Methodology
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The studies selected for the Microbiome Stress Project meet certain criteria to ensure we are not comparing 'apples to oranges' in terms of a meta-analysis. As such, we restrict studies to those assessing bacterial communities using Illumina sequencing of V4 hypervariable region of the 16S rRNA gene (Earth Microbiome primers, 515f/806r). The datasets are categorized on several factors: (1) by experimental vs. observational/gradient-based studies, (2) by stressor type and (3) environment types (specifics listed below).
The detailed methodology of the Microbiome Stress Project is presented in Rocca et al. 2019 (Frontiers in Microbiology)
The detailed methodology of the Microbiome Stress Project is presented in Rocca et al. 2019 (Frontiers in Microbiology)
Sequence processing and downstream analyses:
We are using a standardized pipeline (code available below) to re-process raw sequence data into Exact Sequence Variants (ESVs) using DADA2 (Callahan et al. 2016). The ESVs are all delineated to represent the same 250 bp fragment of the 16S V4 region. We are using Phylofactor (R Package) to determine what portion(s) of the phylogeny respond to various stressors. Machine learning and indicator taxa analyses are also used to identify positive and negative responders to the different stressors.
We are using a standardized pipeline (code available below) to re-process raw sequence data into Exact Sequence Variants (ESVs) using DADA2 (Callahan et al. 2016). The ESVs are all delineated to represent the same 250 bp fragment of the 16S V4 region. We are using Phylofactor (R Package) to determine what portion(s) of the phylogeny respond to various stressors. Machine learning and indicator taxa analyses are also used to identify positive and negative responders to the different stressors.
Microbiome Stress Project Code to Re-Process Datasets into ESVs | |
File Size: | 7 kb |
File Type: | txt |
Environments:
Host-microbiomes, Soil, Water, Sediments, Phyllosphere, Biofilm, Reactor, Litter, Ice...
Natural and Anthropogenic Stressors:
Freeze/Thaw, Salinity, Temperature, pH, Oxic/Anoxic, Precipitation/Drought, UV/Light, Fire, Compaction/Pressure, Tillage, Land use, Agricultural Amendments/Fertilization, Fungicide/Pesticide, Waste water/Sewage sludge, Hydrocarbons (PAHs)/coal, Nanoparticles, Heavy Metals, Antibiotic/Pharmaceutical, PCB, Fracking Fluids and any Emerging Contaminant.
Host-microbiomes, Soil, Water, Sediments, Phyllosphere, Biofilm, Reactor, Litter, Ice...
Natural and Anthropogenic Stressors:
Freeze/Thaw, Salinity, Temperature, pH, Oxic/Anoxic, Precipitation/Drought, UV/Light, Fire, Compaction/Pressure, Tillage, Land use, Agricultural Amendments/Fertilization, Fungicide/Pesticide, Waste water/Sewage sludge, Hydrocarbons (PAHs)/coal, Nanoparticles, Heavy Metals, Antibiotic/Pharmaceutical, PCB, Fracking Fluids and any Emerging Contaminant.