New Ordination Methods for Microbiome Analysis in ERGO

We’ve added to ERGO’s rich suite of tools and workflows for amplicon and metagenome sequencing studies to include ordination plots.

▸ Non-Metric Dimensional Scaling (NMDS)

Non-metric dimensional scaling attempts to closely represent pairwise dissimilarity between samples. It is a robust unconstrained ordination method that uses rank orders commonly used in ecology studies. Unlike many other ordination techniques NMDS iterates to find a solution that fits with an optimal stress value to the number of chosen dimensions. ERGO gives you a simple interface to choose the number of attempts, dimensions, along with an option to specify a previous best stress.

New Non-metric dimensional scaling options in ERGO

▸ Jaccard Indices
In addition to the Bray-Curtis dissimilarity index, ERGO now provides an option for the Jaccard Index and Weighted Jaccard Index. The Jaccard index is based on the presence/absence of species and does not take into account abundance differences, where as the Weighted Jaccard does (Schroeder 2018).
▸ Weighted Unique Fraction (UniFrac) Distance
Weighted UniFrac distance metric utilizes a phylogenetic tree along with taxa abundances to calculate distances between all pairs of samples. This metric uniquely captures the state of evolution that is assumed to reflect a level of adaptation to the sampled environment (Lozupone 2005).
This distance metric is available for BIOM files generated within ERGO. If you have previously performed analysis, your workflow may need to be re-run before you’ll see the option.

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Schroeder, P. J., and Jenkins, D. G.. 2018. How robust are popular beta diversity indices to sampling error? Ecosphere 9( 2):e02100. 10.1002/ecs2.2100

Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005 Dec;71(12):8228-35. doi: 10.1128/AEM.71.12.8228-8235.2005. PMID: 16332807; PMCID: PMC1317376.