Conditions: Spring sampling period in May 2018 in Colorado mountain environment
   Equipment: Not specified
2. Viral DNA extraction
   Fecal samples were processed and viral DNA was extracted using the High Pure viral nucleic acid kit from Roche Diagnostics, USA
   Quantities: Not specifiedDuration: Not specifiedConditions: Standard laboratory conditions
   Equipment: High Pure viral nucleic acid kit, Roche Diagnostics
3. Rolling circle amplification
   Circular DNA was amplified using rolling circle amplification (RCA) with a TempliPhi 2000 kit from GE Healthcare, USA
   Quantities: Not specifiedDuration: Not specifiedConditions: Standard laboratory conditions

Typical Equipment

• High Pure viral nucleic acid kit
• TempliPhi 2000 kit
• Nextera DNA library preparation kit
• Illumina HiSeq 4000 sequencer
• Trimmomatic v0.39
• metaSPAdes v3.12.0
• VirSorter
• RASTtk
• BLASTp
• BBMap

Output Measurements

• microvirus genome sequences
• genome size
• GC content
• gene annotations

Papers Using This Protocol (2)

Species Studied With This Protocol

Places Where Used