Earth Microbiome Vuegen Demo Notebook

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The Earth Microbiome Project (EMP) is a systematic attempt to characterize global microbial taxonomic and functional diversity for the benefit of the planet and humankind. It aimed to sample the Earth’s microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial community structure. The EMP dataset is generated from samples that individual researchers have compiled and contributed to the EMP. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

You can find more information about the Earth Microbiome Project at https://earthmicrobiome.org/ and in the original article.

Exploratory Data Analysis

This section contains the exploratory data analysis of the Earth Microbiome Project (EMP) dataset.

Sample Exploration

Metadata Random Subset

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Animal Samples Map

Plant Samples Map

Saline Samples Map

Physicochemical properties of the EMP samples

Pairwise scatter plots of available physicochemical metadat are shown for temperature, salinity, oxygen, and pH, and for phosphate, nitrate, and ammonium

Metagenomics

Alpha Diversity

This subsection contains the alpha diversity analysis of the EMP dataset.

Alpha Diversity Host Associated Samples

Alpha Diversity Free Living Samples

Average Copy Number

Average Copy Number Emp Ontology Level2

Average Copy Number Emp Ontology Level3

Nestedness

Nestedness Random Subset

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All Samples

Plant Samples

Animal Samples

Non Saline Samples

Shanon entropy analysis

This subsection contains the Shannon entropy analysis of the EMP dataset.

Specificity of sequences and higher taxonomic groups for environment

Environment distribution in all genera and 400 randomly chosen tag sequence. b) and c) Shannon entropy within each taxonomic group.

Network Analysis

Phyla Association Networks

Phyla Counts Subset

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Phyla Correlation Network With 0.5 Threshold Edgelist

Number of nodes: 33

Number of edges: 42