Fall 2019: Investigating the Microbial Communities in Mortality Composts
5
Data visualization with R.
BIT 477/577 Fall 2019 Students and Carlos Goller
Learning Objectives
- To perform basic data analyses using QIIME and a downloaded dataset.
- Given a formatted dataset and an appropriate visualization tool, the participant will be able to accurately summarize the output for different measures of diversity.
- Explain the UniFrac metric of distance and diversity.
- Interpret and evaluate a 2D representation of multidimensional data (ordination plot)
- Visualize metagenomic data with Phyloseq
UniFrac
- Unique Fraction Metric (Unifrac) measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. https://aem.asm.org/content/71/12/8228
PhyloSeq
Ordination plot- visualization of beta diversity for identification of possible data structures.
- PCoA is the most commonly used plot for microbiome data
- Can be obtained via R and Phyloseq
- Ordination guide for Phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html
Main points of Article #3
Nowinski et al. (2019). Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Scientific Data. 6. Article number: 129.
The authors used metatranscriptomics, pipelines, RNAseq, Illumina, DADA2 for this study.
- Sampling was performed using an Environmental Sample Processor (ESP) which provides on-site (in situ) collection and analysis of water samples from the ocean.
- The ESP had two filters: 5.0 uM pore for eukaryotic organisms and 0.22 uM pore to capture bacterial and archaeal microbes.
- Environmental information/measurements were also taken by a CTD (conductivity, temperature, and depth) instrument mounted on the ESP.
- They constructed relative abundance of bacterial and archaeal maps by family.
- Also constructed relative abundance of eukaryotic tax maps
- Why/how did they validate the study?
- Quality control: removed contaminants by removing and filtering of reads
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- BBDuk software
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- Validated to other similar datasets by microbial community standards
- Used spike on controls- used to calibrate abundance organisms by amount of water filtered
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- Calculate relative abundance normalized by volume.
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This study focused mainly on methods; missing results and discussion. It is a data descriptor article, which provides the scientific community with elaborative information and “high-quality materials data” to be able to understand and use in further research.